Starting phenix.real_space_refine on Mon Mar 25 01:03:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pg9_13389/03_2024/7pg9_13389.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 28984 2.51 5 N 8007 2.21 5 O 8055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 86": "NH1" <-> "NH2" Residue "K TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "M PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M ARG 173": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "U TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 143": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X ARG 79": "NH1" <-> "NH2" Residue "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 153": "NH1" <-> "NH2" Residue "Z PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 158": "NH1" <-> "NH2" Residue "Z ARG 186": "NH1" <-> "NH2" Residue "a PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45326 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1729 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1725 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 23.48, per 1000 atoms: 0.52 Number of scatterers: 45326 At special positions: 0 Unit cell: (192.428, 158.16, 133.118, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 8055 8.00 N 8007 7.00 C 28984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.57 Conformation dependent library (CDL) restraints added in 9.4 seconds 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11412 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 70 sheets defined 39.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.852A pdb=" N ASP A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A 11 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.899A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.756A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.635A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.604A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.721A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.546A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.537A pdb=" N GLN B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.923A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.704A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.685A pdb=" N ASN C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.603A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.535A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.523A pdb=" N ILE D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.722A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.871A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.740A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.748A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.527A pdb=" N SER F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.547A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.096A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.704A pdb=" N LEU G 9 " --> pdb=" O GLY G 6 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER G 10 " --> pdb=" O TYR G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 20 through 27 Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.528A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.210A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.025A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.871A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.676A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.950A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.522A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 Processing helix chain 'J' and resid 55 through 78 removed outlier: 3.552A pdb=" N LEU J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.262A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.505A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.626A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 170 removed outlier: 3.526A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLN L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.555A pdb=" N ALA L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.642A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.832A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.539A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.512A pdb=" N MET M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.829A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'O' and resid 22 through 31 removed outlier: 3.543A pdb=" N TYR O 27 " --> pdb=" O TYR O 23 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY O 35 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.755A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.634A pdb=" N CYS O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.604A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 193 through 207 removed outlier: 3.721A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.547A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 123 removed outlier: 3.535A pdb=" N GLN P 111 " --> pdb=" O ALA P 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU P 174 " --> pdb=" O LYS P 170 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.924A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS P 226 " --> pdb=" O PRO P 222 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.705A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.686A pdb=" N ASN Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR Q 179 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.604A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.536A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.524A pdb=" N ILE R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU R 226 " --> pdb=" O PRO R 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.721A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.871A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.739A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.747A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.528A pdb=" N SER T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.547A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 176 removed outlier: 4.097A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 182 Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS T 190 " --> pdb=" O GLU T 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 3.703A pdb=" N LEU U 9 " --> pdb=" O GLY U 6 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 20 through 27 Processing helix chain 'U' and resid 27 through 32 removed outlier: 3.529A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.553A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 4.209A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.024A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.870A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.677A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.949A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.522A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 5 Processing helix chain 'X' and resid 55 through 78 removed outlier: 3.553A pdb=" N LEU X 72 " --> pdb=" O PHE X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 4.261A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.506A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.627A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.527A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS Y 169 " --> pdb=" O GLU Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLN Z 62 " --> pdb=" O LEU Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.556A pdb=" N ALA Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.641A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.831A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.538A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.513A pdb=" N MET a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG b 100 " --> pdb=" O MET b 96 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 3.830A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.847A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 216 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.567A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.575A pdb=" N GLY B 36 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 34 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 213 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.617A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.538A pdb=" N LEU C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 77 removed outlier: 3.637A pdb=" N SER C 75 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.592A pdb=" N HIS D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.635A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 218 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.165A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 164 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.854A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA H 177 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.088A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 47 removed outlier: 3.535A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 124 through 127 removed outlier: 7.622A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.537A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 45 removed outlier: 6.131A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.643A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.905A pdb=" N MET K 118 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.861A pdb=" N SER L 188 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.168A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.849A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.751A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 7.048A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU M 31 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.831A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.531A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.848A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.566A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.575A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER P 34 " --> pdb=" O MET P 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN P 213 " --> pdb=" O GLY P 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.616A pdb=" N ILE P 71 " --> pdb=" O ILE P 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.538A pdb=" N LEU Q 44 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 72 through 77 removed outlier: 3.638A pdb=" N SER Q 75 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.591A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.635A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS R 218 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 69 removed outlier: 4.165A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.854A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA V 177 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.088A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 41 through 47 removed outlier: 3.535A pdb=" N ALA V 101 " --> pdb=" O PHE V 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL V 121 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 127 removed outlier: 7.617A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA W 97 " --> pdb=" O ALA W 46 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.536A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 41 through 45 removed outlier: 6.132A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.643A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.905A pdb=" N MET Y 118 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.860A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.168A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.849A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Z 103 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.752A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 29 through 31 removed outlier: 7.047A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU a 31 " --> pdb=" O SER a 34 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.830A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.532A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE b 189 " --> pdb=" O GLU b 200 " (cutoff:3.500A) 2438 hydrogen bonds defined for protein. 6927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.79 Time building geometry restraints manager: 19.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12846 1.33 - 1.45: 7337 1.45 - 1.57: 25523 1.57 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 46168 Sorted by residual: bond pdb=" CA GLN O 24 " pdb=" C GLN O 24 " ideal model delta sigma weight residual 1.523 1.497 0.027 1.30e-02 5.92e+03 4.16e+00 bond pdb=" N GLN O 24 " pdb=" CA GLN O 24 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.21e-02 6.83e+03 3.35e+00 bond pdb=" N GLN D 215 " pdb=" CA GLN D 215 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.05e+00 bond pdb=" C SER B 15 " pdb=" O SER B 15 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.33e-02 5.65e+03 2.84e+00 bond pdb=" C GLN O 24 " pdb=" O GLN O 24 " ideal model delta sigma weight residual 1.237 1.219 0.017 1.17e-02 7.31e+03 2.21e+00 ... (remaining 46163 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 1031 106.21 - 113.15: 25068 113.15 - 120.10: 15942 120.10 - 127.04: 20298 127.04 - 133.98: 350 Bond angle restraints: 62689 Sorted by residual: angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 110.33 118.92 -8.59 1.29e+00 6.01e-01 4.43e+01 angle pdb=" N ASP A 10 " pdb=" CA ASP A 10 " pdb=" C ASP A 10 " ideal model delta sigma weight residual 111.28 106.23 5.05 1.09e+00 8.42e-01 2.15e+01 angle pdb=" N HIS O 12 " pdb=" CA HIS O 12 " pdb=" C HIS O 12 " ideal model delta sigma weight residual 111.36 115.86 -4.50 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C GLN J 30 " pdb=" N ALA J 31 " pdb=" CA ALA J 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 angle pdb=" C GLN X 30 " pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 ... (remaining 62684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 26832 16.05 - 32.09: 421 32.09 - 48.14: 123 48.14 - 64.18: 11 64.18 - 80.23: 22 Dihedral angle restraints: 27409 sinusoidal: 9534 harmonic: 17875 Sorted by residual: dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N ILE K 25 " pdb=" CA ILE K 25 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N ILE Y 25 " pdb=" CA ILE Y 25 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN F 60 " pdb=" C GLN F 60 " pdb=" N LYS F 61 " pdb=" CA LYS F 61 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 27406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6025 0.055 - 0.109: 1149 0.109 - 0.164: 160 0.164 - 0.219: 7 0.219 - 0.273: 3 Chirality restraints: 7344 Sorted by residual: chirality pdb=" CA GLN D 215 " pdb=" N GLN D 215 " pdb=" C GLN D 215 " pdb=" CB GLN D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA SER D 216 " pdb=" N SER D 216 " pdb=" C SER D 216 " pdb=" CB SER D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA SER R 216 " pdb=" N SER R 216 " pdb=" C SER R 216 " pdb=" CB SER R 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 7341 not shown) Planarity restraints: 7971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C VAL A 183 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 183 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 184 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL O 183 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL O 183 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL O 183 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 184 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER O 17 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO O 18 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO O 18 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 18 " -0.031 5.00e-02 4.00e+02 ... (remaining 7968 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1010 2.70 - 3.25: 43354 3.25 - 3.80: 69704 3.80 - 4.35: 94561 4.35 - 4.90: 160484 Nonbonded interactions: 369113 Sorted by model distance: nonbonded pdb=" O LYS M 49 " pdb=" OG1 THR M 50 " model vdw 2.144 2.440 nonbonded pdb=" O LYS a 49 " pdb=" OG1 THR a 50 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR a 5 " pdb=" O PRO a 103 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR M 5 " pdb=" O PRO M 103 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR D 31 " pdb=" O ARG D 163 " model vdw 2.233 2.440 ... (remaining 369108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 242) selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.230 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 118.870 Find NCS groups from input model: 4.890 Set up NCS constraints: 0.520 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46168 Z= 0.170 Angle : 0.634 8.590 62689 Z= 0.408 Chirality : 0.044 0.273 7344 Planarity : 0.004 0.059 7971 Dihedral : 7.813 80.226 15997 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.09), residues: 6139 helix: -3.35 (0.07), residues: 2162 sheet: -0.87 (0.12), residues: 1470 loop : -0.91 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 215 HIS 0.007 0.001 HIS G 72 PHE 0.020 0.001 PHE K 171 TYR 0.018 0.001 TYR V 136 ARG 0.005 0.000 ARG Z 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1782 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1781 time to evaluate : 5.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7132 (m-30) cc_final: 0.6522 (m-30) REVERT: B 70 HIS cc_start: 0.5995 (p-80) cc_final: 0.5710 (p-80) REVERT: B 71 ILE cc_start: 0.9049 (mt) cc_final: 0.8565 (mt) REVERT: B 94 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7436 (mm110) REVERT: C 6 ASP cc_start: 0.7582 (t0) cc_final: 0.7186 (t0) REVERT: D 110 TYR cc_start: 0.7905 (t80) cc_final: 0.7362 (t80) REVERT: E 13 ASN cc_start: 0.8643 (m-40) cc_final: 0.8338 (m-40) REVERT: G 81 LEU cc_start: 0.8248 (tp) cc_final: 0.7825 (tp) REVERT: G 118 TYR cc_start: 0.7407 (t80) cc_final: 0.7180 (t80) REVERT: H 53 GLN cc_start: 0.7977 (mt0) cc_final: 0.7527 (mt0) REVERT: I 209 THR cc_start: 0.7671 (m) cc_final: 0.7339 (t) REVERT: J 4 SER cc_start: 0.8318 (p) cc_final: 0.8067 (t) REVERT: J 192 ASP cc_start: 0.7304 (p0) cc_final: 0.6943 (p0) REVERT: K 62 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8133 (tttm) REVERT: K 63 ASN cc_start: 0.8178 (m110) cc_final: 0.7882 (m-40) REVERT: K 87 ASN cc_start: 0.7739 (p0) cc_final: 0.7264 (p0) REVERT: K 90 ASP cc_start: 0.7162 (p0) cc_final: 0.6891 (p0) REVERT: K 101 ASN cc_start: 0.7281 (m110) cc_final: 0.7079 (m-40) REVERT: K 139 THR cc_start: 0.8482 (p) cc_final: 0.8107 (p) REVERT: L 33 LYS cc_start: 0.8335 (mttt) cc_final: 0.8081 (mttt) REVERT: M 91 MET cc_start: 0.7716 (ttp) cc_final: 0.7372 (ttm) REVERT: O 39 SER cc_start: 0.8419 (m) cc_final: 0.8207 (m) REVERT: P 57 ASP cc_start: 0.6948 (t0) cc_final: 0.6629 (t0) REVERT: Q 107 CYS cc_start: 0.7361 (m) cc_final: 0.6910 (m) REVERT: R 110 TYR cc_start: 0.7834 (t80) cc_final: 0.6903 (t80) REVERT: S 89 ILE cc_start: 0.8541 (pt) cc_final: 0.8210 (mt) REVERT: T 147 THR cc_start: 0.8187 (p) cc_final: 0.7985 (m) REVERT: V 90 TYR cc_start: 0.7476 (m-80) cc_final: 0.7118 (m-80) REVERT: V 99 ILE cc_start: 0.8926 (tt) cc_final: 0.8600 (mt) REVERT: W 53 ASP cc_start: 0.6460 (m-30) cc_final: 0.6189 (m-30) REVERT: X 164 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6615 (mm-30) REVERT: X 180 SER cc_start: 0.8475 (m) cc_final: 0.7747 (m) REVERT: Y 61 GLN cc_start: 0.7678 (tt0) cc_final: 0.6476 (tt0) REVERT: Y 62 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8117 (tttp) REVERT: Y 90 ASP cc_start: 0.7314 (p0) cc_final: 0.7058 (p0) REVERT: Y 108 ASP cc_start: 0.6930 (t0) cc_final: 0.5031 (t0) REVERT: Y 177 THR cc_start: 0.7623 (p) cc_final: 0.7101 (p) REVERT: a 75 TYR cc_start: 0.8328 (t80) cc_final: 0.7921 (t80) outliers start: 1 outliers final: 0 residues processed: 1782 average time/residue: 0.6328 time to fit residues: 1764.0754 Evaluate side-chains 1098 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 5.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 476 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 552 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 193 GLN B 51 GLN B 87 HIS B 108 GLN B 111 GLN B 147 GLN C 109 GLN C 167 ASN C 230 GLN D 54 GLN D 154 HIS E 23 GLN E 152 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS H 123 GLN I 66 HIS I 91 GLN J 60 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN K 63 ASN K 71 ASN K 101 ASN K 168 GLN L 62 GLN L 85 ASN M 8 ASN M 77 HIS ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 81 HIS N 89 HIS N 108 ASN N 147 GLN N 185 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN ** O 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 120 GLN S 23 GLN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 HIS W 66 HIS X 92 ASN Y 32 HIS Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN a 146 GLN ** b 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 HIS ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 46168 Z= 0.401 Angle : 0.724 9.409 62689 Z= 0.385 Chirality : 0.047 0.196 7344 Planarity : 0.005 0.055 7971 Dihedral : 4.777 27.193 6785 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.17 % Favored : 97.82 % Rotamer: Outliers : 3.47 % Allowed : 13.26 % Favored : 83.27 % 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: -0.90 (0.10), residues: 6139 helix: -0.41 (0.10), residues: 2221 sheet: -0.48 (0.12), residues: 1498 loop : -0.63 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 215 HIS 0.014 0.002 HIS E 227 PHE 0.030 0.002 PHE E 162 TYR 0.029 0.002 TYR Q 97 ARG 0.012 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1094 time to evaluate : 5.374 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: A 123 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 48 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 121 THR cc_start: 0.8595 (p) cc_final: 0.8347 (m) REVERT: C 25 MET cc_start: 0.7567 (mmt) cc_final: 0.7277 (mmp) REVERT: C 206 LEU cc_start: 0.8259 (mp) cc_final: 0.8017 (mp) REVERT: D 84 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9119 (mt) REVERT: D 110 TYR cc_start: 0.8277 (t80) cc_final: 0.7910 (t80) REVERT: E 13 ASN cc_start: 0.8731 (m-40) cc_final: 0.8519 (m-40) REVERT: E 152 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: F 117 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7615 (tp40) REVERT: F 182 CYS cc_start: 0.7173 (m) cc_final: 0.6621 (m) REVERT: G 136 MET cc_start: 0.7533 (mtp) cc_final: 0.7311 (mtp) REVERT: H 95 MET cc_start: 0.7509 (tmm) cc_final: 0.6454 (tmm) REVERT: I 53 ASP cc_start: 0.6589 (t0) cc_final: 0.6222 (t0) REVERT: J 144 GLN cc_start: 0.8397 (mp10) cc_final: 0.8132 (mp10) REVERT: K 90 ASP cc_start: 0.7929 (p0) cc_final: 0.7503 (p0) REVERT: K 163 CYS cc_start: 0.7859 (m) cc_final: 0.7592 (m) REVERT: K 175 LEU cc_start: 0.8905 (mt) cc_final: 0.8583 (mt) REVERT: M 114 ASP cc_start: 0.8399 (p0) cc_final: 0.7861 (p0) REVERT: N 170 GLU cc_start: 0.7484 (pp20) cc_final: 0.7224 (pp20) REVERT: P 162 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7890 (mtp) REVERT: R 90 GLU cc_start: 0.8591 (tp30) cc_final: 0.7226 (tt0) REVERT: R 110 TYR cc_start: 0.8418 (t80) cc_final: 0.7016 (t80) REVERT: R 117 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7611 (ttp80) REVERT: S 89 ILE cc_start: 0.8938 (pt) cc_final: 0.8684 (mt) REVERT: T 117 GLN cc_start: 0.7668 (tp40) cc_final: 0.7365 (tp40) REVERT: T 154 PHE cc_start: 0.7876 (m-80) cc_final: 0.7630 (m-80) REVERT: V 90 TYR cc_start: 0.7844 (m-80) cc_final: 0.7199 (m-80) REVERT: W 57 GLN cc_start: 0.7105 (mt0) cc_final: 0.6870 (mt0) REVERT: X 17 ASN cc_start: 0.7853 (t0) cc_final: 0.7620 (t0) REVERT: Y 13 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8294 (t) REVERT: Y 90 ASP cc_start: 0.7644 (p0) cc_final: 0.7270 (p0) REVERT: b 43 MET cc_start: 0.7675 (tmm) cc_final: 0.7128 (ttp) REVERT: b 96 MET cc_start: 0.7767 (tpp) cc_final: 0.7499 (tpp) REVERT: b 173 MET cc_start: 0.7982 (tpt) cc_final: 0.7703 (mmt) outliers start: 148 outliers final: 87 residues processed: 1177 average time/residue: 0.5794 time to fit residues: 1102.3286 Evaluate side-chains 1037 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 946 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 51 GLN Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 162 MET Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 67 LYS Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 187 LYS Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 63 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 85 CYS Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 0.0030 chunk 171 optimal weight: 10.0000 chunk 459 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 553 optimal weight: 8.9990 chunk 597 optimal weight: 8.9990 chunk 492 optimal weight: 0.6980 chunk 548 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 443 optimal weight: 9.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 40 ASN E 118 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 123 GLN I 91 GLN J 17 ASN J 92 ASN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 61 GLN Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 ASN a 146 GLN b 65 GLN b 147 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46168 Z= 0.201 Angle : 0.617 9.311 62689 Z= 0.323 Chirality : 0.044 0.189 7344 Planarity : 0.004 0.044 7971 Dihedral : 4.544 27.242 6785 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 15.37 % Favored : 82.12 % 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: -0.10 (0.10), residues: 6139 helix: 0.63 (0.11), residues: 2211 sheet: -0.17 (0.13), residues: 1449 loop : -0.49 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 215 HIS 0.011 0.001 HIS E 227 PHE 0.022 0.001 PHE A 191 TYR 0.029 0.001 TYR D 21 ARG 0.009 0.001 ARG V 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1085 time to evaluate : 5.389 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: A 123 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 48 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 135 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8462 (mm) REVERT: D 20 GLU cc_start: 0.7018 (pp20) cc_final: 0.6509 (pp20) REVERT: D 90 GLU cc_start: 0.8133 (tp30) cc_final: 0.7592 (tp30) REVERT: D 110 TYR cc_start: 0.8221 (t80) cc_final: 0.7737 (t80) REVERT: F 182 CYS cc_start: 0.7288 (m) cc_final: 0.6902 (m) REVERT: H 134 TYR cc_start: 0.7951 (m-80) cc_final: 0.7694 (m-80) REVERT: J 177 ASP cc_start: 0.7778 (t0) cc_final: 0.7212 (t0) REVERT: K 59 TYR cc_start: 0.7898 (t80) cc_final: 0.7618 (t80) REVERT: K 68 LYS cc_start: 0.8854 (tptt) cc_final: 0.8512 (tptt) REVERT: K 90 ASP cc_start: 0.7839 (p0) cc_final: 0.7306 (p0) REVERT: L 198 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8346 (tttm) REVERT: M 114 ASP cc_start: 0.8276 (p0) cc_final: 0.7768 (p0) REVERT: N 26 MET cc_start: 0.8109 (mpp) cc_final: 0.6942 (mtm) REVERT: O 122 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8174 (t) REVERT: R 90 GLU cc_start: 0.8644 (tp30) cc_final: 0.8360 (tt0) REVERT: R 117 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7557 (ttp80) REVERT: S 89 ILE cc_start: 0.8921 (pt) cc_final: 0.8648 (mt) REVERT: S 203 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8840 (ttmm) REVERT: T 117 GLN cc_start: 0.7997 (tp40) cc_final: 0.7740 (tp40) REVERT: Y 38 MET cc_start: 0.6790 (tpp) cc_final: 0.6565 (tpp) REVERT: Y 90 ASP cc_start: 0.7505 (p0) cc_final: 0.7091 (p0) REVERT: a 127 VAL cc_start: 0.8735 (m) cc_final: 0.8524 (p) REVERT: b 43 MET cc_start: 0.7586 (tmm) cc_final: 0.7046 (ttp) REVERT: b 96 MET cc_start: 0.7720 (tpp) cc_final: 0.7442 (tpp) REVERT: b 173 MET cc_start: 0.7995 (tpt) cc_final: 0.7657 (mmt) outliers start: 107 outliers final: 60 residues processed: 1135 average time/residue: 0.5656 time to fit residues: 1048.4928 Evaluate side-chains 1036 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 974 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 159 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 187 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 5.9990 chunk 415 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 555 optimal weight: 0.4980 chunk 587 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 526 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 94 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN F 21 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN V 53 GLN X 92 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 46168 Z= 0.345 Angle : 0.657 9.196 62689 Z= 0.344 Chirality : 0.045 0.186 7344 Planarity : 0.004 0.049 7971 Dihedral : 4.614 30.882 6785 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 3.40 % Allowed : 16.10 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.25 (0.10), residues: 6139 helix: 1.06 (0.11), residues: 2233 sheet: -0.09 (0.13), residues: 1470 loop : -0.39 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 215 HIS 0.010 0.001 HIS E 227 PHE 0.026 0.002 PHE T 87 TYR 0.037 0.002 TYR D 21 ARG 0.008 0.001 ARG W 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 994 time to evaluate : 5.290 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: A 123 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 48 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7619 (tm-30) REVERT: D 20 GLU cc_start: 0.7040 (pp20) cc_final: 0.6627 (pp20) REVERT: D 55 ASP cc_start: 0.7578 (t0) cc_final: 0.7147 (t0) REVERT: D 110 TYR cc_start: 0.8354 (t80) cc_final: 0.8105 (t80) REVERT: E 216 GLU cc_start: 0.6135 (tt0) cc_final: 0.5930 (tt0) REVERT: F 182 CYS cc_start: 0.6913 (m) cc_final: 0.6625 (m) REVERT: G 75 MET cc_start: 0.7599 (tpp) cc_final: 0.7067 (ttt) REVERT: H 134 TYR cc_start: 0.7889 (m-80) cc_final: 0.7685 (m-80) REVERT: K 59 TYR cc_start: 0.7986 (t80) cc_final: 0.7755 (t80) REVERT: K 90 ASP cc_start: 0.7910 (p0) cc_final: 0.7420 (p0) REVERT: K 163 CYS cc_start: 0.7871 (m) cc_final: 0.7514 (m) REVERT: M 114 ASP cc_start: 0.8278 (p0) cc_final: 0.7925 (p0) REVERT: N 26 MET cc_start: 0.8050 (mpp) cc_final: 0.7147 (mtm) REVERT: N 64 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8403 (ttpt) REVERT: O 122 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8279 (t) REVERT: O 166 THR cc_start: 0.8291 (m) cc_final: 0.8032 (p) REVERT: Q 68 LEU cc_start: 0.8378 (mp) cc_final: 0.7840 (mp) REVERT: R 90 GLU cc_start: 0.8720 (tp30) cc_final: 0.8127 (tt0) REVERT: R 117 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7713 (ttp80) REVERT: S 203 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8905 (ttmm) REVERT: T 26 MET cc_start: 0.7785 (tpp) cc_final: 0.7559 (mmt) REVERT: T 117 GLN cc_start: 0.8303 (tp40) cc_final: 0.7913 (tp40) REVERT: V 93 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6637 (p0) REVERT: Y 90 ASP cc_start: 0.7773 (p0) cc_final: 0.7392 (p0) REVERT: Y 108 ASP cc_start: 0.6015 (t0) cc_final: 0.5179 (t70) REVERT: a 127 VAL cc_start: 0.8839 (m) cc_final: 0.8631 (p) REVERT: b 43 MET cc_start: 0.7558 (tmm) cc_final: 0.7003 (ttp) REVERT: b 173 MET cc_start: 0.8086 (tpt) cc_final: 0.7815 (mmt) outliers start: 145 outliers final: 108 residues processed: 1072 average time/residue: 0.5647 time to fit residues: 987.0623 Evaluate side-chains 1038 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 928 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 200 LYS Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 51 GLN Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 187 LYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 206 ASP Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain U residue 237 LYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 0.6980 chunk 333 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 437 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 501 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 8.9990 chunk 527 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN E 118 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 86 ASN G 110 HIS H 7 GLN H 62 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN O 24 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN V 53 GLN X 92 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 46168 Z= 0.195 Angle : 0.607 10.207 62689 Z= 0.315 Chirality : 0.043 0.183 7344 Planarity : 0.004 0.045 7971 Dihedral : 4.438 29.038 6785 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.62 % Allowed : 17.97 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 6139 helix: 1.37 (0.11), residues: 2215 sheet: -0.04 (0.13), residues: 1476 loop : -0.31 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 215 HIS 0.009 0.001 HIS S 227 PHE 0.025 0.001 PHE T 87 TYR 0.035 0.001 TYR D 21 ARG 0.008 0.000 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1013 time to evaluate : 5.607 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: A 123 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 224 ASN cc_start: 0.7290 (p0) cc_final: 0.6985 (p0) REVERT: B 48 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 26 GLU cc_start: 0.6676 (tp30) cc_final: 0.6412 (tp30) REVERT: C 30 HIS cc_start: 0.7497 (m-70) cc_final: 0.7132 (m-70) REVERT: D 20 GLU cc_start: 0.6851 (pp20) cc_final: 0.6623 (pp20) REVERT: D 90 GLU cc_start: 0.8147 (tp30) cc_final: 0.7773 (tp30) REVERT: D 110 TYR cc_start: 0.8307 (t80) cc_final: 0.7793 (t80) REVERT: F 182 CYS cc_start: 0.6945 (m) cc_final: 0.6710 (m) REVERT: G 75 MET cc_start: 0.7613 (tpp) cc_final: 0.7016 (ttt) REVERT: H 90 TYR cc_start: 0.7557 (m-10) cc_final: 0.7228 (m-80) REVERT: K 8 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7806 (tm-30) REVERT: K 38 MET cc_start: 0.7119 (mmm) cc_final: 0.6533 (mmm) REVERT: K 44 LEU cc_start: 0.8676 (tp) cc_final: 0.8358 (tt) REVERT: K 68 LYS cc_start: 0.8852 (tptt) cc_final: 0.8593 (tptt) REVERT: K 90 ASP cc_start: 0.7911 (p0) cc_final: 0.7481 (p0) REVERT: N 26 MET cc_start: 0.7961 (mpp) cc_final: 0.7188 (mtm) REVERT: O 122 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8243 (t) REVERT: P 48 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7860 (tm-30) REVERT: Q 68 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (mp) REVERT: R 110 TYR cc_start: 0.8439 (t80) cc_final: 0.7702 (t80) REVERT: R 117 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7622 (ttp80) REVERT: T 117 GLN cc_start: 0.8320 (tp40) cc_final: 0.7968 (tp40) REVERT: Y 38 MET cc_start: 0.7115 (tpp) cc_final: 0.6894 (tpp) REVERT: Y 90 ASP cc_start: 0.7637 (p0) cc_final: 0.7285 (p0) REVERT: Z 97 MET cc_start: 0.7406 (tmm) cc_final: 0.7167 (tmm) REVERT: b 43 MET cc_start: 0.7433 (tmm) cc_final: 0.7041 (ttp) REVERT: b 96 MET cc_start: 0.7642 (tpp) cc_final: 0.7388 (tpp) REVERT: b 173 MET cc_start: 0.8130 (tpt) cc_final: 0.7887 (mmt) outliers start: 112 outliers final: 72 residues processed: 1069 average time/residue: 0.6106 time to fit residues: 1069.2513 Evaluate side-chains 1005 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 931 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 107 CYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 10.0000 chunk 529 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 345 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 588 optimal weight: 0.9980 chunk 488 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 308 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 172 GLN B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN E 118 ASN J 32 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN T 86 ASN V 53 GLN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 92 ASN Y 32 HIS Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46168 Z= 0.178 Angle : 0.613 10.943 62689 Z= 0.315 Chirality : 0.043 0.192 7344 Planarity : 0.004 0.051 7971 Dihedral : 4.349 31.561 6785 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.81 % Allowed : 18.63 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.58 (0.11), residues: 6139 helix: 1.49 (0.11), residues: 2207 sheet: -0.05 (0.13), residues: 1492 loop : -0.23 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 215 HIS 0.011 0.001 HIS F 69 PHE 0.024 0.001 PHE U 135 TYR 0.034 0.001 TYR K 59 ARG 0.009 0.000 ARG W 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1002 time to evaluate : 5.406 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: A 123 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 48 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 26 GLU cc_start: 0.6635 (tp30) cc_final: 0.6187 (tp30) REVERT: C 30 HIS cc_start: 0.7422 (m-70) cc_final: 0.6913 (m-70) REVERT: D 20 GLU cc_start: 0.6893 (pp20) cc_final: 0.6623 (pp20) REVERT: D 110 TYR cc_start: 0.8305 (t80) cc_final: 0.8011 (t80) REVERT: E 60 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: E 149 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7975 (tmmt) REVERT: E 189 MET cc_start: 0.6422 (ptp) cc_final: 0.6128 (ptp) REVERT: G 75 MET cc_start: 0.7640 (tpp) cc_final: 0.7065 (ttt) REVERT: G 136 MET cc_start: 0.7492 (mtp) cc_final: 0.7201 (mtp) REVERT: G 179 LEU cc_start: 0.7812 (tp) cc_final: 0.7585 (tt) REVERT: H 37 ILE cc_start: 0.8745 (mp) cc_final: 0.8497 (mp) REVERT: H 90 TYR cc_start: 0.7672 (m-10) cc_final: 0.7463 (m-10) REVERT: J 3 MET cc_start: 0.7366 (mmm) cc_final: 0.6736 (mmm) REVERT: K 8 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7901 (tm-30) REVERT: K 38 MET cc_start: 0.7080 (mmm) cc_final: 0.6455 (mmm) REVERT: K 44 LEU cc_start: 0.8637 (tp) cc_final: 0.8359 (tt) REVERT: K 90 ASP cc_start: 0.7819 (p0) cc_final: 0.7433 (p0) REVERT: N 26 MET cc_start: 0.7867 (mpp) cc_final: 0.7150 (mtm) REVERT: P 48 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7790 (tm-30) REVERT: P 118 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8271 (tm-30) REVERT: Q 68 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7969 (mp) REVERT: R 90 GLU cc_start: 0.8541 (tp30) cc_final: 0.8002 (tt0) REVERT: S 107 MET cc_start: 0.8298 (ttm) cc_final: 0.8096 (ttm) REVERT: T 117 GLN cc_start: 0.8404 (tp40) cc_final: 0.8078 (tp40) REVERT: Y 38 MET cc_start: 0.7114 (tpp) cc_final: 0.6855 (tpp) REVERT: Y 90 ASP cc_start: 0.7491 (p0) cc_final: 0.7269 (p0) REVERT: Z 100 MET cc_start: 0.7822 (mtm) cc_final: 0.7583 (mtt) REVERT: a 169 ASP cc_start: 0.6468 (p0) cc_final: 0.6263 (p0) REVERT: b 43 MET cc_start: 0.7426 (tmm) cc_final: 0.7075 (ttt) REVERT: b 173 MET cc_start: 0.8161 (tpt) cc_final: 0.7846 (mmt) outliers start: 120 outliers final: 85 residues processed: 1059 average time/residue: 0.6086 time to fit residues: 1059.4957 Evaluate side-chains 1028 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 941 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 107 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 chunk 429 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 495 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 586 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN F 86 ASN G 32 ASN J 168 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 106 GLN W 57 GLN W 85 GLN X 92 ASN Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46168 Z= 0.217 Angle : 0.629 11.490 62689 Z= 0.323 Chirality : 0.043 0.217 7344 Planarity : 0.004 0.048 7971 Dihedral : 4.317 30.051 6785 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.02 % Allowed : 19.78 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.66 (0.11), residues: 6139 helix: 1.57 (0.11), residues: 2209 sheet: 0.01 (0.13), residues: 1478 loop : -0.22 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 215 HIS 0.008 0.001 HIS F 69 PHE 0.029 0.001 PHE U 135 TYR 0.026 0.001 TYR G 149 ARG 0.015 0.000 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 966 time to evaluate : 5.328 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: A 123 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 48 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 26 GLU cc_start: 0.6672 (tp30) cc_final: 0.6164 (tp30) REVERT: C 30 HIS cc_start: 0.7425 (m-70) cc_final: 0.6835 (m-70) REVERT: D 20 GLU cc_start: 0.6924 (pp20) cc_final: 0.6684 (pp20) REVERT: D 110 TYR cc_start: 0.8362 (t80) cc_final: 0.8044 (t80) REVERT: E 60 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: G 75 MET cc_start: 0.7644 (tpp) cc_final: 0.7116 (ttt) REVERT: H 90 TYR cc_start: 0.7750 (m-10) cc_final: 0.7158 (m-10) REVERT: K 38 MET cc_start: 0.7222 (mmm) cc_final: 0.6580 (mmm) REVERT: K 44 LEU cc_start: 0.8677 (tp) cc_final: 0.8364 (tt) REVERT: K 45 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8293 (mp) REVERT: K 90 ASP cc_start: 0.7849 (p0) cc_final: 0.7468 (p0) REVERT: L 100 MET cc_start: 0.8359 (mpp) cc_final: 0.7975 (mtm) REVERT: N 26 MET cc_start: 0.7935 (mpp) cc_final: 0.7276 (mtm) REVERT: Q 68 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8041 (mp) REVERT: R 90 GLU cc_start: 0.8537 (tp30) cc_final: 0.7947 (tt0) REVERT: S 107 MET cc_start: 0.8332 (ttm) cc_final: 0.8080 (ttm) REVERT: T 117 GLN cc_start: 0.8498 (tp40) cc_final: 0.8237 (tp40) REVERT: X 170 MET cc_start: 0.7966 (tpt) cc_final: 0.7653 (tpt) REVERT: Y 90 ASP cc_start: 0.7520 (p0) cc_final: 0.7310 (p0) REVERT: Z 100 MET cc_start: 0.7812 (mtm) cc_final: 0.7587 (mtt) REVERT: a 169 ASP cc_start: 0.6498 (p0) cc_final: 0.6260 (p0) REVERT: b 43 MET cc_start: 0.7382 (tmm) cc_final: 0.7053 (ttp) outliers start: 129 outliers final: 86 residues processed: 1030 average time/residue: 0.5466 time to fit residues: 921.0137 Evaluate side-chains 1017 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 928 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 106 GLN Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 349 optimal weight: 0.0770 chunk 176 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 372 optimal weight: 10.0000 chunk 399 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 460 optimal weight: 9.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN E 204 GLN G 32 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 ASN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN V 106 GLN X 92 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46168 Z= 0.189 Angle : 0.635 12.332 62689 Z= 0.325 Chirality : 0.043 0.242 7344 Planarity : 0.004 0.049 7971 Dihedral : 4.282 30.550 6785 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.48 % Allowed : 20.17 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.72 (0.11), residues: 6139 helix: 1.64 (0.11), residues: 2205 sheet: 0.03 (0.13), residues: 1496 loop : -0.21 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 215 HIS 0.007 0.001 HIS S 227 PHE 0.028 0.001 PHE T 87 TYR 0.027 0.001 TYR R 153 ARG 0.014 0.000 ARG W 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 987 time to evaluate : 5.485 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: A 123 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 48 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 101 GLN cc_start: 0.7612 (mm110) cc_final: 0.7359 (mm110) REVERT: C 26 GLU cc_start: 0.6490 (tp30) cc_final: 0.6133 (tp30) REVERT: C 30 HIS cc_start: 0.7383 (m-70) cc_final: 0.6755 (m-70) REVERT: D 20 GLU cc_start: 0.6861 (pp20) cc_final: 0.6659 (pp20) REVERT: D 110 TYR cc_start: 0.8378 (t80) cc_final: 0.8126 (t80) REVERT: G 75 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7089 (ttt) REVERT: G 179 LEU cc_start: 0.7523 (tt) cc_final: 0.7284 (tt) REVERT: H 37 ILE cc_start: 0.8725 (mp) cc_final: 0.8392 (mp) REVERT: H 90 TYR cc_start: 0.7638 (m-10) cc_final: 0.7264 (m-10) REVERT: H 93 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6565 (p0) REVERT: I 30 ASN cc_start: 0.7721 (t0) cc_final: 0.7366 (t0) REVERT: I 57 GLN cc_start: 0.7124 (tt0) cc_final: 0.6823 (tt0) REVERT: K 38 MET cc_start: 0.7283 (mmm) cc_final: 0.6737 (mmm) REVERT: K 44 LEU cc_start: 0.8623 (tp) cc_final: 0.8371 (tt) REVERT: K 90 ASP cc_start: 0.7825 (p0) cc_final: 0.7439 (p0) REVERT: M 131 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7342 (tm-30) REVERT: N 26 MET cc_start: 0.7874 (mpp) cc_final: 0.7232 (mtm) REVERT: P 48 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8096 (tm-30) REVERT: Q 68 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8021 (mp) REVERT: R 90 GLU cc_start: 0.8518 (tp30) cc_final: 0.7933 (tt0) REVERT: T 117 GLN cc_start: 0.8485 (tp40) cc_final: 0.8237 (tp40) REVERT: V 95 MET cc_start: 0.6666 (tmm) cc_final: 0.5985 (tmm) REVERT: X 145 MET cc_start: 0.7815 (pmm) cc_final: 0.7588 (pmm) REVERT: X 170 MET cc_start: 0.8112 (tpt) cc_final: 0.7848 (tpt) REVERT: Y 166 GLU cc_start: 0.6867 (tp30) cc_final: 0.5355 (tp30) REVERT: Z 97 MET cc_start: 0.7552 (tmm) cc_final: 0.7217 (tmm) REVERT: a 54 CYS cc_start: 0.7202 (m) cc_final: 0.6905 (m) REVERT: a 91 MET cc_start: 0.7741 (tmm) cc_final: 0.7513 (tmm) REVERT: a 169 ASP cc_start: 0.6854 (p0) cc_final: 0.6545 (p0) REVERT: b 43 MET cc_start: 0.7379 (tmm) cc_final: 0.7026 (ttt) outliers start: 106 outliers final: 86 residues processed: 1034 average time/residue: 0.5671 time to fit residues: 959.9432 Evaluate side-chains 1026 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 937 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 106 GLN Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 3.9990 chunk 561 optimal weight: 1.9990 chunk 512 optimal weight: 3.9990 chunk 546 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 237 optimal weight: 0.7980 chunk 428 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 493 optimal weight: 0.9990 chunk 516 optimal weight: 8.9990 chunk 544 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN G 32 ASN H 106 GLN K 63 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 ASN P 51 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46168 Z= 0.198 Angle : 0.659 13.163 62689 Z= 0.336 Chirality : 0.043 0.290 7344 Planarity : 0.004 0.049 7971 Dihedral : 4.290 28.354 6785 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.39 % Allowed : 20.76 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 6139 helix: 1.65 (0.11), residues: 2221 sheet: 0.05 (0.13), residues: 1500 loop : -0.20 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 215 HIS 0.008 0.001 HIS S 99 PHE 0.027 0.001 PHE U 135 TYR 0.029 0.001 TYR W 90 ARG 0.010 0.000 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 967 time to evaluate : 4.332 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: A 123 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 224 ASN cc_start: 0.7099 (p0) cc_final: 0.5926 (p0) REVERT: A 228 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6367 (ptt-90) REVERT: B 48 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 101 GLN cc_start: 0.7759 (mm110) cc_final: 0.7401 (mm110) REVERT: D 20 GLU cc_start: 0.6848 (pp20) cc_final: 0.6191 (pp20) REVERT: D 110 TYR cc_start: 0.8434 (t80) cc_final: 0.8189 (t80) REVERT: F 115 LYS cc_start: 0.8460 (tttm) cc_final: 0.8063 (tttm) REVERT: G 75 MET cc_start: 0.7639 (tpp) cc_final: 0.7124 (ttt) REVERT: H 90 TYR cc_start: 0.7695 (m-10) cc_final: 0.7257 (m-10) REVERT: H 93 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6577 (p0) REVERT: I 30 ASN cc_start: 0.7806 (t0) cc_final: 0.7424 (t0) REVERT: J 44 MET cc_start: 0.7398 (mmp) cc_final: 0.7191 (mmm) REVERT: J 105 GLU cc_start: 0.7539 (mp0) cc_final: 0.7309 (mp0) REVERT: J 144 GLN cc_start: 0.8138 (mp10) cc_final: 0.7785 (mp10) REVERT: K 19 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7740 (mtp85) REVERT: K 38 MET cc_start: 0.7252 (mmm) cc_final: 0.6705 (mmm) REVERT: K 44 LEU cc_start: 0.8622 (tp) cc_final: 0.8393 (tt) REVERT: K 90 ASP cc_start: 0.7822 (p0) cc_final: 0.7417 (p0) REVERT: L 97 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7101 (ttp) REVERT: M 131 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7336 (tm-30) REVERT: N 26 MET cc_start: 0.7852 (mpp) cc_final: 0.7238 (mtm) REVERT: P 48 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7979 (tm-30) REVERT: Q 68 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8050 (mp) REVERT: R 90 GLU cc_start: 0.8479 (tp30) cc_final: 0.7910 (tt0) REVERT: S 206 MET cc_start: 0.7464 (mmm) cc_final: 0.7224 (mmm) REVERT: T 117 GLN cc_start: 0.8492 (tp40) cc_final: 0.8251 (tp40) REVERT: V 95 MET cc_start: 0.6745 (tmm) cc_final: 0.6051 (tmm) REVERT: W 19 ARG cc_start: 0.8478 (ttm170) cc_final: 0.8221 (ttm170) REVERT: W 30 ASN cc_start: 0.7818 (t0) cc_final: 0.7590 (t0) REVERT: X 170 MET cc_start: 0.8070 (tpt) cc_final: 0.7798 (tpt) REVERT: Z 97 MET cc_start: 0.7636 (tmm) cc_final: 0.7350 (tmm) REVERT: a 54 CYS cc_start: 0.7246 (m) cc_final: 0.6970 (m) REVERT: a 91 MET cc_start: 0.7757 (tmm) cc_final: 0.7544 (tmm) REVERT: a 169 ASP cc_start: 0.6831 (p0) cc_final: 0.6602 (p0) REVERT: b 43 MET cc_start: 0.7270 (tmm) cc_final: 0.6907 (ttt) outliers start: 102 outliers final: 85 residues processed: 1013 average time/residue: 0.5843 time to fit residues: 963.2533 Evaluate side-chains 1021 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 933 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 107 CYS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 10.0000 chunk 577 optimal weight: 0.8980 chunk 352 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 chunk 605 optimal weight: 10.0000 chunk 557 optimal weight: 4.9990 chunk 482 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 372 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN E 204 GLN G 32 ASN ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 ASN P 51 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 63 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46168 Z= 0.284 Angle : 0.698 13.955 62689 Z= 0.356 Chirality : 0.044 0.301 7344 Planarity : 0.004 0.050 7971 Dihedral : 4.374 28.040 6785 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.18 % Allowed : 21.04 % Favored : 76.78 % 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: 0.75 (0.11), residues: 6139 helix: 1.68 (0.11), residues: 2210 sheet: 0.06 (0.13), residues: 1500 loop : -0.21 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 215 HIS 0.007 0.001 HIS S 99 PHE 0.032 0.001 PHE U 135 TYR 0.028 0.001 TYR W 90 ARG 0.008 0.001 ARG P 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 928 time to evaluate : 5.437 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 123 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 224 ASN cc_start: 0.7162 (p0) cc_final: 0.5967 (p0) REVERT: A 228 ARG cc_start: 0.6612 (ttp-110) cc_final: 0.6384 (ptt-90) REVERT: B 48 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 26 GLU cc_start: 0.6312 (tp30) cc_final: 0.5320 (tp30) REVERT: D 20 GLU cc_start: 0.6781 (pp20) cc_final: 0.6385 (pp20) REVERT: D 110 TYR cc_start: 0.8443 (t80) cc_final: 0.8155 (t80) REVERT: F 90 GLN cc_start: 0.7718 (tp40) cc_final: 0.7449 (tp40) REVERT: G 75 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7081 (ttt) REVERT: H 93 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6810 (p0) REVERT: I 30 ASN cc_start: 0.7913 (t0) cc_final: 0.7566 (t0) REVERT: I 83 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8718 (mm) REVERT: J 144 GLN cc_start: 0.8141 (mp10) cc_final: 0.7828 (mp10) REVERT: J 157 MET cc_start: 0.7984 (mmm) cc_final: 0.7185 (tpt) REVERT: K 38 MET cc_start: 0.7280 (mmm) cc_final: 0.6679 (mmm) REVERT: K 90 ASP cc_start: 0.7897 (p0) cc_final: 0.7500 (p0) REVERT: L 97 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7241 (ttp) REVERT: M 131 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7384 (tm-30) REVERT: N 26 MET cc_start: 0.7942 (mpp) cc_final: 0.7380 (mtm) REVERT: P 48 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8144 (tm-30) REVERT: Q 68 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8318 (mp) REVERT: R 90 GLU cc_start: 0.8495 (tp30) cc_final: 0.7922 (tt0) REVERT: S 206 MET cc_start: 0.7529 (mmm) cc_final: 0.7249 (mmm) REVERT: S 228 MET cc_start: 0.6963 (ttm) cc_final: 0.6747 (mtp) REVERT: T 117 GLN cc_start: 0.8547 (tp40) cc_final: 0.8280 (tp40) REVERT: V 95 MET cc_start: 0.6764 (tmm) cc_final: 0.6147 (tmm) REVERT: W 19 ARG cc_start: 0.8570 (ttm170) cc_final: 0.8321 (ttm170) REVERT: X 170 MET cc_start: 0.8225 (tpt) cc_final: 0.7933 (tpt) REVERT: Z 97 MET cc_start: 0.7661 (tmm) cc_final: 0.7367 (tmm) REVERT: a 54 CYS cc_start: 0.7274 (m) cc_final: 0.6968 (m) REVERT: a 169 ASP cc_start: 0.6881 (p0) cc_final: 0.6654 (p0) REVERT: b 43 MET cc_start: 0.7307 (tmm) cc_final: 0.6955 (ttt) outliers start: 93 outliers final: 77 residues processed: 974 average time/residue: 0.5724 time to fit residues: 910.2861 Evaluate side-chains 984 residues out of total 5144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 902 time to evaluate : 5.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 8 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 ASN Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 107 CYS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 185 LYS Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 157 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 2.9990 chunk 513 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 496 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN F 60 GLN F 121 GLN G 32 ASN H 7 GLN ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 152 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN ** Y 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.052146 restraints weight = 144238.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054383 restraints weight = 65748.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055888 restraints weight = 38440.323| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46168 Z= 0.254 Angle : 0.694 14.147 62689 Z= 0.354 Chirality : 0.044 0.281 7344 Planarity : 0.004 0.062 7971 Dihedral : 4.386 28.187 6785 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 21.34 % Favored : 76.45 % 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: 0.75 (0.11), residues: 6139 helix: 1.65 (0.11), residues: 2218 sheet: 0.06 (0.13), residues: 1500 loop : -0.19 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 215 HIS 0.007 0.001 HIS E 227 PHE 0.028 0.001 PHE U 135 TYR 0.026 0.001 TYR W 90 ARG 0.011 0.001 ARG V 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14707.07 seconds wall clock time: 262 minutes 22.26 seconds (15742.26 seconds total)