Starting phenix.real_space_refine on Sun Mar 24 15:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr2_21875/03_2024/6wr2_21875.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 168 5.16 5 C 13445 2.51 5 N 3675 2.21 5 O 4022 1.98 5 H 21361 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ASP 18": "OD1" <-> "OD2" Residue "h ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 194": "OE1" <-> "OE2" Residue "i ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 194": "OE1" <-> "OE2" Residue "k ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k GLU 56": "OE1" <-> "OE2" Residue "k ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l GLU 194": "OE1" <-> "OE2" Residue "m ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 8": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42671 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "h" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2944 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "i" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "j" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2956 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "k" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2976 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "l" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "m" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2971 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "n" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3017 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3105 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 16.38, per 1000 atoms: 0.38 Number of scatterers: 42671 At special positions: 0 Unit cell: (112.23, 113.1, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 O 4022 8.00 N 3675 7.00 C 13445 6.00 H 21361 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.78 Conformation dependent library (CDL) restraints added in 4.1 seconds 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 49 sheets defined 49.5% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.537A pdb=" N GLU h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 54 Processing helix chain 'h' and resid 69 through 83 removed outlier: 3.567A pdb=" N GLY h 73 " --> pdb=" O VAL h 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 169 Processing helix chain 'h' and resid 176 through 183 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.779A pdb=" N GLU i 26 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 54 Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.658A pdb=" N GLY i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 105 Processing helix chain 'i' and resid 132 through 158 Processing helix chain 'i' and resid 160 through 169 Processing helix chain 'i' and resid 176 through 182 Processing helix chain 'j' and resid 19 through 25 Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 3.606A pdb=" N GLY j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 105 Processing helix chain 'j' and resid 132 through 158 Processing helix chain 'j' and resid 160 through 169 Processing helix chain 'j' and resid 176 through 182 Processing helix chain 'k' and resid 19 through 25 Processing helix chain 'k' and resid 36 through 54 Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.677A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 Processing helix chain 'k' and resid 132 through 158 Processing helix chain 'k' and resid 160 through 169 Processing helix chain 'k' and resid 176 through 182 Processing helix chain 'l' and resid 19 through 25 Processing helix chain 'l' and resid 36 through 54 Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.770A pdb=" N GLY l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 Processing helix chain 'l' and resid 160 through 169 Processing helix chain 'l' and resid 176 through 182 Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.875A pdb=" N GLU m 26 " --> pdb=" O ARG m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 54 Processing helix chain 'm' and resid 69 through 83 removed outlier: 3.594A pdb=" N GLY m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 105 Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 169 Processing helix chain 'm' and resid 176 through 183 Processing helix chain 'n' and resid 19 through 26 removed outlier: 3.550A pdb=" N GLU n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 69 through 83 removed outlier: 3.588A pdb=" N GLY n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 105 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 169 Processing helix chain 'n' and resid 176 through 182 Processing helix chain 'n' and resid 191 through 196 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.644A pdb=" N GLY M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 25 Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 70 through 83 removed outlier: 3.683A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 191 through 196 removed outlier: 3.654A pdb=" N ASN N 195 " --> pdb=" O HIS N 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.540A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.726A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 26 Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.665A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 132 through 158 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.630A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 132 through 158 Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.696A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 132 through 158 Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.551A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.660A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 169 Processing helix chain 'L' and resid 176 through 183 Processing sheet with id=AA1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.338A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.338A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 125 through 131 Processing sheet with id=AA5, first strand: chain 'i' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.355A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.355A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE i 112 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR i 89 " --> pdb=" O PHE i 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER i 187 " --> pdb=" O ARG i 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 125 through 131 Processing sheet with id=AA9, first strand: chain 'j' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.316A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'j' and resid 125 through 131 Processing sheet with id=AB4, first strand: chain 'k' and resid 5 through 8 removed outlier: 4.119A pdb=" N GLU k 8 " --> pdb=" O ARG k 15 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG k 15 " --> pdb=" O GLU k 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.395A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER k 187 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'k' and resid 118 through 121 Processing sheet with id=AB7, first strand: chain 'k' and resid 125 through 131 Processing sheet with id=AB8, first strand: chain 'l' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.428A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG l 118 " --> pdb=" O CYS l 91 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY l 93 " --> pdb=" O ARG l 118 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N MET l 120 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.428A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'l' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.465A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'm' and resid 118 through 121 Processing sheet with id=AC6, first strand: chain 'm' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'n' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.308A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.308A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AD3, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.294A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 28 through 32 removed outlier: 5.294A pdb=" N SER M 65 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD6, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.245A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY N 93 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.245A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER N 187 " --> pdb=" O ARG N 111 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.643A pdb=" N ILE H 29 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN H 64 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 31 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG H 118 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY H 93 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N MET H 120 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.643A pdb=" N ILE H 29 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN H 64 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 31 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 5 through 8 Processing sheet with id=AE3, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.319A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.319A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER I 187 " --> pdb=" O ARG I 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 5 through 8 Processing sheet with id=AE6, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.664A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.664A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.299A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY K 93 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N MET K 120 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.299A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AF3, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.257A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG L 118 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY L 93 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N MET L 120 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.257A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) 1211 hydrogen bonds defined for protein. 3561 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: 16.55 Time building geometry restraints manager: 33.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21333 1.03 - 1.22: 68 1.22 - 1.42: 8790 1.42 - 1.62: 12491 1.62 - 1.82: 308 Bond restraints: 42990 Sorted by residual: bond pdb=" CA LEU M 189 " pdb=" CB LEU M 189 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.76e-02 3.23e+03 7.55e+00 bond pdb=" CA ALA M 96 " pdb=" CB ALA M 96 " ideal model delta sigma weight residual 1.527 1.489 0.038 1.49e-02 4.50e+03 6.52e+00 bond pdb=" CG1 ILE L 63 " pdb=" CD1 ILE L 63 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.50e+00 bond pdb=" CG1 ILE M 63 " pdb=" CD1 ILE M 63 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.46e+00 bond pdb=" CG1 ILE N 63 " pdb=" CD1 ILE N 63 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 ... (remaining 42985 not shown) Histogram of bond angle deviations from ideal: 96.47 - 103.46: 339 103.46 - 110.45: 41509 110.45 - 117.45: 16611 117.45 - 124.44: 17033 124.44 - 131.43: 2239 Bond angle restraints: 77731 Sorted by residual: angle pdb=" N SER M 65 " pdb=" CA SER M 65 " pdb=" C SER M 65 " ideal model delta sigma weight residual 109.64 115.61 -5.97 1.56e+00 4.11e-01 1.47e+01 angle pdb=" N ASP K 18 " pdb=" CA ASP K 18 " pdb=" C ASP K 18 " ideal model delta sigma weight residual 110.55 106.07 4.48 1.35e+00 5.49e-01 1.10e+01 angle pdb=" C PHE N 17 " pdb=" CA PHE N 17 " pdb=" CB PHE N 17 " ideal model delta sigma weight residual 109.56 102.34 7.22 2.22e+00 2.03e-01 1.06e+01 angle pdb=" N ASP I 18 " pdb=" CA ASP I 18 " pdb=" C ASP I 18 " ideal model delta sigma weight residual 110.55 106.17 4.38 1.35e+00 5.49e-01 1.05e+01 angle pdb=" N ASP J 18 " pdb=" CA ASP J 18 " pdb=" C ASP J 18 " ideal model delta sigma weight residual 110.55 106.30 4.25 1.35e+00 5.49e-01 9.93e+00 ... (remaining 77726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 17734 17.62 - 35.23: 1722 35.23 - 52.85: 481 52.85 - 70.47: 125 70.47 - 88.08: 11 Dihedral angle restraints: 20073 sinusoidal: 11191 harmonic: 8882 Sorted by residual: dihedral pdb=" CB MET I 120 " pdb=" CG MET I 120 " pdb=" SD MET I 120 " pdb=" CE MET I 120 " ideal model delta sinusoidal sigma weight residual 60.00 117.36 -57.36 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB MET H 120 " pdb=" CG MET H 120 " pdb=" SD MET H 120 " pdb=" CE MET H 120 " ideal model delta sinusoidal sigma weight residual 180.00 122.97 57.03 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB MET j 120 " pdb=" CG MET j 120 " pdb=" SD MET j 120 " pdb=" CE MET j 120 " ideal model delta sinusoidal sigma weight residual 60.00 112.44 -52.44 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 20070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1770 0.041 - 0.083: 960 0.083 - 0.124: 473 0.124 - 0.165: 78 0.165 - 0.207: 21 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA PRO j 115 " pdb=" N PRO j 115 " pdb=" C PRO j 115 " pdb=" CB PRO j 115 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO k 115 " pdb=" N PRO k 115 " pdb=" C PRO k 115 " pdb=" CB PRO k 115 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL i 185 " pdb=" CA VAL i 185 " pdb=" CG1 VAL i 185 " pdb=" CG2 VAL i 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3299 not shown) Planarity restraints: 6387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO M 66 " -0.029 2.00e-02 2.50e+03 5.72e-02 3.28e+01 pdb=" C PRO M 66 " 0.099 2.00e-02 2.50e+03 pdb=" O PRO M 66 " -0.036 2.00e-02 2.50e+03 pdb=" N GLY M 67 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 12 " -0.307 9.50e-02 1.11e+02 1.02e-01 1.11e+01 pdb=" NE ARG I 12 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG I 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG I 12 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 12 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG I 12 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG I 12 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG I 12 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG I 12 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 118 " -0.286 9.50e-02 1.11e+02 9.55e-02 9.68e+00 pdb=" NE ARG H 118 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 118 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 118 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 118 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG H 118 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG H 118 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG H 118 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG H 118 " -0.005 2.00e-02 2.50e+03 ... (remaining 6384 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 5256 2.24 - 2.83: 98910 2.83 - 3.42: 110512 3.42 - 4.01: 162083 4.01 - 4.60: 256374 Nonbonded interactions: 633135 Sorted by model distance: nonbonded pdb=" HG1 THR M 10 " pdb=" O GLY M 13 " model vdw 1.649 1.850 nonbonded pdb=" HG1 THR N 10 " pdb=" O GLY N 13 " model vdw 1.653 1.850 nonbonded pdb=" O MET K 153 " pdb=" HG1 THR K 157 " model vdw 1.681 1.850 nonbonded pdb=" O MET M 153 " pdb=" HG1 THR M 157 " model vdw 1.684 1.850 nonbonded pdb=" O ALA m 72 " pdb=" HG SER m 75 " model vdw 1.685 1.850 ... (remaining 633130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'I' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'J' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'K' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'L' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'M' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'N' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'h' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 through 16 or (resid 17 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HZ )) or resid 18 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or na \ me HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 \ or name HH21 or name HH22)) or resid 193)) selection = (chain 'i' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'j' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) selection = (chain 'k' and (resid 2 through 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD \ 2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) o \ r resid 193)) selection = (chain 'l' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 193)) selection = (chain 'm' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 193)) selection = (chain 'n' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 8 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HZ )) or resid 18 through 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name H \ H22)) or resid 193)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.640 Extract box with map and model: 14.840 Check model and map are aligned: 0.570 Set scattering table: 0.380 Process input model: 125.520 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.014 0.095 21629 Z= 0.961 Angle : 0.878 8.483 29139 Z= 0.474 Chirality : 0.059 0.207 3302 Planarity : 0.006 0.132 3789 Dihedral : 12.474 88.083 8173 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2675 helix: 1.12 (0.14), residues: 1389 sheet: 0.11 (0.26), residues: 292 loop : -1.78 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS K 122 PHE 0.042 0.002 PHE N 17 TYR 0.013 0.002 TYR m 62 ARG 0.005 0.001 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 3.139 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: h 57 LYS cc_start: 0.7174 (mtpp) cc_final: 0.6771 (mtmt) REVERT: h 129 GLN cc_start: 0.7592 (mt0) cc_final: 0.6848 (mm-40) REVERT: h 191 HIS cc_start: 0.7493 (m90) cc_final: 0.7210 (m-70) REVERT: i 21 SER cc_start: 0.7320 (m) cc_final: 0.6690 (m) REVERT: i 22 ARG cc_start: 0.7594 (tpt90) cc_final: 0.7145 (tpt90) REVERT: j 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6312 (mt-10) REVERT: k 26 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6347 (mt-10) REVERT: k 41 ASN cc_start: 0.7009 (t0) cc_final: 0.6798 (t0) REVERT: l 108 LYS cc_start: 0.7572 (tptm) cc_final: 0.7154 (tppt) REVERT: l 168 THR cc_start: 0.5356 (p) cc_final: 0.5132 (p) REVERT: l 169 GLU cc_start: 0.6374 (mm-30) cc_final: 0.5934 (tm-30) REVERT: M 118 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6073 (ptp-170) REVERT: M 186 ASP cc_start: 0.7701 (m-30) cc_final: 0.7394 (m-30) REVERT: I 57 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6942 (ttmt) REVERT: I 118 ARG cc_start: 0.7074 (mmt180) cc_final: 0.5850 (ttp-170) REVERT: J 57 LYS cc_start: 0.6867 (mtpp) cc_final: 0.6604 (ttpt) REVERT: J 118 ARG cc_start: 0.6631 (mmt180) cc_final: 0.6195 (ttm170) REVERT: K 84 LYS cc_start: 0.7504 (mtpt) cc_final: 0.7026 (mmpt) REVERT: K 118 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.5877 (ptt180) REVERT: L 56 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6864 (mp0) REVERT: L 84 LYS cc_start: 0.7085 (mtpt) cc_final: 0.6881 (ttpt) REVERT: L 117 SER cc_start: 0.8098 (p) cc_final: 0.7540 (m) REVERT: L 118 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.5950 (ptm160) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 2.7467 time to fit residues: 1716.4419 Evaluate side-chains 398 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 41 ASN h 116 ASN i 41 ASN j 41 ASN j 81 GLN l 159 GLN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 41 ASN M 41 ASN N 159 GLN H 41 ASN I 41 ASN J 41 ASN K 41 ASN L 9 GLN L 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21629 Z= 0.240 Angle : 0.530 6.381 29139 Z= 0.277 Chirality : 0.042 0.185 3302 Planarity : 0.004 0.039 3789 Dihedral : 3.663 21.831 2949 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.35 % Allowed : 11.23 % Favored : 87.42 % 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: 0.82 (0.16), residues: 2675 helix: 1.86 (0.14), residues: 1378 sheet: 0.07 (0.28), residues: 285 loop : -1.20 (0.16), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS k 191 PHE 0.018 0.001 PHE m 101 TYR 0.011 0.001 TYR k 77 ARG 0.004 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 522 time to evaluate : 5.393 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: h 26 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5711 (mt-10) REVERT: h 57 LYS cc_start: 0.7448 (mtpp) cc_final: 0.7031 (mtmt) REVERT: h 60 TYR cc_start: 0.7945 (m-80) cc_final: 0.7733 (m-80) REVERT: h 129 GLN cc_start: 0.7692 (mt0) cc_final: 0.7217 (mm110) REVERT: i 22 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7464 (tpt90) REVERT: i 54 ASN cc_start: 0.8095 (t0) cc_final: 0.7826 (t0) REVERT: i 151 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6139 (mt-10) REVERT: j 41 ASN cc_start: 0.7370 (t0) cc_final: 0.6812 (t0) REVERT: j 120 MET cc_start: 0.8229 (tmm) cc_final: 0.8011 (tmm) REVERT: j 144 LYS cc_start: 0.7332 (mttt) cc_final: 0.7007 (mttp) REVERT: j 181 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6498 (mp0) REVERT: k 26 GLU cc_start: 0.6722 (mt-10) cc_final: 0.5783 (tp30) REVERT: k 41 ASN cc_start: 0.7282 (t0) cc_final: 0.6901 (t0) REVERT: l 108 LYS cc_start: 0.7906 (tptm) cc_final: 0.7466 (tppt) REVERT: l 169 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6160 (tm-30) REVERT: m 118 ARG cc_start: 0.6604 (mtt-85) cc_final: 0.6088 (ptt180) REVERT: m 169 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5912 (tm-30) REVERT: n 141 GLU cc_start: 0.6898 (tp30) cc_final: 0.6667 (tp30) REVERT: n 178 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6961 (mt-10) REVERT: M 14 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.5072 (tp30) REVERT: M 118 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6113 (ptt180) REVERT: M 148 ARG cc_start: 0.7267 (tpt170) cc_final: 0.7020 (tpm-80) REVERT: M 186 ASP cc_start: 0.8070 (m-30) cc_final: 0.7758 (m-30) REVERT: H 84 LYS cc_start: 0.6906 (mtpt) cc_final: 0.6611 (mtpp) REVERT: H 92 MET cc_start: 0.8273 (ptp) cc_final: 0.7888 (ptm) REVERT: H 120 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7887 (ttm) REVERT: H 136 GLU cc_start: 0.6723 (tt0) cc_final: 0.6523 (tt0) REVERT: H 144 LYS cc_start: 0.7548 (mttt) cc_final: 0.7345 (mttt) REVERT: I 57 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7266 (ttmt) REVERT: I 84 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7154 (mttm) REVERT: J 25 LYS cc_start: 0.7171 (tttm) cc_final: 0.6906 (ttpp) REVERT: J 118 ARG cc_start: 0.6853 (mmt180) cc_final: 0.6327 (ttm170) REVERT: K 15 ARG cc_start: 0.6942 (ttm170) cc_final: 0.6037 (ttm170) REVERT: K 54 ASN cc_start: 0.7790 (t0) cc_final: 0.7524 (t0) REVERT: K 57 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7039 (ttpt) REVERT: K 84 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7431 (mmpt) REVERT: K 118 ARG cc_start: 0.7020 (mtt-85) cc_final: 0.6084 (ptt180) REVERT: L 54 ASN cc_start: 0.7491 (t0) cc_final: 0.6974 (t0) REVERT: L 57 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7143 (ttpt) REVERT: L 118 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6159 (ptt180) REVERT: L 144 LYS cc_start: 0.7081 (mttt) cc_final: 0.6801 (mttp) outliers start: 31 outliers final: 14 residues processed: 537 average time/residue: 2.8856 time to fit residues: 1792.5710 Evaluate side-chains 459 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 443 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain M residue 14 GLU Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain L residue 153 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 41 ASN i 41 ASN l 41 ASN l 123 GLN l 129 GLN m 116 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 116 ASN N 129 GLN H 41 ASN I 41 ASN J 41 ASN J 129 GLN K 41 ASN L 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21629 Z= 0.298 Angle : 0.532 5.382 29139 Z= 0.280 Chirality : 0.043 0.158 3302 Planarity : 0.004 0.043 3789 Dihedral : 3.876 21.165 2949 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.09 % Allowed : 13.15 % Favored : 84.76 % 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: 0.99 (0.16), residues: 2675 helix: 1.90 (0.15), residues: 1374 sheet: 0.18 (0.30), residues: 248 loop : -0.91 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS k 191 PHE 0.016 0.001 PHE k 101 TYR 0.010 0.001 TYR k 77 ARG 0.005 0.000 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 524 time to evaluate : 2.819 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: h 22 ARG cc_start: 0.7757 (tpt90) cc_final: 0.7508 (tpt90) REVERT: h 57 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7225 (mtmt) REVERT: h 129 GLN cc_start: 0.7765 (mt0) cc_final: 0.7405 (mm-40) REVERT: i 22 ARG cc_start: 0.7822 (tpt90) cc_final: 0.7564 (tpt90) REVERT: i 54 ASN cc_start: 0.8046 (t0) cc_final: 0.7842 (t0) REVERT: i 144 LYS cc_start: 0.7265 (mttt) cc_final: 0.7014 (mttt) REVERT: j 41 ASN cc_start: 0.7284 (t0) cc_final: 0.6805 (t0) REVERT: j 144 LYS cc_start: 0.7372 (mttt) cc_final: 0.7039 (mttp) REVERT: k 26 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6486 (mm-30) REVERT: k 41 ASN cc_start: 0.7378 (t0) cc_final: 0.7088 (t0) REVERT: k 47 MET cc_start: 0.7755 (mtt) cc_final: 0.7285 (mtt) REVERT: l 22 ARG cc_start: 0.7429 (tpt90) cc_final: 0.7181 (tpt90) REVERT: l 108 LYS cc_start: 0.8385 (tptm) cc_final: 0.7768 (tppt) REVERT: l 129 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7697 (mp10) REVERT: l 144 LYS cc_start: 0.7078 (mtmt) cc_final: 0.6762 (mtmt) REVERT: l 169 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6559 (tm-30) REVERT: m 108 LYS cc_start: 0.7952 (tptm) cc_final: 0.7195 (mppt) REVERT: m 118 ARG cc_start: 0.7089 (mtt-85) cc_final: 0.6041 (ptt180) REVERT: n 22 ARG cc_start: 0.7369 (tpt90) cc_final: 0.7132 (tpt90) REVERT: n 92 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7230 (ptt) REVERT: n 108 LYS cc_start: 0.8368 (tptm) cc_final: 0.7741 (mmtm) REVERT: n 140 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6554 (mtm-85) REVERT: n 141 GLU cc_start: 0.7225 (tp30) cc_final: 0.7020 (tp30) REVERT: M 118 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.6277 (ptt180) REVERT: M 148 ARG cc_start: 0.7298 (tpt170) cc_final: 0.7035 (tpm-80) REVERT: N 22 ARG cc_start: 0.7677 (tpt90) cc_final: 0.7352 (tpm-80) REVERT: N 34 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7584 (tp40) REVERT: N 41 ASN cc_start: 0.6869 (m-40) cc_final: 0.6413 (m110) REVERT: N 57 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7926 (mttt) REVERT: N 143 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7088 (mm) REVERT: N 181 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6783 (mt-10) REVERT: H 15 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7585 (ttm170) REVERT: H 120 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: H 144 LYS cc_start: 0.7552 (mttt) cc_final: 0.7309 (mttp) REVERT: H 153 MET cc_start: 0.7768 (mmm) cc_final: 0.7269 (tpt) REVERT: I 57 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7578 (ttmt) REVERT: I 92 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7796 (ptm) REVERT: I 98 MET cc_start: 0.7294 (tpt) cc_final: 0.7088 (tpt) REVERT: I 171 ASP cc_start: 0.8150 (m-30) cc_final: 0.7617 (m-30) REVERT: J 25 LYS cc_start: 0.7356 (tttm) cc_final: 0.7122 (ttpp) REVERT: J 56 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6573 (mp0) REVERT: J 118 ARG cc_start: 0.7024 (mmt180) cc_final: 0.6222 (ttm170) REVERT: J 149 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7179 (mmm) REVERT: K 15 ARG cc_start: 0.7318 (ttm170) cc_final: 0.6444 (ttm170) REVERT: K 84 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7147 (mmtt) REVERT: K 118 ARG cc_start: 0.7315 (mtt-85) cc_final: 0.6307 (ptt180) REVERT: K 144 LYS cc_start: 0.7453 (mttt) cc_final: 0.7168 (mttp) REVERT: K 180 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7420 (t) REVERT: K 190 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7478 (m) REVERT: L 25 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7759 (tttp) REVERT: L 118 ARG cc_start: 0.7510 (mtt-85) cc_final: 0.6336 (ptp-170) REVERT: L 140 ARG cc_start: 0.6807 (mtp180) cc_final: 0.6519 (mtm110) REVERT: L 144 LYS cc_start: 0.7225 (mttt) cc_final: 0.7009 (mttp) outliers start: 48 outliers final: 15 residues processed: 543 average time/residue: 2.9969 time to fit residues: 1843.8990 Evaluate side-chains 492 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 470 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 92 MET Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 180 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 190 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 41 ASN i 41 ASN m 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 GLN M 34 GLN M 41 ASN H 34 GLN L 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21629 Z= 0.337 Angle : 0.552 6.013 29139 Z= 0.293 Chirality : 0.044 0.150 3302 Planarity : 0.004 0.034 3789 Dihedral : 4.208 22.484 2949 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.44 % Allowed : 14.50 % Favored : 83.06 % 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: 0.87 (0.16), residues: 2675 helix: 1.75 (0.15), residues: 1363 sheet: 0.24 (0.30), residues: 238 loop : -0.87 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS m 122 PHE 0.010 0.001 PHE l 173 TYR 0.011 0.002 TYR k 77 ARG 0.004 0.000 ARG m 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 513 time to evaluate : 2.805 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: h 25 LYS cc_start: 0.7433 (mtpp) cc_final: 0.7206 (mtpp) REVERT: h 41 ASN cc_start: 0.8105 (t0) cc_final: 0.7844 (t0) REVERT: h 57 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7557 (mtmt) REVERT: h 92 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7362 (ptt) REVERT: h 108 LYS cc_start: 0.8081 (tptm) cc_final: 0.7459 (tppt) REVERT: h 129 GLN cc_start: 0.7734 (mt0) cc_final: 0.7323 (mm-40) REVERT: h 153 MET cc_start: 0.7913 (mmm) cc_final: 0.7309 (tpt) REVERT: i 20 TYR cc_start: 0.8011 (m-80) cc_final: 0.7769 (m-10) REVERT: i 22 ARG cc_start: 0.7875 (tpt90) cc_final: 0.7627 (tpt90) REVERT: i 92 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7672 (ptt) REVERT: i 108 LYS cc_start: 0.8704 (tptm) cc_final: 0.8485 (tptp) REVERT: j 22 ARG cc_start: 0.8017 (tpt90) cc_final: 0.7570 (tpt90) REVERT: j 26 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6008 (mt-10) REVERT: j 41 ASN cc_start: 0.7439 (t0) cc_final: 0.6945 (t0) REVERT: k 26 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6478 (mm-30) REVERT: k 144 LYS cc_start: 0.7293 (mtmm) cc_final: 0.6897 (mtmt) REVERT: l 144 LYS cc_start: 0.7164 (ttmt) cc_final: 0.6877 (mtmt) REVERT: l 162 GLU cc_start: 0.7130 (mp0) cc_final: 0.6830 (mp0) REVERT: m 25 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7242 (mtpp) REVERT: m 108 LYS cc_start: 0.8388 (tptm) cc_final: 0.7768 (tppt) REVERT: m 118 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.5968 (ptt180) REVERT: m 153 MET cc_start: 0.7981 (mmt) cc_final: 0.7576 (mmt) REVERT: m 162 GLU cc_start: 0.7061 (mp0) cc_final: 0.6859 (mp0) REVERT: n 22 ARG cc_start: 0.7813 (tpt90) cc_final: 0.7484 (tpt90) REVERT: n 140 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6737 (mtm-85) REVERT: n 144 LYS cc_start: 0.6763 (mttt) cc_final: 0.6401 (mttt) REVERT: M 118 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6269 (ptt180) REVERT: M 190 THR cc_start: 0.8202 (t) cc_final: 0.7948 (m) REVERT: N 22 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7755 (tpm-80) REVERT: N 34 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7817 (tp40) REVERT: N 41 ASN cc_start: 0.7048 (m-40) cc_final: 0.6598 (m110) REVERT: N 53 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6490 (mm-30) REVERT: N 57 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8019 (mttt) REVERT: N 84 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6482 (mttp) REVERT: H 41 ASN cc_start: 0.7685 (m110) cc_final: 0.7387 (m110) REVERT: H 108 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7840 (tmtt) REVERT: H 120 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: H 153 MET cc_start: 0.7847 (mmm) cc_final: 0.7441 (tpt) REVERT: I 56 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7045 (mp0) REVERT: I 57 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7728 (mttt) REVERT: I 144 LYS cc_start: 0.7469 (mttt) cc_final: 0.7152 (mttt) REVERT: I 171 ASP cc_start: 0.8228 (m-30) cc_final: 0.7680 (m-30) REVERT: J 15 ARG cc_start: 0.7726 (ttm170) cc_final: 0.7477 (ttp-170) REVERT: J 56 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7204 (mp0) REVERT: J 118 ARG cc_start: 0.7122 (mmt180) cc_final: 0.6229 (ptp-170) REVERT: J 144 LYS cc_start: 0.7454 (mttt) cc_final: 0.7236 (mttp) REVERT: J 149 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: K 15 ARG cc_start: 0.7522 (ttm170) cc_final: 0.6615 (ttm170) REVERT: K 84 LYS cc_start: 0.7440 (mtpt) cc_final: 0.6858 (mmtm) REVERT: K 118 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.6464 (ptt180) REVERT: K 129 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7161 (mm110) REVERT: K 144 LYS cc_start: 0.7551 (mttt) cc_final: 0.7267 (mttp) REVERT: K 148 ARG cc_start: 0.7320 (tpt170) cc_final: 0.7100 (mmm160) REVERT: K 190 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7886 (m) REVERT: L 118 ARG cc_start: 0.7591 (mtt-85) cc_final: 0.6281 (ptp-170) REVERT: L 144 LYS cc_start: 0.7146 (mttt) cc_final: 0.6903 (mttp) REVERT: L 181 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6897 (mt-10) outliers start: 56 outliers final: 22 residues processed: 529 average time/residue: 3.1528 time to fit residues: 1890.6114 Evaluate side-chains 493 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 463 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN m 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN H 34 GLN J 41 ASN L 9 GLN L 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21629 Z= 0.241 Angle : 0.489 5.212 29139 Z= 0.257 Chirality : 0.041 0.139 3302 Planarity : 0.003 0.044 3789 Dihedral : 4.053 22.433 2949 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.26 % Allowed : 16.20 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2675 helix: 1.87 (0.15), residues: 1369 sheet: -0.19 (0.26), residues: 367 loop : -0.73 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 122 PHE 0.011 0.001 PHE H 17 TYR 0.008 0.001 TYR m 60 ARG 0.006 0.000 ARG l 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 482 time to evaluate : 3.308 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: h 57 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7609 (mtmt) REVERT: h 92 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7003 (ptt) REVERT: h 108 LYS cc_start: 0.8064 (tptm) cc_final: 0.7441 (tppt) REVERT: h 129 GLN cc_start: 0.7748 (mt0) cc_final: 0.7408 (mm-40) REVERT: i 20 TYR cc_start: 0.7985 (m-80) cc_final: 0.7784 (m-80) REVERT: i 22 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7599 (tpt90) REVERT: i 57 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7714 (mttp) REVERT: i 108 LYS cc_start: 0.8673 (tptm) cc_final: 0.8350 (tptp) REVERT: j 22 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7562 (tpt90) REVERT: j 26 GLU cc_start: 0.6390 (mt-10) cc_final: 0.6044 (mt-10) REVERT: j 41 ASN cc_start: 0.7445 (t0) cc_final: 0.7132 (t0) REVERT: j 144 LYS cc_start: 0.7325 (mttt) cc_final: 0.6990 (mttp) REVERT: k 26 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6476 (mm-30) REVERT: k 34 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7752 (tp40) REVERT: k 47 MET cc_start: 0.7831 (mtt) cc_final: 0.7581 (mtt) REVERT: k 92 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6977 (ptt) REVERT: k 144 LYS cc_start: 0.7281 (mtmm) cc_final: 0.6901 (mtmt) REVERT: l 37 ASP cc_start: 0.6855 (m-30) cc_final: 0.6590 (m-30) REVERT: l 140 ARG cc_start: 0.7511 (ttm170) cc_final: 0.6876 (mtm-85) REVERT: l 162 GLU cc_start: 0.7112 (mp0) cc_final: 0.6752 (mp0) REVERT: m 25 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7279 (mtpp) REVERT: m 84 LYS cc_start: 0.7125 (mtpp) cc_final: 0.6513 (mttp) REVERT: m 108 LYS cc_start: 0.8430 (tptm) cc_final: 0.7829 (tppt) REVERT: m 118 ARG cc_start: 0.7356 (mtt-85) cc_final: 0.6015 (ptt180) REVERT: m 153 MET cc_start: 0.7952 (mmt) cc_final: 0.7693 (mmt) REVERT: m 162 GLU cc_start: 0.7110 (mp0) cc_final: 0.6905 (mp0) REVERT: n 22 ARG cc_start: 0.7780 (tpt90) cc_final: 0.7405 (tpt90) REVERT: n 140 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6723 (mtm-85) REVERT: n 144 LYS cc_start: 0.6815 (mttt) cc_final: 0.6448 (mttt) REVERT: M 15 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: M 118 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.6272 (ptt180) REVERT: M 190 THR cc_start: 0.8184 (t) cc_final: 0.7943 (m) REVERT: N 34 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7855 (tp40) REVERT: N 41 ASN cc_start: 0.7031 (m-40) cc_final: 0.6586 (m110) REVERT: N 53 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6467 (mm-30) REVERT: N 57 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7933 (mttt) REVERT: H 108 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7859 (tmtt) REVERT: H 120 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: H 153 MET cc_start: 0.7839 (mmm) cc_final: 0.7408 (tpt) REVERT: I 56 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7067 (mp0) REVERT: I 57 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7758 (mttt) REVERT: I 144 LYS cc_start: 0.7422 (mttt) cc_final: 0.7095 (mttt) REVERT: I 171 ASP cc_start: 0.8186 (m-30) cc_final: 0.7644 (m-30) REVERT: J 56 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7234 (mp0) REVERT: J 118 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6280 (ptp-170) REVERT: J 144 LYS cc_start: 0.7431 (mttt) cc_final: 0.7221 (mttp) REVERT: J 149 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7245 (mmm) REVERT: K 15 ARG cc_start: 0.7529 (ttm170) cc_final: 0.6587 (ttm170) REVERT: K 84 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6791 (mmtm) REVERT: K 118 ARG cc_start: 0.7538 (mtt-85) cc_final: 0.6443 (ptt180) REVERT: K 129 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: K 144 LYS cc_start: 0.7498 (mttt) cc_final: 0.7271 (mttp) REVERT: K 190 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7815 (m) REVERT: L 5 MET cc_start: 0.8237 (mmm) cc_final: 0.7889 (mmm) REVERT: L 98 MET cc_start: 0.7762 (tpt) cc_final: 0.7212 (tpt) REVERT: L 118 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.6282 (ptt180) REVERT: L 144 LYS cc_start: 0.7136 (mttt) cc_final: 0.6892 (mttp) outliers start: 52 outliers final: 27 residues processed: 499 average time/residue: 3.0180 time to fit residues: 1705.1696 Evaluate side-chains 500 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 464 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN M 41 ASN H 34 GLN I 9 GLN I 34 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21629 Z= 0.401 Angle : 0.550 5.612 29139 Z= 0.295 Chirality : 0.044 0.150 3302 Planarity : 0.004 0.037 3789 Dihedral : 4.274 22.587 2949 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.35 % Allowed : 16.63 % Favored : 81.02 % 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: 0.83 (0.16), residues: 2675 helix: 1.70 (0.15), residues: 1361 sheet: 0.21 (0.28), residues: 295 loop : -0.93 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS m 122 PHE 0.015 0.001 PHE H 17 TYR 0.015 0.002 TYR k 62 ARG 0.004 0.000 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 474 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5407 (mp) REVERT: h 57 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7686 (mtmt) REVERT: h 108 LYS cc_start: 0.8098 (tptm) cc_final: 0.7450 (tppt) REVERT: h 129 GLN cc_start: 0.7774 (mt0) cc_final: 0.7374 (mm-40) REVERT: i 22 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7608 (tpt90) REVERT: i 57 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7676 (mttt) REVERT: i 108 LYS cc_start: 0.8716 (tptm) cc_final: 0.8394 (tptp) REVERT: j 22 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7581 (tpt90) REVERT: j 26 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6162 (mt-10) REVERT: j 41 ASN cc_start: 0.7487 (t0) cc_final: 0.7209 (t0) REVERT: j 53 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6561 (mm-30) REVERT: j 144 LYS cc_start: 0.7344 (mttt) cc_final: 0.6998 (mttp) REVERT: k 26 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6404 (mm-30) REVERT: k 92 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7231 (ptt) REVERT: k 108 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8215 (tmtt) REVERT: k 144 LYS cc_start: 0.7333 (mtmm) cc_final: 0.6933 (mtmt) REVERT: l 37 ASP cc_start: 0.6880 (m-30) cc_final: 0.6633 (m-30) REVERT: m 25 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7395 (mtpp) REVERT: m 108 LYS cc_start: 0.8495 (tptm) cc_final: 0.7879 (tppt) REVERT: m 118 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.5947 (ptp-170) REVERT: m 153 MET cc_start: 0.7901 (mmt) cc_final: 0.7675 (mmt) REVERT: m 162 GLU cc_start: 0.7228 (mp0) cc_final: 0.6947 (mp0) REVERT: n 22 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7431 (tpt90) REVERT: n 108 LYS cc_start: 0.8594 (tptm) cc_final: 0.7593 (mmtm) REVERT: n 140 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6789 (mtm-85) REVERT: n 144 LYS cc_start: 0.7050 (mttt) cc_final: 0.6652 (mttt) REVERT: M 86 ASP cc_start: 0.8223 (m-30) cc_final: 0.8016 (m-30) REVERT: N 34 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7934 (tp40) REVERT: N 41 ASN cc_start: 0.7218 (m-40) cc_final: 0.6771 (m110) REVERT: N 53 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6415 (mm-30) REVERT: N 57 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7912 (mttt) REVERT: H 108 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7887 (tmtt) REVERT: H 120 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (ttm) REVERT: H 153 MET cc_start: 0.7852 (mmm) cc_final: 0.7451 (tpt) REVERT: I 15 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7184 (ttm170) REVERT: I 56 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7136 (mp0) REVERT: I 57 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7731 (mttt) REVERT: I 144 LYS cc_start: 0.7445 (mttt) cc_final: 0.7111 (mttt) REVERT: I 171 ASP cc_start: 0.8321 (m-30) cc_final: 0.7732 (m-30) REVERT: J 41 ASN cc_start: 0.6821 (m-40) cc_final: 0.6589 (m110) REVERT: J 56 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7272 (mp0) REVERT: J 118 ARG cc_start: 0.7253 (mmt180) cc_final: 0.6287 (ptp-170) REVERT: J 144 LYS cc_start: 0.7446 (mttt) cc_final: 0.7231 (mttp) REVERT: J 149 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: K 15 ARG cc_start: 0.7520 (ttm170) cc_final: 0.6710 (tpt170) REVERT: K 25 LYS cc_start: 0.7685 (tttm) cc_final: 0.7369 (tttt) REVERT: K 84 LYS cc_start: 0.7430 (mtpt) cc_final: 0.6844 (mmtm) REVERT: K 118 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.6372 (ptt180) REVERT: K 129 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: K 144 LYS cc_start: 0.7521 (mttt) cc_final: 0.7192 (mttt) REVERT: K 190 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7887 (m) REVERT: L 5 MET cc_start: 0.8241 (mmm) cc_final: 0.7905 (mmm) REVERT: L 15 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7236 (ptp-170) REVERT: L 34 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7530 (tp40) REVERT: L 118 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.6281 (ptp-170) REVERT: L 140 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6560 (mtm110) REVERT: L 144 LYS cc_start: 0.7062 (mttt) cc_final: 0.6757 (mttp) REVERT: L 172 ARG cc_start: 0.7484 (ttt90) cc_final: 0.7208 (tpp80) outliers start: 54 outliers final: 32 residues processed: 493 average time/residue: 3.1796 time to fit residues: 1780.4166 Evaluate side-chains 499 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 458 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 129 GLN H 34 GLN I 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21629 Z= 0.207 Angle : 0.475 5.676 29139 Z= 0.249 Chirality : 0.041 0.142 3302 Planarity : 0.003 0.036 3789 Dihedral : 4.081 22.160 2949 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.92 % Allowed : 16.85 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2675 helix: 1.90 (0.15), residues: 1364 sheet: 0.39 (0.29), residues: 279 loop : -0.77 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS m 122 PHE 0.009 0.001 PHE H 17 TYR 0.009 0.001 TYR m 60 ARG 0.004 0.000 ARG l 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 465 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 57 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7652 (mtmt) REVERT: h 108 LYS cc_start: 0.8139 (tptm) cc_final: 0.7480 (tppt) REVERT: h 129 GLN cc_start: 0.7773 (mt0) cc_final: 0.7434 (mm-40) REVERT: i 22 ARG cc_start: 0.7960 (tpt90) cc_final: 0.7647 (tpt90) REVERT: i 57 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7651 (mttt) REVERT: i 108 LYS cc_start: 0.8692 (tptm) cc_final: 0.8382 (tptp) REVERT: j 22 ARG cc_start: 0.8017 (tpt90) cc_final: 0.7591 (tpt90) REVERT: j 26 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6122 (mt-10) REVERT: j 41 ASN cc_start: 0.7443 (t0) cc_final: 0.7152 (t0) REVERT: j 53 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6549 (mm-30) REVERT: j 144 LYS cc_start: 0.7372 (mttt) cc_final: 0.7037 (mttp) REVERT: k 26 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6438 (mm-30) REVERT: k 34 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7733 (tp40) REVERT: k 92 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6986 (ptt) REVERT: k 108 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8224 (tmtt) REVERT: k 144 LYS cc_start: 0.7279 (mtmm) cc_final: 0.6895 (mtmt) REVERT: l 37 ASP cc_start: 0.6805 (m-30) cc_final: 0.6591 (m-30) REVERT: l 140 ARG cc_start: 0.7493 (ttm170) cc_final: 0.6941 (mtm-85) REVERT: l 181 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6198 (mm-30) REVERT: m 84 LYS cc_start: 0.7230 (mtpp) cc_final: 0.6604 (mttp) REVERT: m 108 LYS cc_start: 0.8520 (tptm) cc_final: 0.7871 (tppt) REVERT: m 118 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6000 (ptt180) REVERT: m 162 GLU cc_start: 0.7143 (mp0) cc_final: 0.6924 (mp0) REVERT: n 22 ARG cc_start: 0.7822 (tpt90) cc_final: 0.7434 (tpt90) REVERT: n 108 LYS cc_start: 0.8603 (tptm) cc_final: 0.7618 (mmtm) REVERT: n 140 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6814 (mtm-85) REVERT: n 144 LYS cc_start: 0.7040 (mttt) cc_final: 0.6797 (mtmt) REVERT: N 34 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7940 (tp40) REVERT: N 41 ASN cc_start: 0.7047 (m-40) cc_final: 0.6607 (m110) REVERT: N 53 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6351 (mm-30) REVERT: N 57 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7888 (mttt) REVERT: N 181 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6775 (mp0) REVERT: H 108 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7898 (tmtt) REVERT: H 120 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8243 (ttm) REVERT: H 153 MET cc_start: 0.7836 (mmm) cc_final: 0.7247 (tpt) REVERT: I 56 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7130 (mp0) REVERT: I 57 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7769 (mttt) REVERT: I 144 LYS cc_start: 0.7409 (mttt) cc_final: 0.7092 (mttt) REVERT: I 171 ASP cc_start: 0.8310 (m-30) cc_final: 0.7780 (m-30) REVERT: J 56 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7248 (mp0) REVERT: J 118 ARG cc_start: 0.7248 (mmt180) cc_final: 0.6282 (ptp-170) REVERT: J 149 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7162 (mmm) REVERT: K 15 ARG cc_start: 0.7563 (ttm170) cc_final: 0.6767 (tpt170) REVERT: K 25 LYS cc_start: 0.7625 (tttm) cc_final: 0.7313 (tttt) REVERT: K 84 LYS cc_start: 0.7386 (mtpt) cc_final: 0.6761 (mmtm) REVERT: K 118 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.6413 (ptt180) REVERT: K 129 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: K 144 LYS cc_start: 0.7491 (mttt) cc_final: 0.7238 (mttp) REVERT: K 190 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (m) REVERT: L 5 MET cc_start: 0.8221 (mmm) cc_final: 0.7940 (mmm) REVERT: L 15 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7249 (ptp-170) REVERT: L 34 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7517 (tp40) REVERT: L 118 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.6302 (ptt180) REVERT: L 144 LYS cc_start: 0.7047 (mttt) cc_final: 0.6842 (mttp) outliers start: 44 outliers final: 29 residues processed: 477 average time/residue: 3.0340 time to fit residues: 1635.1840 Evaluate side-chains 491 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 455 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 129 GLN H 34 GLN H 41 ASN I 34 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21629 Z= 0.395 Angle : 0.541 5.143 29139 Z= 0.290 Chirality : 0.043 0.148 3302 Planarity : 0.004 0.052 3789 Dihedral : 4.270 21.457 2949 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.26 % Allowed : 16.63 % Favored : 81.11 % 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: 0.86 (0.16), residues: 2675 helix: 1.73 (0.15), residues: 1361 sheet: 0.37 (0.28), residues: 281 loop : -0.95 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS m 122 PHE 0.013 0.001 PHE H 17 TYR 0.014 0.002 TYR m 60 ARG 0.006 0.000 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 469 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 2 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5738 (mt) REVERT: h 57 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7745 (mtmt) REVERT: h 108 LYS cc_start: 0.8087 (tptm) cc_final: 0.7401 (tppt) REVERT: h 129 GLN cc_start: 0.7786 (mt0) cc_final: 0.7438 (mm-40) REVERT: i 22 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7656 (tpt90) REVERT: i 108 LYS cc_start: 0.8730 (tptm) cc_final: 0.8413 (tptp) REVERT: j 22 ARG cc_start: 0.8072 (tpt90) cc_final: 0.7639 (tpt90) REVERT: j 26 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6239 (mt-10) REVERT: j 41 ASN cc_start: 0.7478 (t0) cc_final: 0.7196 (t0) REVERT: j 53 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6570 (mm-30) REVERT: j 144 LYS cc_start: 0.7346 (mttt) cc_final: 0.7124 (mttp) REVERT: k 26 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6418 (mm-30) REVERT: k 34 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7822 (tp40) REVERT: k 47 MET cc_start: 0.7907 (mtt) cc_final: 0.7705 (mtm) REVERT: k 92 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7251 (ptt) REVERT: k 108 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8249 (tmtt) REVERT: k 144 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6939 (mtmt) REVERT: l 37 ASP cc_start: 0.6863 (m-30) cc_final: 0.6623 (m-30) REVERT: l 140 ARG cc_start: 0.7509 (ttm170) cc_final: 0.7036 (ttp-110) REVERT: l 181 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6207 (mm-30) REVERT: m 47 MET cc_start: 0.7970 (mtt) cc_final: 0.7728 (mtt) REVERT: m 108 LYS cc_start: 0.8430 (tptm) cc_final: 0.7730 (tppt) REVERT: m 162 GLU cc_start: 0.7226 (mp0) cc_final: 0.6923 (mp0) REVERT: n 22 ARG cc_start: 0.7847 (tpt90) cc_final: 0.7436 (tpt90) REVERT: n 108 LYS cc_start: 0.8631 (tptm) cc_final: 0.7503 (mmtm) REVERT: n 140 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6841 (mtm-85) REVERT: n 144 LYS cc_start: 0.7094 (mttt) cc_final: 0.6834 (mtmt) REVERT: N 34 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7992 (tp40) REVERT: N 41 ASN cc_start: 0.7252 (m-40) cc_final: 0.6806 (m110) REVERT: N 53 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6443 (mm-30) REVERT: N 57 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7886 (mttt) REVERT: N 181 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6770 (mp0) REVERT: H 108 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7859 (tmtt) REVERT: H 120 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8356 (ttm) REVERT: H 153 MET cc_start: 0.7833 (mmm) cc_final: 0.7272 (tpt) REVERT: I 56 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7118 (mp0) REVERT: I 57 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7757 (mttt) REVERT: I 144 LYS cc_start: 0.7437 (mttt) cc_final: 0.7106 (mttt) REVERT: I 171 ASP cc_start: 0.8324 (m-30) cc_final: 0.7722 (m-30) REVERT: J 56 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7254 (mp0) REVERT: J 86 ASP cc_start: 0.8168 (m-30) cc_final: 0.7955 (m-30) REVERT: J 118 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6228 (ptp-170) REVERT: J 149 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7223 (mmm) REVERT: K 15 ARG cc_start: 0.7514 (ttm170) cc_final: 0.6772 (tpt170) REVERT: K 25 LYS cc_start: 0.7666 (tttm) cc_final: 0.7369 (tttt) REVERT: K 84 LYS cc_start: 0.7437 (mtpt) cc_final: 0.6802 (mmtm) REVERT: K 118 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.6372 (ptt180) REVERT: K 129 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7070 (mp10) REVERT: K 144 LYS cc_start: 0.7451 (mttt) cc_final: 0.7179 (mttt) REVERT: K 190 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7902 (m) REVERT: L 5 MET cc_start: 0.8267 (mmm) cc_final: 0.7970 (mmm) REVERT: L 15 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7307 (ptp-170) REVERT: L 34 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7643 (tp40) REVERT: L 118 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.6338 (ptp-170) REVERT: L 140 ARG cc_start: 0.6935 (mtp180) cc_final: 0.6584 (mtm110) REVERT: L 144 LYS cc_start: 0.7060 (mttt) cc_final: 0.6852 (mttp) REVERT: L 172 ARG cc_start: 0.7464 (ttt90) cc_final: 0.7135 (tpp80) outliers start: 52 outliers final: 33 residues processed: 489 average time/residue: 3.1641 time to fit residues: 1761.1935 Evaluate side-chains 502 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 461 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 6 VAL Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 6 VAL Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN H 34 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21629 Z= 0.269 Angle : 0.494 4.950 29139 Z= 0.261 Chirality : 0.041 0.145 3302 Planarity : 0.004 0.037 3789 Dihedral : 4.198 21.251 2949 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.05 % Allowed : 16.94 % Favored : 81.02 % 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: 0.95 (0.16), residues: 2675 helix: 1.77 (0.15), residues: 1367 sheet: 0.40 (0.28), residues: 286 loop : -0.87 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS m 122 PHE 0.009 0.001 PHE H 17 TYR 0.010 0.001 TYR m 60 ARG 0.005 0.000 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 464 time to evaluate : 3.512 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: h 2 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5705 (mt) REVERT: h 57 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7755 (mtmt) REVERT: h 108 LYS cc_start: 0.8124 (tptm) cc_final: 0.7428 (tppt) REVERT: h 129 GLN cc_start: 0.7787 (mt0) cc_final: 0.7442 (mm-40) REVERT: i 22 ARG cc_start: 0.7986 (tpt90) cc_final: 0.7626 (tpt90) REVERT: i 108 LYS cc_start: 0.8741 (tptm) cc_final: 0.8407 (tptp) REVERT: j 22 ARG cc_start: 0.8044 (tpt90) cc_final: 0.7632 (tpt90) REVERT: j 26 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6254 (mt-10) REVERT: j 41 ASN cc_start: 0.7465 (t0) cc_final: 0.7189 (t0) REVERT: j 53 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6555 (mm-30) REVERT: j 144 LYS cc_start: 0.7378 (mttt) cc_final: 0.7042 (mttp) REVERT: k 26 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6434 (mm-30) REVERT: k 34 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7699 (tp40) REVERT: k 92 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7085 (ptt) REVERT: k 108 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8194 (tmtt) REVERT: k 144 LYS cc_start: 0.7311 (mtmm) cc_final: 0.6918 (mtmt) REVERT: l 37 ASP cc_start: 0.6813 (m-30) cc_final: 0.6591 (m-30) REVERT: l 140 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7030 (ttp-110) REVERT: l 181 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6169 (mm-30) REVERT: m 47 MET cc_start: 0.7959 (mtt) cc_final: 0.7711 (mtt) REVERT: m 108 LYS cc_start: 0.8449 (tptm) cc_final: 0.7725 (tppt) REVERT: m 162 GLU cc_start: 0.7184 (mp0) cc_final: 0.6902 (mp0) REVERT: n 22 ARG cc_start: 0.7756 (tpt90) cc_final: 0.7425 (tpt90) REVERT: n 108 LYS cc_start: 0.8645 (tptm) cc_final: 0.7496 (mmtm) REVERT: n 140 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6807 (mtm-85) REVERT: n 144 LYS cc_start: 0.7066 (mttt) cc_final: 0.6812 (mtmt) REVERT: N 34 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7995 (tp40) REVERT: N 41 ASN cc_start: 0.7188 (m-40) cc_final: 0.6753 (m110) REVERT: N 53 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6400 (mm-30) REVERT: N 57 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7878 (mttt) REVERT: N 181 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6712 (mp0) REVERT: H 108 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7827 (tmtt) REVERT: H 120 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8330 (ttm) REVERT: H 153 MET cc_start: 0.7840 (mmm) cc_final: 0.7263 (tpt) REVERT: I 56 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7190 (mp0) REVERT: I 57 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7761 (mttt) REVERT: I 84 LYS cc_start: 0.7360 (mtpp) cc_final: 0.6999 (ttpt) REVERT: I 144 LYS cc_start: 0.7399 (mttt) cc_final: 0.7079 (mttt) REVERT: I 171 ASP cc_start: 0.8314 (m-30) cc_final: 0.7756 (m-30) REVERT: J 56 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7245 (mp0) REVERT: J 118 ARG cc_start: 0.7266 (mmt180) cc_final: 0.6212 (ptp-170) REVERT: J 149 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: K 15 ARG cc_start: 0.7540 (ttm170) cc_final: 0.6795 (tpt170) REVERT: K 25 LYS cc_start: 0.7648 (tttm) cc_final: 0.7320 (tttt) REVERT: K 84 LYS cc_start: 0.7418 (mtpt) cc_final: 0.6785 (mmtm) REVERT: K 118 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.6385 (ptt180) REVERT: K 129 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: K 190 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7883 (m) REVERT: L 5 MET cc_start: 0.8296 (mmm) cc_final: 0.8031 (mmm) REVERT: L 15 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7254 (ptp-170) REVERT: L 34 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7571 (tp40) REVERT: L 118 ARG cc_start: 0.7605 (mtt-85) cc_final: 0.6311 (ptp-170) REVERT: L 172 ARG cc_start: 0.7444 (ttt90) cc_final: 0.7181 (tpp80) outliers start: 47 outliers final: 32 residues processed: 481 average time/residue: 3.1072 time to fit residues: 1685.7196 Evaluate side-chains 496 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 456 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 122 HIS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN H 34 GLN I 34 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 129 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21629 Z= 0.298 Angle : 0.502 6.797 29139 Z= 0.266 Chirality : 0.042 0.144 3302 Planarity : 0.004 0.037 3789 Dihedral : 4.191 21.191 2949 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.00 % Allowed : 17.33 % Favored : 80.67 % 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: 0.96 (0.16), residues: 2675 helix: 1.79 (0.15), residues: 1367 sheet: 0.42 (0.28), residues: 286 loop : -0.89 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS m 122 PHE 0.015 0.001 PHE m 17 TYR 0.010 0.001 TYR m 60 ARG 0.005 0.000 ARG K 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5350 Ramachandran restraints generated. 2675 Oldfield, 0 Emsley, 2675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 465 time to evaluate : 3.369 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: h 2 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5690 (mt) REVERT: h 57 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7736 (mtmt) REVERT: h 108 LYS cc_start: 0.8127 (tptm) cc_final: 0.7402 (tppt) REVERT: h 129 GLN cc_start: 0.7785 (mt0) cc_final: 0.7425 (mm-40) REVERT: i 22 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7631 (tpt90) REVERT: i 108 LYS cc_start: 0.8714 (tptm) cc_final: 0.8383 (tptp) REVERT: j 22 ARG cc_start: 0.8037 (tpt90) cc_final: 0.7648 (tpt90) REVERT: j 26 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6207 (mt-10) REVERT: j 41 ASN cc_start: 0.7464 (t0) cc_final: 0.7186 (t0) REVERT: j 53 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6559 (mm-30) REVERT: j 144 LYS cc_start: 0.7381 (mttt) cc_final: 0.7163 (mttp) REVERT: k 26 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6463 (mm-30) REVERT: k 34 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7826 (tp40) REVERT: k 92 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7141 (ptt) REVERT: k 108 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8148 (tmtt) REVERT: k 144 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6928 (mtmt) REVERT: l 37 ASP cc_start: 0.6819 (m-30) cc_final: 0.6595 (m-30) REVERT: l 140 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7018 (ttp-110) REVERT: l 181 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6188 (mm-30) REVERT: m 47 MET cc_start: 0.7952 (mtt) cc_final: 0.7710 (mtt) REVERT: m 108 LYS cc_start: 0.8525 (tptm) cc_final: 0.7771 (tppt) REVERT: m 162 GLU cc_start: 0.7208 (mp0) cc_final: 0.6926 (mp0) REVERT: n 22 ARG cc_start: 0.7833 (tpt90) cc_final: 0.7409 (tpt90) REVERT: n 108 LYS cc_start: 0.8655 (tptm) cc_final: 0.7490 (mmtm) REVERT: n 140 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6841 (mtm-85) REVERT: n 144 LYS cc_start: 0.7081 (mttt) cc_final: 0.6824 (mtmt) REVERT: N 15 ARG cc_start: 0.7281 (ttm170) cc_final: 0.6227 (mmt180) REVERT: N 34 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7995 (tp40) REVERT: N 41 ASN cc_start: 0.7218 (m-40) cc_final: 0.6783 (m110) REVERT: N 53 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6357 (mm-30) REVERT: N 57 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7884 (mttt) REVERT: N 181 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6666 (mp0) REVERT: H 108 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7832 (tmtt) REVERT: H 120 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8366 (ttm) REVERT: H 153 MET cc_start: 0.7844 (mmm) cc_final: 0.7265 (tpt) REVERT: I 56 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7171 (mp0) REVERT: I 57 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7764 (mttt) REVERT: I 84 LYS cc_start: 0.7389 (mtpp) cc_final: 0.7088 (ttpt) REVERT: I 144 LYS cc_start: 0.7388 (mttt) cc_final: 0.7065 (mttt) REVERT: I 171 ASP cc_start: 0.8308 (m-30) cc_final: 0.7730 (m-30) REVERT: J 56 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7241 (mp0) REVERT: J 118 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6192 (ptp-170) REVERT: J 149 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7140 (mmm) REVERT: K 15 ARG cc_start: 0.7527 (ttm170) cc_final: 0.6777 (tpt170) REVERT: K 25 LYS cc_start: 0.7645 (tttm) cc_final: 0.7323 (tttt) REVERT: K 84 LYS cc_start: 0.7423 (mtpt) cc_final: 0.6780 (mmtm) REVERT: K 118 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.6412 (ptt180) REVERT: K 129 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: K 190 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7893 (m) REVERT: L 5 MET cc_start: 0.8295 (mmm) cc_final: 0.8031 (mmm) REVERT: L 15 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7243 (ptp-170) REVERT: L 34 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7671 (tp40) REVERT: L 118 ARG cc_start: 0.7599 (mtt-85) cc_final: 0.6320 (ptp-170) REVERT: L 172 ARG cc_start: 0.7449 (ttt90) cc_final: 0.7141 (tpp80) outliers start: 46 outliers final: 32 residues processed: 482 average time/residue: 3.1962 time to fit residues: 1752.0273 Evaluate side-chains 500 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 460 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain h residue 2 LEU Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 17 PHE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 58 ASP Chi-restraints excluded: chain j residue 190 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 108 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 153 MET Chi-restraints excluded: chain l residue 88 SER Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain l residue 122 HIS Chi-restraints excluded: chain l residue 190 THR Chi-restraints excluded: chain m residue 113 CYS Chi-restraints excluded: chain m residue 190 THR Chi-restraints excluded: chain n residue 36 GLU Chi-restraints excluded: chain n residue 190 THR Chi-restraints excluded: chain M residue 15 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN k 41 ASN k 129 GLN l 41 ASN ** m 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 129 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.088238 restraints weight = 67201.113| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.29 r_work: 0.2908 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21629 Z= 0.253 Angle : 0.489 5.602 29139 Z= 0.258 Chirality : 0.041 0.144 3302 Planarity : 0.004 0.037 3789 Dihedral : 4.160 22.961 2949 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 17.54 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2675 helix: 1.85 (0.15), residues: 1364 sheet: 0.37 (0.29), residues: 278 loop : -0.75 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS m 122 PHE 0.014 0.001 PHE m 17 TYR 0.009 0.001 TYR m 60 ARG 0.005 0.000 ARG K 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22733.65 seconds wall clock time: 394 minutes 35.38 seconds (23675.38 seconds total)