Starting phenix.real_space_refine on Mon Mar 11 18:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjk_22896/03_2024/7kjk_22896.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.019 sd= 0.596 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 36972 2.51 5 N 9822 2.21 5 O 12156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A5 ARG 104": "NH1" <-> "NH2" Residue "A5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A5 ARG 149": "NH1" <-> "NH2" Residue "A5 GLU 156": "OE1" <-> "OE2" Residue "A5 ASP 160": "OD1" <-> "OD2" Residue "B5 ARG 104": "NH1" <-> "NH2" Residue "B5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 ARG 149": "NH1" <-> "NH2" Residue "B5 GLU 156": "OE1" <-> "OE2" Residue "B5 ASP 160": "OD1" <-> "OD2" Residue "C5 ARG 104": "NH1" <-> "NH2" Residue "C5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 ARG 149": "NH1" <-> "NH2" Residue "C5 GLU 156": "OE1" <-> "OE2" Residue "C5 ASP 160": "OD1" <-> "OD2" Residue "D5 ARG 104": "NH1" <-> "NH2" Residue "D5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 ARG 149": "NH1" <-> "NH2" Residue "D5 GLU 156": "OE1" <-> "OE2" Residue "D5 ASP 160": "OD1" <-> "OD2" Residue "E5 ARG 104": "NH1" <-> "NH2" Residue "E5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 ARG 149": "NH1" <-> "NH2" Residue "E5 GLU 156": "OE1" <-> "OE2" Residue "E5 ASP 160": "OD1" <-> "OD2" Residue "F5 ARG 104": "NH1" <-> "NH2" Residue "F5 TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 ARG 149": "NH1" <-> "NH2" Residue "F5 GLU 156": "OE1" <-> "OE2" Residue "F5 ASP 160": "OD1" <-> "OD2" Residue "A3 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 GLU 39": "OE1" <-> "OE2" Residue "A3 GLU 55": "OE1" <-> "OE2" Residue "A3 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ARG 31": "NH1" <-> "NH2" Residue "B3 ARG 35": "NH1" <-> "NH2" Residue "B3 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 55": "OE1" <-> "OE2" Residue "B3 GLU 93": "OE1" <-> "OE2" Residue "B3 GLU 106": "OE1" <-> "OE2" Residue "C3 ARG 35": "NH1" <-> "NH2" Residue "C3 GLU 55": "OE1" <-> "OE2" Residue "C3 ASP 121": "OD1" <-> "OD2" Residue "D3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 GLU 110": "OE1" <-> "OE2" Residue "D3 ASP 121": "OD1" <-> "OD2" Residue "E3 GLU 10": "OE1" <-> "OE2" Residue "E3 ARG 31": "NH1" <-> "NH2" Residue "E3 ARG 35": "NH1" <-> "NH2" Residue "E3 GLU 55": "OE1" <-> "OE2" Residue "F3 ARG 35": "NH1" <-> "NH2" Residue "F3 GLU 55": "OE1" <-> "OE2" Residue "F3 ASP 75": "OD1" <-> "OD2" Residue "F3 ASP 123": "OD1" <-> "OD2" Residue "G3 GLU 39": "OE1" <-> "OE2" Residue "G3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G3 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G3 GLU 110": "OE1" <-> "OE2" Residue "G3 ASP 121": "OD1" <-> "OD2" Residue "H3 ARG 31": "NH1" <-> "NH2" Residue "H3 ARG 35": "NH1" <-> "NH2" Residue "I3 ARG 35": "NH1" <-> "NH2" Residue "J3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J3 GLU 55": "OE1" <-> "OE2" Residue "K3 ARG 31": "NH1" <-> "NH2" Residue "K3 ARG 35": "NH1" <-> "NH2" Residue "K3 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K3 GLU 55": "OE1" <-> "OE2" Residue "K3 GLU 93": "OE1" <-> "OE2" Residue "L3 ARG 35": "NH1" <-> "NH2" Residue "L3 GLU 55": "OE1" <-> "OE2" Residue "M3 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M3 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N3 GLU 10": "OE1" <-> "OE2" Residue "N3 ARG 31": "NH1" <-> "NH2" Residue "N3 ARG 35": "NH1" <-> "NH2" Residue "N3 GLU 55": "OE1" <-> "OE2" Residue "N3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O3 ARG 35": "NH1" <-> "NH2" Residue "O3 GLU 55": "OE1" <-> "OE2" Residue "P3 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P3 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q3 ARG 31": "NH1" <-> "NH2" Residue "Q3 ARG 35": "NH1" <-> "NH2" Residue "Q3 ASP 50": "OD1" <-> "OD2" Residue "Q3 GLU 55": "OE1" <-> "OE2" Residue "R3 ARG 35": "NH1" <-> "NH2" Residue "A4 ARG 25": "NH1" <-> "NH2" Residue "A4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 ARG 25": "NH1" <-> "NH2" Residue "B4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 ARG 25": "NH1" <-> "NH2" Residue "C4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 ARG 25": "NH1" <-> "NH2" Residue "D4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E4 ARG 25": "NH1" <-> "NH2" Residue "E4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 ARG 25": "NH1" <-> "NH2" Residue "F4 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A7 ARG 53": "NH1" <-> "NH2" Residue "A7 GLU 83": "OE1" <-> "OE2" Residue "A7 ARG 130": "NH1" <-> "NH2" Residue "A7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 ARG 53": "NH1" <-> "NH2" Residue "B7 GLU 83": "OE1" <-> "OE2" Residue "B7 ARG 130": "NH1" <-> "NH2" Residue "B7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C7 ARG 53": "NH1" <-> "NH2" Residue "C7 GLU 83": "OE1" <-> "OE2" Residue "C7 ARG 130": "NH1" <-> "NH2" Residue "C7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D7 ARG 53": "NH1" <-> "NH2" Residue "D7 GLU 83": "OE1" <-> "OE2" Residue "D7 ARG 130": "NH1" <-> "NH2" Residue "D7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E7 ARG 53": "NH1" <-> "NH2" Residue "E7 GLU 83": "OE1" <-> "OE2" Residue "E7 ARG 130": "NH1" <-> "NH2" Residue "E7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 ARG 53": "NH1" <-> "NH2" Residue "F7 GLU 83": "OE1" <-> "OE2" Residue "F7 ARG 130": "NH1" <-> "NH2" Residue "F7 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 62": "OE1" <-> "OE2" Residue "A6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 146": "OE1" <-> "OE2" Residue "A6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 360": "OE1" <-> "OE2" Residue "A6 GLU 379": "OE1" <-> "OE2" Residue "A6 GLU 419": "OE1" <-> "OE2" Residue "A6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 62": "OE1" <-> "OE2" Residue "B6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 146": "OE1" <-> "OE2" Residue "B6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 360": "OE1" <-> "OE2" Residue "B6 GLU 379": "OE1" <-> "OE2" Residue "B6 GLU 419": "OE1" <-> "OE2" Residue "B6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 GLU 62": "OE1" <-> "OE2" Residue "C6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 GLU 146": "OE1" <-> "OE2" Residue "C6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 GLU 360": "OE1" <-> "OE2" Residue "C6 GLU 379": "OE1" <-> "OE2" Residue "C6 GLU 419": "OE1" <-> "OE2" Residue "C6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 GLU 62": "OE1" <-> "OE2" Residue "D6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 GLU 146": "OE1" <-> "OE2" Residue "D6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 GLU 360": "OE1" <-> "OE2" Residue "D6 GLU 379": "OE1" <-> "OE2" Residue "D6 GLU 419": "OE1" <-> "OE2" Residue "D6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 GLU 62": "OE1" <-> "OE2" Residue "E6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 GLU 146": "OE1" <-> "OE2" Residue "E6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 GLU 360": "OE1" <-> "OE2" Residue "E6 GLU 379": "OE1" <-> "OE2" Residue "E6 GLU 419": "OE1" <-> "OE2" Residue "E6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 GLU 62": "OE1" <-> "OE2" Residue "F6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 GLU 146": "OE1" <-> "OE2" Residue "F6 TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 GLU 360": "OE1" <-> "OE2" Residue "F6 GLU 379": "OE1" <-> "OE2" Residue "F6 GLU 419": "OE1" <-> "OE2" Residue "F6 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59088 Number of models: 1 Model: "" Number of chains: 42 Chain: "A5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "B5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "C5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "D5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "E5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "F5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1267 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 1, 'TRANS': 157} Chain: "A3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "B3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "E3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "F3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "H3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "K3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "L3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "N3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "O3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "Q3" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R3" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "C4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "E4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "F4" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 918 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "B7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "C7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "D7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "E7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F7" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "B6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "C6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "D6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "E6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "F6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Time building chain proxies: 23.26, per 1000 atoms: 0.39 Number of scatterers: 59088 At special positions: 0 Unit cell: (204.12, 208.17, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 12156 8.00 N 9822 7.00 C 36972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.17 Conformation dependent library (CDL) restraints added in 8.1 seconds 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14400 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 112 sheets defined 28.7% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A5' and resid 3 through 14 Processing helix chain 'A5' and resid 82 through 94 removed outlier: 3.580A pdb=" N PHEA5 90 " --> pdb=" O ASNA5 86 " (cutoff:3.500A) Processing helix chain 'A5' and resid 96 through 103 Processing helix chain 'B5' and resid 3 through 14 Processing helix chain 'B5' and resid 82 through 94 removed outlier: 3.580A pdb=" N PHEB5 90 " --> pdb=" O ASNB5 86 " (cutoff:3.500A) Processing helix chain 'B5' and resid 96 through 103 Processing helix chain 'C5' and resid 3 through 14 Processing helix chain 'C5' and resid 82 through 94 removed outlier: 3.580A pdb=" N PHEC5 90 " --> pdb=" O ASNC5 86 " (cutoff:3.500A) Processing helix chain 'C5' and resid 96 through 103 Processing helix chain 'D5' and resid 3 through 14 Processing helix chain 'D5' and resid 82 through 94 removed outlier: 3.581A pdb=" N PHED5 90 " --> pdb=" O ASND5 86 " (cutoff:3.500A) Processing helix chain 'D5' and resid 96 through 103 Processing helix chain 'E5' and resid 3 through 14 Processing helix chain 'E5' and resid 82 through 94 removed outlier: 3.580A pdb=" N PHEE5 90 " --> pdb=" O ASNE5 86 " (cutoff:3.500A) Processing helix chain 'E5' and resid 96 through 103 Processing helix chain 'F5' and resid 3 through 14 Processing helix chain 'F5' and resid 82 through 94 removed outlier: 3.580A pdb=" N PHEF5 90 " --> pdb=" O ASNF5 86 " (cutoff:3.500A) Processing helix chain 'F5' and resid 96 through 103 Processing helix chain 'A3' and resid 44 through 46 No H-bonds generated for 'chain 'A3' and resid 44 through 46' Processing helix chain 'A3' and resid 88 through 94 Processing helix chain 'A3' and resid 96 through 126 Processing helix chain 'B3' and resid 44 through 46 No H-bonds generated for 'chain 'B3' and resid 44 through 46' Processing helix chain 'B3' and resid 87 through 95 Processing helix chain 'B3' and resid 99 through 126 Processing helix chain 'C3' and resid 10 through 14 Processing helix chain 'C3' and resid 44 through 46 No H-bonds generated for 'chain 'C3' and resid 44 through 46' Processing helix chain 'C3' and resid 87 through 93 removed outlier: 3.659A pdb=" N GLUC3 93 " --> pdb=" O ILEC3 89 " (cutoff:3.500A) Processing helix chain 'C3' and resid 99 through 105 removed outlier: 3.627A pdb=" N GLNC3 105 " --> pdb=" O VALC3 101 " (cutoff:3.500A) Processing helix chain 'C3' and resid 106 through 123 removed outlier: 4.037A pdb=" N GLUC3 110 " --> pdb=" O GLUC3 106 " (cutoff:3.500A) Processing helix chain 'C3' and resid 124 through 126 No H-bonds generated for 'chain 'C3' and resid 124 through 126' Processing helix chain 'D3' and resid 87 through 94 Processing helix chain 'D3' and resid 96 through 126 Processing helix chain 'E3' and resid 44 through 46 No H-bonds generated for 'chain 'E3' and resid 44 through 46' Processing helix chain 'E3' and resid 87 through 95 Processing helix chain 'E3' and resid 99 through 126 Processing helix chain 'F3' and resid 10 through 14 removed outlier: 3.692A pdb=" N LEUF3 13 " --> pdb=" O GLUF3 10 " (cutoff:3.500A) Processing helix chain 'F3' and resid 44 through 46 No H-bonds generated for 'chain 'F3' and resid 44 through 46' Processing helix chain 'F3' and resid 87 through 93 removed outlier: 3.663A pdb=" N GLUF3 93 " --> pdb=" O ILEF3 89 " (cutoff:3.500A) Processing helix chain 'F3' and resid 99 through 105 removed outlier: 3.700A pdb=" N GLNF3 105 " --> pdb=" O VALF3 101 " (cutoff:3.500A) Processing helix chain 'F3' and resid 106 through 123 removed outlier: 3.977A pdb=" N GLUF3 110 " --> pdb=" O GLUF3 106 " (cutoff:3.500A) Processing helix chain 'F3' and resid 124 through 126 No H-bonds generated for 'chain 'F3' and resid 124 through 126' Processing helix chain 'G3' and resid 44 through 46 No H-bonds generated for 'chain 'G3' and resid 44 through 46' Processing helix chain 'G3' and resid 87 through 94 Processing helix chain 'G3' and resid 96 through 126 Processing helix chain 'H3' and resid 44 through 46 No H-bonds generated for 'chain 'H3' and resid 44 through 46' Processing helix chain 'H3' and resid 87 through 95 Processing helix chain 'H3' and resid 99 through 126 Processing helix chain 'I3' and resid 10 through 14 removed outlier: 3.571A pdb=" N LEUI3 13 " --> pdb=" O GLUI3 10 " (cutoff:3.500A) Processing helix chain 'I3' and resid 44 through 46 No H-bonds generated for 'chain 'I3' and resid 44 through 46' Processing helix chain 'I3' and resid 87 through 93 removed outlier: 3.651A pdb=" N GLUI3 93 " --> pdb=" O ILEI3 89 " (cutoff:3.500A) Processing helix chain 'I3' and resid 99 through 105 removed outlier: 3.672A pdb=" N GLNI3 105 " --> pdb=" O VALI3 101 " (cutoff:3.500A) Processing helix chain 'I3' and resid 106 through 123 removed outlier: 4.002A pdb=" N GLUI3 110 " --> pdb=" O GLUI3 106 " (cutoff:3.500A) Processing helix chain 'I3' and resid 124 through 126 No H-bonds generated for 'chain 'I3' and resid 124 through 126' Processing helix chain 'J3' and resid 44 through 46 No H-bonds generated for 'chain 'J3' and resid 44 through 46' Processing helix chain 'J3' and resid 88 through 95 Processing helix chain 'J3' and resid 96 through 126 Processing helix chain 'K3' and resid 44 through 46 No H-bonds generated for 'chain 'K3' and resid 44 through 46' Processing helix chain 'K3' and resid 87 through 95 Processing helix chain 'K3' and resid 99 through 126 Processing helix chain 'L3' and resid 10 through 14 removed outlier: 3.542A pdb=" N LEUL3 13 " --> pdb=" O GLUL3 10 " (cutoff:3.500A) Processing helix chain 'L3' and resid 44 through 46 No H-bonds generated for 'chain 'L3' and resid 44 through 46' Processing helix chain 'L3' and resid 87 through 93 removed outlier: 3.704A pdb=" N GLUL3 93 " --> pdb=" O ILEL3 89 " (cutoff:3.500A) Processing helix chain 'L3' and resid 99 through 105 removed outlier: 3.545A pdb=" N GLNL3 105 " --> pdb=" O VALL3 101 " (cutoff:3.500A) Processing helix chain 'L3' and resid 106 through 123 removed outlier: 3.814A pdb=" N GLUL3 110 " --> pdb=" O GLUL3 106 " (cutoff:3.500A) Processing helix chain 'M3' and resid 44 through 46 No H-bonds generated for 'chain 'M3' and resid 44 through 46' Processing helix chain 'M3' and resid 87 through 95 Processing helix chain 'M3' and resid 96 through 126 Processing helix chain 'N3' and resid 44 through 46 No H-bonds generated for 'chain 'N3' and resid 44 through 46' Processing helix chain 'N3' and resid 87 through 95 Processing helix chain 'N3' and resid 99 through 126 Processing helix chain 'O3' and resid 10 through 14 removed outlier: 3.527A pdb=" N LEUO3 13 " --> pdb=" O GLUO3 10 " (cutoff:3.500A) Processing helix chain 'O3' and resid 44 through 46 No H-bonds generated for 'chain 'O3' and resid 44 through 46' Processing helix chain 'O3' and resid 87 through 93 removed outlier: 3.666A pdb=" N GLUO3 93 " --> pdb=" O ILEO3 89 " (cutoff:3.500A) Processing helix chain 'O3' and resid 99 through 105 Processing helix chain 'O3' and resid 106 through 123 removed outlier: 3.914A pdb=" N GLUO3 110 " --> pdb=" O GLUO3 106 " (cutoff:3.500A) Processing helix chain 'O3' and resid 124 through 126 No H-bonds generated for 'chain 'O3' and resid 124 through 126' Processing helix chain 'P3' and resid 44 through 46 No H-bonds generated for 'chain 'P3' and resid 44 through 46' Processing helix chain 'P3' and resid 87 through 94 Processing helix chain 'P3' and resid 96 through 126 Processing helix chain 'Q3' and resid 44 through 46 No H-bonds generated for 'chain 'Q3' and resid 44 through 46' Processing helix chain 'Q3' and resid 87 through 95 Processing helix chain 'Q3' and resid 99 through 126 Processing helix chain 'R3' and resid 10 through 14 removed outlier: 3.563A pdb=" N LEUR3 13 " --> pdb=" O GLUR3 10 " (cutoff:3.500A) Processing helix chain 'R3' and resid 44 through 46 No H-bonds generated for 'chain 'R3' and resid 44 through 46' Processing helix chain 'R3' and resid 87 through 93 removed outlier: 3.695A pdb=" N GLUR3 93 " --> pdb=" O ILER3 89 " (cutoff:3.500A) Processing helix chain 'R3' and resid 99 through 105 removed outlier: 3.690A pdb=" N GLNR3 105 " --> pdb=" O VALR3 101 " (cutoff:3.500A) Processing helix chain 'R3' and resid 106 through 123 removed outlier: 3.907A pdb=" N GLUR3 110 " --> pdb=" O GLUR3 106 " (cutoff:3.500A) Processing helix chain 'R3' and resid 124 through 126 No H-bonds generated for 'chain 'R3' and resid 124 through 126' Processing helix chain 'A4' and resid 6 through 11 removed outlier: 4.725A pdb=" N META4 11 " --> pdb=" O SERA4 7 " (cutoff:3.500A) Processing helix chain 'B4' and resid 6 through 11 removed outlier: 4.723A pdb=" N METB4 11 " --> pdb=" O SERB4 7 " (cutoff:3.500A) Processing helix chain 'C4' and resid 6 through 11 removed outlier: 4.724A pdb=" N METC4 11 " --> pdb=" O SERC4 7 " (cutoff:3.500A) Processing helix chain 'D4' and resid 6 through 11 removed outlier: 4.724A pdb=" N METD4 11 " --> pdb=" O SERD4 7 " (cutoff:3.500A) Processing helix chain 'E4' and resid 6 through 11 removed outlier: 4.725A pdb=" N METE4 11 " --> pdb=" O SERE4 7 " (cutoff:3.500A) Processing helix chain 'F4' and resid 6 through 11 removed outlier: 4.724A pdb=" N METF4 11 " --> pdb=" O SERF4 7 " (cutoff:3.500A) Processing helix chain 'A7' and resid 69 through 80 Processing helix chain 'B7' and resid 69 through 80 Processing helix chain 'C7' and resid 69 through 80 Processing helix chain 'D7' and resid 69 through 80 Processing helix chain 'E7' and resid 69 through 80 Processing helix chain 'F7' and resid 69 through 80 Processing helix chain 'A6' and resid 3 through 6 removed outlier: 3.780A pdb=" N GLUA6 6 " --> pdb=" O SERA6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A6' and resid 3 through 6' Processing helix chain 'A6' and resid 48 through 57 Processing helix chain 'A6' and resid 60 through 71 Processing helix chain 'A6' and resid 75 through 80 Processing helix chain 'A6' and resid 108 through 119 removed outlier: 3.976A pdb=" N LEUA6 112 " --> pdb=" O SERA6 108 " (cutoff:3.500A) Proline residue: A6 114 - end of helix Processing helix chain 'A6' and resid 146 through 158 removed outlier: 3.679A pdb=" N VALA6 150 " --> pdb=" O GLUA6 146 " (cutoff:3.500A) Processing helix chain 'A6' and resid 195 through 200 Processing helix chain 'A6' and resid 223 through 225 No H-bonds generated for 'chain 'A6' and resid 223 through 225' Processing helix chain 'A6' and resid 226 through 235 removed outlier: 4.139A pdb=" N ILEA6 230 " --> pdb=" O GLYA6 226 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASNA6 235 " --> pdb=" O LYSA6 231 " (cutoff:3.500A) Processing helix chain 'A6' and resid 246 through 248 No H-bonds generated for 'chain 'A6' and resid 246 through 248' Processing helix chain 'A6' and resid 249 through 261 Processing helix chain 'A6' and resid 269 through 273 Processing helix chain 'A6' and resid 279 through 288 Processing helix chain 'A6' and resid 302 through 313 removed outlier: 3.911A pdb=" N ALAA6 306 " --> pdb=" O ARGA6 302 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HISA6 313 " --> pdb=" O META6 309 " (cutoff:3.500A) Processing helix chain 'A6' and resid 339 through 350 Processing helix chain 'A6' and resid 371 through 394 Processing helix chain 'A6' and resid 403 through 423 removed outlier: 3.666A pdb=" N THRA6 414 " --> pdb=" O ILEA6 410 " (cutoff:3.500A) Processing helix chain 'A6' and resid 440 through 452 Processing helix chain 'A6' and resid 464 through 469 Processing helix chain 'B6' and resid 3 through 7 removed outlier: 3.780A pdb=" N GLUB6 6 " --> pdb=" O SERB6 3 " (cutoff:3.500A) Processing helix chain 'B6' and resid 48 through 57 Processing helix chain 'B6' and resid 60 through 71 Processing helix chain 'B6' and resid 75 through 80 Processing helix chain 'B6' and resid 108 through 119 removed outlier: 3.975A pdb=" N LEUB6 112 " --> pdb=" O SERB6 108 " (cutoff:3.500A) Proline residue: B6 114 - end of helix Processing helix chain 'B6' and resid 146 through 158 removed outlier: 3.678A pdb=" N VALB6 150 " --> pdb=" O GLUB6 146 " (cutoff:3.500A) Processing helix chain 'B6' and resid 195 through 200 Processing helix chain 'B6' and resid 223 through 225 No H-bonds generated for 'chain 'B6' and resid 223 through 225' Processing helix chain 'B6' and resid 226 through 235 removed outlier: 4.139A pdb=" N ILEB6 230 " --> pdb=" O GLYB6 226 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASNB6 235 " --> pdb=" O LYSB6 231 " (cutoff:3.500A) Processing helix chain 'B6' and resid 246 through 248 No H-bonds generated for 'chain 'B6' and resid 246 through 248' Processing helix chain 'B6' and resid 249 through 261 Processing helix chain 'B6' and resid 269 through 273 Processing helix chain 'B6' and resid 279 through 288 Processing helix chain 'B6' and resid 302 through 313 removed outlier: 3.910A pdb=" N ALAB6 306 " --> pdb=" O ARGB6 302 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HISB6 313 " --> pdb=" O METB6 309 " (cutoff:3.500A) Processing helix chain 'B6' and resid 339 through 350 Processing helix chain 'B6' and resid 371 through 394 Processing helix chain 'B6' and resid 403 through 423 removed outlier: 3.666A pdb=" N THRB6 414 " --> pdb=" O ILEB6 410 " (cutoff:3.500A) Processing helix chain 'B6' and resid 440 through 452 Processing helix chain 'B6' and resid 464 through 469 Processing helix chain 'C6' and resid 3 through 6 removed outlier: 3.780A pdb=" N GLUC6 6 " --> pdb=" O SERC6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C6' and resid 3 through 6' Processing helix chain 'C6' and resid 48 through 57 Processing helix chain 'C6' and resid 60 through 71 Processing helix chain 'C6' and resid 75 through 80 Processing helix chain 'C6' and resid 108 through 119 removed outlier: 3.976A pdb=" N LEUC6 112 " --> pdb=" O SERC6 108 " (cutoff:3.500A) Proline residue: C6 114 - end of helix Processing helix chain 'C6' and resid 146 through 158 removed outlier: 3.678A pdb=" N VALC6 150 " --> pdb=" O GLUC6 146 " (cutoff:3.500A) Processing helix chain 'C6' and resid 195 through 200 Processing helix chain 'C6' and resid 223 through 225 No H-bonds generated for 'chain 'C6' and resid 223 through 225' Processing helix chain 'C6' and resid 226 through 235 removed outlier: 4.139A pdb=" N ILEC6 230 " --> pdb=" O GLYC6 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASNC6 235 " --> pdb=" O LYSC6 231 " (cutoff:3.500A) Processing helix chain 'C6' and resid 246 through 248 No H-bonds generated for 'chain 'C6' and resid 246 through 248' Processing helix chain 'C6' and resid 249 through 261 Processing helix chain 'C6' and resid 269 through 273 Processing helix chain 'C6' and resid 279 through 288 Processing helix chain 'C6' and resid 302 through 313 removed outlier: 3.911A pdb=" N ALAC6 306 " --> pdb=" O ARGC6 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HISC6 313 " --> pdb=" O METC6 309 " (cutoff:3.500A) Processing helix chain 'C6' and resid 339 through 350 Processing helix chain 'C6' and resid 371 through 394 Processing helix chain 'C6' and resid 403 through 423 removed outlier: 3.666A pdb=" N THRC6 414 " --> pdb=" O ILEC6 410 " (cutoff:3.500A) Processing helix chain 'C6' and resid 440 through 452 Processing helix chain 'C6' and resid 464 through 469 Processing helix chain 'D6' and resid 3 through 6 removed outlier: 3.781A pdb=" N GLUD6 6 " --> pdb=" O SERD6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D6' and resid 3 through 6' Processing helix chain 'D6' and resid 48 through 57 Processing helix chain 'D6' and resid 60 through 71 Processing helix chain 'D6' and resid 75 through 80 Processing helix chain 'D6' and resid 108 through 119 removed outlier: 3.975A pdb=" N LEUD6 112 " --> pdb=" O SERD6 108 " (cutoff:3.500A) Proline residue: D6 114 - end of helix Processing helix chain 'D6' and resid 146 through 158 removed outlier: 3.678A pdb=" N VALD6 150 " --> pdb=" O GLUD6 146 " (cutoff:3.500A) Processing helix chain 'D6' and resid 195 through 200 Processing helix chain 'D6' and resid 223 through 225 No H-bonds generated for 'chain 'D6' and resid 223 through 225' Processing helix chain 'D6' and resid 226 through 235 removed outlier: 4.139A pdb=" N ILED6 230 " --> pdb=" O GLYD6 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASND6 235 " --> pdb=" O LYSD6 231 " (cutoff:3.500A) Processing helix chain 'D6' and resid 246 through 248 No H-bonds generated for 'chain 'D6' and resid 246 through 248' Processing helix chain 'D6' and resid 249 through 261 Processing helix chain 'D6' and resid 269 through 273 Processing helix chain 'D6' and resid 279 through 288 Processing helix chain 'D6' and resid 302 through 313 removed outlier: 3.910A pdb=" N ALAD6 306 " --> pdb=" O ARGD6 302 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HISD6 313 " --> pdb=" O METD6 309 " (cutoff:3.500A) Processing helix chain 'D6' and resid 339 through 350 Processing helix chain 'D6' and resid 371 through 394 Processing helix chain 'D6' and resid 403 through 423 removed outlier: 3.666A pdb=" N THRD6 414 " --> pdb=" O ILED6 410 " (cutoff:3.500A) Processing helix chain 'D6' and resid 440 through 452 Processing helix chain 'D6' and resid 464 through 469 Processing helix chain 'E6' and resid 3 through 6 removed outlier: 3.780A pdb=" N GLUE6 6 " --> pdb=" O SERE6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E6' and resid 3 through 6' Processing helix chain 'E6' and resid 48 through 57 Processing helix chain 'E6' and resid 60 through 71 Processing helix chain 'E6' and resid 75 through 80 Processing helix chain 'E6' and resid 108 through 119 removed outlier: 3.975A pdb=" N LEUE6 112 " --> pdb=" O SERE6 108 " (cutoff:3.500A) Proline residue: E6 114 - end of helix Processing helix chain 'E6' and resid 146 through 158 removed outlier: 3.678A pdb=" N VALE6 150 " --> pdb=" O GLUE6 146 " (cutoff:3.500A) Processing helix chain 'E6' and resid 195 through 200 Processing helix chain 'E6' and resid 223 through 225 No H-bonds generated for 'chain 'E6' and resid 223 through 225' Processing helix chain 'E6' and resid 226 through 235 removed outlier: 4.139A pdb=" N ILEE6 230 " --> pdb=" O GLYE6 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASNE6 235 " --> pdb=" O LYSE6 231 " (cutoff:3.500A) Processing helix chain 'E6' and resid 246 through 248 No H-bonds generated for 'chain 'E6' and resid 246 through 248' Processing helix chain 'E6' and resid 249 through 261 Processing helix chain 'E6' and resid 269 through 273 Processing helix chain 'E6' and resid 279 through 288 Processing helix chain 'E6' and resid 302 through 313 removed outlier: 3.910A pdb=" N ALAE6 306 " --> pdb=" O ARGE6 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HISE6 313 " --> pdb=" O METE6 309 " (cutoff:3.500A) Processing helix chain 'E6' and resid 339 through 350 Processing helix chain 'E6' and resid 371 through 394 Processing helix chain 'E6' and resid 403 through 423 removed outlier: 3.666A pdb=" N THRE6 414 " --> pdb=" O ILEE6 410 " (cutoff:3.500A) Processing helix chain 'E6' and resid 440 through 452 Processing helix chain 'E6' and resid 464 through 469 Processing helix chain 'F6' and resid 3 through 6 removed outlier: 3.780A pdb=" N GLUF6 6 " --> pdb=" O SERF6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F6' and resid 3 through 6' Processing helix chain 'F6' and resid 48 through 57 Processing helix chain 'F6' and resid 60 through 71 Processing helix chain 'F6' and resid 75 through 80 Processing helix chain 'F6' and resid 108 through 119 removed outlier: 3.975A pdb=" N LEUF6 112 " --> pdb=" O SERF6 108 " (cutoff:3.500A) Proline residue: F6 114 - end of helix Processing helix chain 'F6' and resid 146 through 158 removed outlier: 3.678A pdb=" N VALF6 150 " --> pdb=" O GLUF6 146 " (cutoff:3.500A) Processing helix chain 'F6' and resid 195 through 200 Processing helix chain 'F6' and resid 223 through 225 No H-bonds generated for 'chain 'F6' and resid 223 through 225' Processing helix chain 'F6' and resid 226 through 235 removed outlier: 4.138A pdb=" N ILEF6 230 " --> pdb=" O GLYF6 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASNF6 235 " --> pdb=" O LYSF6 231 " (cutoff:3.500A) Processing helix chain 'F6' and resid 246 through 248 No H-bonds generated for 'chain 'F6' and resid 246 through 248' Processing helix chain 'F6' and resid 249 through 261 Processing helix chain 'F6' and resid 269 through 273 Processing helix chain 'F6' and resid 279 through 288 Processing helix chain 'F6' and resid 302 through 313 removed outlier: 3.910A pdb=" N ALAF6 306 " --> pdb=" O ARGF6 302 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HISF6 313 " --> pdb=" O METF6 309 " (cutoff:3.500A) Processing helix chain 'F6' and resid 339 through 350 Processing helix chain 'F6' and resid 371 through 394 Processing helix chain 'F6' and resid 403 through 423 removed outlier: 3.667A pdb=" N THRF6 414 " --> pdb=" O ILEF6 410 " (cutoff:3.500A) Processing helix chain 'F6' and resid 440 through 452 Processing helix chain 'F6' and resid 464 through 469 Processing sheet with id=AA1, first strand: chain 'A5' and resid 23 through 24 removed outlier: 3.695A pdb=" N VALA5 42 " --> pdb=" O GLNA5 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEA5 74 " --> pdb=" O PHEA5 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEA5 135 " --> pdb=" O ILEA5 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLNA5 115 " --> pdb=" O ASPA5 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SERB5 69 " --> pdb=" O LEUB5 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALB5 42 " --> pdb=" O GLNB5 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B5' and resid 23 through 24 removed outlier: 3.696A pdb=" N VALB5 42 " --> pdb=" O GLNB5 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEB5 74 " --> pdb=" O PHEB5 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEB5 135 " --> pdb=" O ILEB5 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLNB5 115 " --> pdb=" O ASPB5 134 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SERC5 69 " --> pdb=" O LEUC5 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALC5 42 " --> pdb=" O GLNC5 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C5' and resid 23 through 24 removed outlier: 3.696A pdb=" N VALC5 42 " --> pdb=" O GLNC5 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEC5 74 " --> pdb=" O PHEC5 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEC5 135 " --> pdb=" O ILEC5 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLNC5 115 " --> pdb=" O ASPC5 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SERD5 69 " --> pdb=" O LEUD5 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALD5 42 " --> pdb=" O GLND5 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D5' and resid 23 through 24 removed outlier: 3.696A pdb=" N VALD5 42 " --> pdb=" O GLND5 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILED5 74 " --> pdb=" O PHED5 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHED5 135 " --> pdb=" O ILED5 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLND5 115 " --> pdb=" O ASPD5 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SERE5 69 " --> pdb=" O LEUE5 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VALE5 42 " --> pdb=" O GLNE5 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E5' and resid 23 through 24 removed outlier: 3.695A pdb=" N VALE5 42 " --> pdb=" O GLNE5 24 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILEE5 74 " --> pdb=" O PHEE5 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEE5 135 " --> pdb=" O ILEE5 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLNE5 115 " --> pdb=" O ASPE5 134 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SERF5 69 " --> pdb=" O LEUF5 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALF5 42 " --> pdb=" O GLNF5 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F5' and resid 23 through 24 removed outlier: 3.696A pdb=" N VALF5 42 " --> pdb=" O GLNF5 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILEF5 74 " --> pdb=" O PHEF5 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEF5 135 " --> pdb=" O ILEF5 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLNF5 115 " --> pdb=" O ASPF5 134 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SERA5 69 " --> pdb=" O LEUA5 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VALA5 42 " --> pdb=" O GLNA5 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A5' and resid 55 through 57 Processing sheet with id=AA8, first strand: chain 'A5' and resid 121 through 122 removed outlier: 3.626A pdb=" N GLNA5 121 " --> pdb=" O GLYA5 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYA5 128 " --> pdb=" O GLNA5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A5' and resid 155 through 159 removed outlier: 6.848A pdb=" N GLUA5 156 " --> pdb=" O ILEA6 478 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VALA6 480 " --> pdb=" O GLUA5 156 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEUA5 158 " --> pdb=" O VALA6 480 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B5' and resid 55 through 57 Processing sheet with id=AB2, first strand: chain 'B5' and resid 121 through 122 removed outlier: 3.626A pdb=" N GLNB5 121 " --> pdb=" O GLYB5 128 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLYB5 128 " --> pdb=" O GLNB5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B5' and resid 155 through 159 removed outlier: 6.856A pdb=" N GLUB5 156 " --> pdb=" O ILEB6 478 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VALB6 480 " --> pdb=" O GLUB5 156 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEUB5 158 " --> pdb=" O VALB6 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C5' and resid 55 through 57 removed outlier: 8.630A pdb=" N LEUF3 36 " --> pdb=" O SERC5 142 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYRC5 144 " --> pdb=" O LEUF3 36 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THRF3 38 " --> pdb=" O TYRC5 144 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHEF3 57 " --> pdb=" O LYSF3 27 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILEF3 62 " --> pdb=" O LYSF3 72 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYSF3 72 " --> pdb=" O ILEF3 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C5' and resid 121 through 122 removed outlier: 3.627A pdb=" N GLNC5 121 " --> pdb=" O GLYC5 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYC5 128 " --> pdb=" O GLNC5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C5' and resid 156 through 159 removed outlier: 7.361A pdb=" N GLUC5 156 " --> pdb=" O ILEC6 478 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VALC6 480 " --> pdb=" O GLUC5 156 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEUC5 158 " --> pdb=" O VALC6 480 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D5' and resid 55 through 57 Processing sheet with id=AB8, first strand: chain 'D5' and resid 121 through 122 removed outlier: 3.627A pdb=" N GLND5 121 " --> pdb=" O GLYD5 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYD5 128 " --> pdb=" O GLND5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D5' and resid 155 through 159 removed outlier: 6.848A pdb=" N GLUD5 156 " --> pdb=" O ILED6 478 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VALD6 480 " --> pdb=" O GLUD5 156 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEUD5 158 " --> pdb=" O VALD6 480 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E5' and resid 55 through 57 Processing sheet with id=AC2, first strand: chain 'E5' and resid 121 through 122 removed outlier: 3.626A pdb=" N GLNE5 121 " --> pdb=" O GLYE5 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYE5 128 " --> pdb=" O GLNE5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E5' and resid 155 through 159 removed outlier: 6.936A pdb=" N GLUE5 156 " --> pdb=" O ILEE6 478 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N VALE6 480 " --> pdb=" O GLUE5 156 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEUE5 158 " --> pdb=" O VALE6 480 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F5' and resid 55 through 57 removed outlier: 8.634A pdb=" N LEUO3 36 " --> pdb=" O SERF5 142 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYRF5 144 " --> pdb=" O LEUO3 36 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N THRO3 38 " --> pdb=" O TYRF5 144 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHEO3 57 " --> pdb=" O LYSO3 27 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILEO3 62 " --> pdb=" O LYSO3 72 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYSO3 72 " --> pdb=" O ILEO3 62 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F5' and resid 121 through 122 removed outlier: 3.626A pdb=" N GLNF5 121 " --> pdb=" O GLYF5 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYF5 128 " --> pdb=" O GLNF5 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F5' and resid 155 through 159 removed outlier: 7.002A pdb=" N GLUF5 156 " --> pdb=" O ILEF6 478 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N VALF6 480 " --> pdb=" O GLUF5 156 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEUF5 158 " --> pdb=" O VALF6 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A3' and resid 4 through 8 Processing sheet with id=AC8, first strand: chain 'A3' and resid 37 through 42 removed outlier: 6.365A pdb=" N GLYA3 56 " --> pdb=" O SERA3 77 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SERA3 77 " --> pdb=" O GLYA3 56 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HISA3 58 " --> pdb=" O ASPA3 75 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASPA3 75 " --> pdb=" O HISA3 58 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILEA3 60 " --> pdb=" O LEUA3 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 5 through 8 Processing sheet with id=AD1, first strand: chain 'B3' and resid 38 through 42 removed outlier: 6.423A pdb=" N GLYB3 56 " --> pdb=" O SERB3 77 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SERB3 77 " --> pdb=" O GLYB3 56 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HISB3 58 " --> pdb=" O ASPB3 75 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASPB3 75 " --> pdb=" O HISB3 58 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILEB3 60 " --> pdb=" O LEUB3 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C3' and resid 48 through 53 removed outlier: 3.788A pdb=" N ILEC3 86 " --> pdb=" O GLNC3 4 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C3' and resid 35 through 42 removed outlier: 4.540A pdb=" N PHEC3 57 " --> pdb=" O LYSC3 27 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILEC3 62 " --> pdb=" O LYSC3 72 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYSC3 72 " --> pdb=" O ILEC3 62 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D3' and resid 4 through 8 removed outlier: 3.510A pdb=" N VALD3 5 " --> pdb=" O PHED3 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D3' and resid 37 through 42 removed outlier: 3.763A pdb=" N GLYD3 74 " --> pdb=" O ILED3 60 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILED3 62 " --> pdb=" O LYSD3 72 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYSD3 72 " --> pdb=" O ILED3 62 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E3' and resid 3 through 8 Processing sheet with id=AD7, first strand: chain 'E3' and resid 38 through 42 removed outlier: 6.440A pdb=" N GLYE3 56 " --> pdb=" O SERE3 77 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SERE3 77 " --> pdb=" O GLYE3 56 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HISE3 58 " --> pdb=" O ASPE3 75 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASPE3 75 " --> pdb=" O HISE3 58 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILEE3 60 " --> pdb=" O LEUE3 73 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F3' and resid 48 through 53 removed outlier: 3.942A pdb=" N ILEF3 86 " --> pdb=" O GLNF3 4 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G3' and resid 4 through 8 Processing sheet with id=AE1, first strand: chain 'G3' and resid 38 through 42 removed outlier: 6.363A pdb=" N GLYG3 56 " --> pdb=" O SERG3 77 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SERG3 77 " --> pdb=" O GLYG3 56 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HISG3 58 " --> pdb=" O ASPG3 75 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASPG3 75 " --> pdb=" O HISG3 58 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILEG3 60 " --> pdb=" O LEUG3 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H3' and resid 3 through 8 Processing sheet with id=AE3, first strand: chain 'H3' and resid 39 through 42 removed outlier: 6.825A pdb=" N ILEH3 62 " --> pdb=" O LYSH3 72 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYSH3 72 " --> pdb=" O ILEH3 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I3' and resid 48 through 53 removed outlier: 3.960A pdb=" N ILEI3 86 " --> pdb=" O GLNI3 4 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I3' and resid 35 through 42 removed outlier: 4.609A pdb=" N PHEI3 57 " --> pdb=" O LYSI3 27 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILEI3 62 " --> pdb=" O LYSI3 72 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYSI3 72 " --> pdb=" O ILEI3 62 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J3' and resid 4 through 8 Processing sheet with id=AE7, first strand: chain 'J3' and resid 38 through 42 removed outlier: 6.362A pdb=" N GLYJ3 56 " --> pdb=" O SERJ3 77 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SERJ3 77 " --> pdb=" O GLYJ3 56 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HISJ3 58 " --> pdb=" O ASPJ3 75 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASPJ3 75 " --> pdb=" O HISJ3 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILEJ3 60 " --> pdb=" O LEUJ3 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K3' and resid 3 through 8 Processing sheet with id=AE9, first strand: chain 'K3' and resid 38 through 42 removed outlier: 6.937A pdb=" N ILEK3 62 " --> pdb=" O LYSK3 72 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYSK3 72 " --> pdb=" O ILEK3 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L3' and resid 48 through 53 removed outlier: 3.955A pdb=" N ILEL3 86 " --> pdb=" O GLNL3 4 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L3' and resid 35 through 42 removed outlier: 4.580A pdb=" N PHEL3 57 " --> pdb=" O LYSL3 27 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILEL3 62 " --> pdb=" O LYSL3 72 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYSL3 72 " --> pdb=" O ILEL3 62 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M3' and resid 4 through 8 Processing sheet with id=AF4, first strand: chain 'M3' and resid 37 through 42 removed outlier: 6.364A pdb=" N GLYM3 56 " --> pdb=" O SERM3 77 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SERM3 77 " --> pdb=" O GLYM3 56 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HISM3 58 " --> pdb=" O ASPM3 75 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASPM3 75 " --> pdb=" O HISM3 58 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILEM3 60 " --> pdb=" O LEUM3 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N3' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'N3' and resid 38 through 42 removed outlier: 6.576A pdb=" N GLYN3 56 " --> pdb=" O SERN3 77 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SERN3 77 " --> pdb=" O GLYN3 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HISN3 58 " --> pdb=" O ASPN3 75 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASPN3 75 " --> pdb=" O HISN3 58 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILEN3 60 " --> pdb=" O LEUN3 73 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O3' and resid 48 through 53 removed outlier: 3.962A pdb=" N ILEO3 86 " --> pdb=" O GLNO3 4 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P3' and resid 4 through 8 Processing sheet with id=AF9, first strand: chain 'P3' and resid 38 through 42 removed outlier: 6.336A pdb=" N GLYP3 56 " --> pdb=" O SERP3 77 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SERP3 77 " --> pdb=" O GLYP3 56 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HISP3 58 " --> pdb=" O ASPP3 75 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASPP3 75 " --> pdb=" O HISP3 58 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILEP3 60 " --> pdb=" O LEUP3 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q3' and resid 48 through 53 removed outlier: 5.857A pdb=" N GLNQ3 4 " --> pdb=" O ILEQ3 86 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q3' and resid 38 through 42 removed outlier: 7.506A pdb=" N PHEQ3 57 " --> pdb=" O LYSQ3 27 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLYQ3 56 " --> pdb=" O SERQ3 77 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SERQ3 77 " --> pdb=" O GLYQ3 56 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HISQ3 58 " --> pdb=" O ASPQ3 75 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASPQ3 75 " --> pdb=" O HISQ3 58 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILEQ3 60 " --> pdb=" O LEUQ3 73 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R3' and resid 48 through 53 removed outlier: 3.978A pdb=" N ILER3 86 " --> pdb=" O GLNR3 4 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R3' and resid 35 through 42 removed outlier: 4.610A pdb=" N PHER3 57 " --> pdb=" O LYSR3 27 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILER3 62 " --> pdb=" O LYSR3 72 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYSR3 72 " --> pdb=" O ILER3 62 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A4' and resid 91 through 93 removed outlier: 3.755A pdb=" N GLUA4 22 " --> pdb=" O ILEA4 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILEA4 33 " --> pdb=" O GLUA4 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALA4 26 " --> pdb=" O VALA4 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLNA4 44 " --> pdb=" O TRPA4 64 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILEA4 63 " --> pdb=" O GLYA4 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B4' and resid 91 through 93 removed outlier: 3.755A pdb=" N GLUB4 22 " --> pdb=" O ILEB4 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILEB4 33 " --> pdb=" O GLUB4 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALB4 26 " --> pdb=" O VALB4 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNB4 44 " --> pdb=" O TRPB4 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEB4 63 " --> pdb=" O GLYB4 103 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C4' and resid 91 through 93 removed outlier: 3.755A pdb=" N GLUC4 22 " --> pdb=" O ILEC4 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILEC4 33 " --> pdb=" O GLUC4 22 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALC4 26 " --> pdb=" O VALC4 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNC4 44 " --> pdb=" O TRPC4 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEC4 63 " --> pdb=" O GLYC4 103 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D4' and resid 91 through 93 removed outlier: 3.756A pdb=" N GLUD4 22 " --> pdb=" O ILED4 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILED4 33 " --> pdb=" O GLUD4 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALD4 26 " --> pdb=" O VALD4 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLND4 44 " --> pdb=" O TRPD4 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILED4 63 " --> pdb=" O GLYD4 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E4' and resid 91 through 93 removed outlier: 3.756A pdb=" N GLUE4 22 " --> pdb=" O ILEE4 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILEE4 33 " --> pdb=" O GLUE4 22 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VALE4 26 " --> pdb=" O VALE4 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNE4 44 " --> pdb=" O TRPE4 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEE4 63 " --> pdb=" O GLYE4 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F4' and resid 91 through 93 removed outlier: 3.756A pdb=" N GLUF4 22 " --> pdb=" O ILEF4 33 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILEF4 33 " --> pdb=" O GLUF4 22 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALF4 26 " --> pdb=" O VALF4 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNF4 44 " --> pdb=" O TRPF4 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEF4 63 " --> pdb=" O GLYF4 103 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A7' and resid 5 through 6 removed outlier: 5.905A pdb=" N PHEA7 87 " --> pdb=" O THRA7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRA7 110 " --> pdb=" O PHEA7 87 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SERA7 112 " --> pdb=" O GLUA7 135 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A7' and resid 18 through 19 removed outlier: 5.905A pdb=" N PHEA7 87 " --> pdb=" O THRA7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRA7 110 " --> pdb=" O PHEA7 87 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A7' and resid 39 through 43 removed outlier: 3.506A pdb=" N THRA7 41 " --> pdb=" O SERA7 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLYA7 47 " --> pdb=" O SERA7 43 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B7' and resid 5 through 6 removed outlier: 5.905A pdb=" N PHEB7 87 " --> pdb=" O THRB7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRB7 110 " --> pdb=" O PHEB7 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERB7 112 " --> pdb=" O GLUB7 135 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B7' and resid 18 through 19 removed outlier: 5.905A pdb=" N PHEB7 87 " --> pdb=" O THRB7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRB7 110 " --> pdb=" O PHEB7 87 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B7' and resid 39 through 43 removed outlier: 3.507A pdb=" N THRB7 41 " --> pdb=" O SERB7 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLYB7 47 " --> pdb=" O SERB7 43 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C7' and resid 5 through 6 removed outlier: 5.905A pdb=" N PHEC7 87 " --> pdb=" O THRC7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRC7 110 " --> pdb=" O PHEC7 87 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SERC7 112 " --> pdb=" O GLUC7 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C7' and resid 18 through 19 removed outlier: 5.905A pdb=" N PHEC7 87 " --> pdb=" O THRC7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRC7 110 " --> pdb=" O PHEC7 87 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C7' and resid 39 through 43 removed outlier: 3.505A pdb=" N THRC7 41 " --> pdb=" O SERC7 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLYC7 47 " --> pdb=" O SERC7 43 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D7' and resid 5 through 6 removed outlier: 5.905A pdb=" N PHED7 87 " --> pdb=" O THRD7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRD7 110 " --> pdb=" O PHED7 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERD7 112 " --> pdb=" O GLUD7 135 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D7' and resid 18 through 19 removed outlier: 5.905A pdb=" N PHED7 87 " --> pdb=" O THRD7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRD7 110 " --> pdb=" O PHED7 87 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D7' and resid 39 through 43 removed outlier: 3.505A pdb=" N THRD7 41 " --> pdb=" O SERD7 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLYD7 47 " --> pdb=" O SERD7 43 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E7' and resid 5 through 6 removed outlier: 5.904A pdb=" N PHEE7 87 " --> pdb=" O THRE7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRE7 110 " --> pdb=" O PHEE7 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERE7 112 " --> pdb=" O GLUE7 135 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E7' and resid 18 through 19 removed outlier: 5.904A pdb=" N PHEE7 87 " --> pdb=" O THRE7 110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THRE7 110 " --> pdb=" O PHEE7 87 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E7' and resid 39 through 43 removed outlier: 3.505A pdb=" N THRE7 41 " --> pdb=" O SERE7 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLYE7 47 " --> pdb=" O SERE7 43 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F7' and resid 5 through 6 removed outlier: 5.905A pdb=" N PHEF7 87 " --> pdb=" O THRF7 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THRF7 110 " --> pdb=" O PHEF7 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERF7 112 " --> pdb=" O GLUF7 135 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F7' and resid 18 through 19 removed outlier: 5.905A pdb=" N PHEF7 87 " --> pdb=" O THRF7 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THRF7 110 " --> pdb=" O PHEF7 87 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F7' and resid 39 through 43 removed outlier: 3.506A pdb=" N THRF7 41 " --> pdb=" O SERF7 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLYF7 47 " --> pdb=" O SERF7 43 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A6' and resid 8 through 11 removed outlier: 6.478A pdb=" N ARGA6 9 " --> pdb=" O ILEB6 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'A6' and resid 27 through 31 removed outlier: 3.823A pdb=" N THRA6 31 " --> pdb=" O GLYA6 86 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A6' and resid 161 through 166 Processing sheet with id=AJ5, first strand: chain 'A6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALA6 264 " --> pdb=" O ARGA6 293 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEUA6 295 " --> pdb=" O VALA6 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLUA6 266 " --> pdb=" O LEUA6 295 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'A6' and resid 353 through 356 Processing sheet with id=AJ7, first strand: chain 'A6' and resid 489 through 492 removed outlier: 6.545A pdb=" N GLUA6 489 " --> pdb=" O ARGF6 9 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N SERF6 11 " --> pdb=" O GLUA6 489 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILEA6 491 " --> pdb=" O SERF6 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'B6' and resid 10 through 11 removed outlier: 3.911A pdb=" N SERB6 11 " --> pdb=" O ILEC6 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'B6' and resid 27 through 31 removed outlier: 3.824A pdb=" N THRB6 31 " --> pdb=" O GLYB6 86 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'B6' and resid 161 through 166 Processing sheet with id=AK2, first strand: chain 'B6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALB6 264 " --> pdb=" O ARGB6 293 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEUB6 295 " --> pdb=" O VALB6 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLUB6 266 " --> pdb=" O LEUB6 295 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'B6' and resid 353 through 356 Processing sheet with id=AK4, first strand: chain 'C6' and resid 8 through 11 removed outlier: 6.467A pdb=" N ARGC6 9 " --> pdb=" O ILED6 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'C6' and resid 27 through 31 removed outlier: 3.823A pdb=" N THRC6 31 " --> pdb=" O GLYC6 86 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'C6' and resid 161 through 166 Processing sheet with id=AK7, first strand: chain 'C6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALC6 264 " --> pdb=" O ARGC6 293 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEUC6 295 " --> pdb=" O VALC6 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLUC6 266 " --> pdb=" O LEUC6 295 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'C6' and resid 353 through 356 Processing sheet with id=AK9, first strand: chain 'D6' and resid 8 through 11 removed outlier: 6.464A pdb=" N ARGD6 9 " --> pdb=" O ILEE6 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'D6' and resid 27 through 31 removed outlier: 3.824A pdb=" N THRD6 31 " --> pdb=" O GLYD6 86 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'D6' and resid 161 through 166 Processing sheet with id=AL3, first strand: chain 'D6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALD6 264 " --> pdb=" O ARGD6 293 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEUD6 295 " --> pdb=" O VALD6 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLUD6 266 " --> pdb=" O LEUD6 295 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'D6' and resid 353 through 356 Processing sheet with id=AL5, first strand: chain 'E6' and resid 8 through 11 removed outlier: 6.624A pdb=" N ARGE6 9 " --> pdb=" O ILEF6 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'E6' and resid 27 through 31 removed outlier: 3.823A pdb=" N THRE6 31 " --> pdb=" O GLYE6 86 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'E6' and resid 161 through 166 Processing sheet with id=AL8, first strand: chain 'E6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALE6 264 " --> pdb=" O ARGE6 293 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEUE6 295 " --> pdb=" O VALE6 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLUE6 266 " --> pdb=" O LEUE6 295 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'E6' and resid 353 through 356 Processing sheet with id=AM1, first strand: chain 'F6' and resid 27 through 31 removed outlier: 3.823A pdb=" N THRF6 31 " --> pdb=" O GLYF6 86 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'F6' and resid 161 through 166 Processing sheet with id=AM3, first strand: chain 'F6' and resid 238 through 239 removed outlier: 6.107A pdb=" N VALF6 264 " --> pdb=" O ARGF6 293 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEUF6 295 " --> pdb=" O VALF6 264 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLUF6 266 " --> pdb=" O LEUF6 295 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'F6' and resid 353 through 356 2505 hydrogen bonds defined for protein. 6903 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: 23.61 Time building geometry restraints manager: 21.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19728 1.34 - 1.46: 12297 1.46 - 1.58: 27711 1.58 - 1.70: 0 1.70 - 1.82: 252 Bond restraints: 59988 Sorted by residual: bond pdb=" CB PHEB3 70 " pdb=" CG PHEB3 70 " ideal model delta sigma weight residual 1.502 1.425 0.077 2.30e-02 1.89e+03 1.13e+01 bond pdb=" CG LYSH3 27 " pdb=" CD LYSH3 27 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.39e+00 bond pdb=" CG1 ILEH3 9 " pdb=" CD1 ILEH3 9 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.53e+00 bond pdb=" CG1 ILEE3 9 " pdb=" CD1 ILEE3 9 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.28e+00 bond pdb=" CG LEUG3 13 " pdb=" CD1 LEUG3 13 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 ... (remaining 59983 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.23: 661 104.23 - 111.68: 29010 111.68 - 119.13: 20400 119.13 - 126.58: 30998 126.58 - 134.03: 441 Bond angle restraints: 81510 Sorted by residual: angle pdb=" NE ARGB3 23 " pdb=" CZ ARGB3 23 " pdb=" NH1 ARGB3 23 " ideal model delta sigma weight residual 121.50 115.35 6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CG LYSQ3 59 " pdb=" CD LYSQ3 59 " pdb=" CE LYSQ3 59 " ideal model delta sigma weight residual 111.30 123.21 -11.91 2.30e+00 1.89e-01 2.68e+01 angle pdb=" CG LYSH3 59 " pdb=" CD LYSH3 59 " pdb=" CE LYSH3 59 " ideal model delta sigma weight residual 111.30 121.93 -10.63 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CA LYSQ3 59 " pdb=" CB LYSQ3 59 " pdb=" CG LYSQ3 59 " ideal model delta sigma weight residual 114.10 123.06 -8.96 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CA LYSH3 59 " pdb=" CB LYSH3 59 " pdb=" CG LYSH3 59 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.98e+01 ... (remaining 81505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 32350 17.43 - 34.86: 3038 34.86 - 52.30: 480 52.30 - 69.73: 145 69.73 - 87.16: 65 Dihedral angle restraints: 36078 sinusoidal: 13674 harmonic: 22404 Sorted by residual: dihedral pdb=" CA ASPB5 14 " pdb=" C ASPB5 14 " pdb=" N LEUB5 15 " pdb=" CA LEUB5 15 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASPD5 14 " pdb=" C ASPD5 14 " pdb=" N LEUD5 15 " pdb=" CA LEUD5 15 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASPA5 14 " pdb=" C ASPA5 14 " pdb=" N LEUA5 15 " pdb=" CA LEUA5 15 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 36075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 8122 0.072 - 0.145: 1416 0.145 - 0.217: 130 0.217 - 0.290: 14 0.290 - 0.362: 2 Chirality restraints: 9684 Sorted by residual: chirality pdb=" CB VALD3 102 " pdb=" CA VALD3 102 " pdb=" CG1 VALD3 102 " pdb=" CG2 VALD3 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VALP3 102 " pdb=" CA VALP3 102 " pdb=" CG1 VALP3 102 " pdb=" CG2 VALP3 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VALJ3 102 " pdb=" CA VALJ3 102 " pdb=" CG1 VALJ3 102 " pdb=" CG2 VALJ3 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 9681 not shown) Planarity restraints: 10548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPB4 64 " -0.058 2.00e-02 2.50e+03 5.08e-02 6.46e+01 pdb=" CG TRPB4 64 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 TRPB4 64 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRPB4 64 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRPB4 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRPB4 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRPB4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRPB4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRPB4 64 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRPB4 64 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPE4 64 " -0.058 2.00e-02 2.50e+03 5.08e-02 6.44e+01 pdb=" CG TRPE4 64 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 TRPE4 64 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRPE4 64 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRPE4 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRPE4 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRPE4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRPE4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRPE4 64 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRPE4 64 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPC4 64 " -0.058 2.00e-02 2.50e+03 5.07e-02 6.42e+01 pdb=" CG TRPC4 64 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 TRPC4 64 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRPC4 64 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRPC4 64 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRPC4 64 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRPC4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRPC4 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRPC4 64 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRPC4 64 " -0.007 2.00e-02 2.50e+03 ... (remaining 10545 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 763 2.52 - 3.11: 52195 3.11 - 3.71: 92925 3.71 - 4.30: 130373 4.30 - 4.90: 210355 Nonbonded interactions: 486611 Sorted by model distance: nonbonded pdb=" NH2 ARGC6 9 " pdb=" OD2 ASPD6 490 " model vdw 1.919 2.520 nonbonded pdb=" OH TYRA5 18 " pdb=" O GLYA5 38 " model vdw 1.928 2.440 nonbonded pdb=" OH TYRE5 18 " pdb=" O GLYE5 38 " model vdw 1.929 2.440 nonbonded pdb=" OH TYRF5 18 " pdb=" O GLYF5 38 " model vdw 1.929 2.440 nonbonded pdb=" OH TYRB5 18 " pdb=" O GLYB5 38 " model vdw 1.929 2.440 ... (remaining 486606 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 'A3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'B3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'C3' selection = (chain 'D3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'F3' selection = (chain 'G3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'H3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'I3' selection = (chain 'J3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'K3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'L3' selection = (chain 'M3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'N3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'O3' selection = (chain 'P3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'Q3' and (resid 1 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'R3' } ncs_group { reference = chain 'A4' selection = chain 'B4' selection = chain 'C4' selection = chain 'D4' selection = chain 'E4' selection = chain 'F4' } ncs_group { reference = chain 'A5' selection = chain 'B5' selection = chain 'C5' selection = chain 'D5' selection = chain 'E5' selection = chain 'F5' } ncs_group { reference = chain 'A6' selection = chain 'B6' selection = chain 'C6' selection = chain 'D6' selection = chain 'E6' selection = chain 'F6' } ncs_group { reference = chain 'A7' selection = chain 'B7' selection = chain 'C7' selection = chain 'D7' selection = chain 'E7' selection = chain 'F7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.780 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: 0.070 Extract box with map and model: 27.140 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 125.480 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.009 0.107 59988 Z= 0.590 Angle : 0.940 13.830 81510 Z= 0.514 Chirality : 0.053 0.362 9684 Planarity : 0.005 0.083 10548 Dihedral : 14.473 87.161 21678 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 1.45 % Allowed : 1.86 % Favored : 96.68 % 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: -3.10 (0.09), residues: 7656 helix: -0.62 (0.12), residues: 1878 sheet: -2.27 (0.11), residues: 1980 loop : -2.69 (0.09), residues: 3798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.009 TRPE4 64 HIS 0.007 0.002 HISA3 58 PHE 0.086 0.003 PHEB3 70 TYR 0.039 0.003 TYRB3 41 ARG 0.041 0.002 ARGB3 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2460 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 2364 time to evaluate : 5.213 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: A5 39 TYR cc_start: 0.8882 (m-10) cc_final: 0.8677 (m-80) REVERT: A5 82 ASP cc_start: 0.8670 (p0) cc_final: 0.7718 (p0) REVERT: B5 65 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B5 82 ASP cc_start: 0.8655 (p0) cc_final: 0.7693 (p0) REVERT: C5 62 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C5 82 ASP cc_start: 0.8648 (p0) cc_final: 0.7611 (p0) REVERT: C5 146 GLU cc_start: 0.8159 (tt0) cc_final: 0.7952 (tt0) REVERT: D5 62 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D5 76 LEU cc_start: 0.8864 (mt) cc_final: 0.8649 (mt) REVERT: D5 146 GLU cc_start: 0.8129 (tt0) cc_final: 0.7852 (tt0) REVERT: E5 82 ASP cc_start: 0.8628 (p0) cc_final: 0.8077 (p0) REVERT: E5 139 TYR cc_start: 0.8684 (p90) cc_final: 0.8356 (p90) REVERT: F5 65 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7785 (tm-30) REVERT: F5 82 ASP cc_start: 0.8699 (p0) cc_final: 0.7769 (p0) REVERT: F5 114 SER cc_start: 0.9077 (t) cc_final: 0.8857 (t) REVERT: B3 49 TYR cc_start: 0.7998 (p90) cc_final: 0.7767 (p90) REVERT: B3 59 LYS cc_start: 0.8754 (mttm) cc_final: 0.8549 (mttm) REVERT: E3 9 ILE cc_start: 0.7239 (mm) cc_final: 0.6951 (tp) REVERT: E3 35 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8149 (ttm-80) REVERT: F3 49 TYR cc_start: 0.7682 (p90) cc_final: 0.7457 (p90) REVERT: G3 62 ILE cc_start: 0.8304 (mp) cc_final: 0.7904 (mm) REVERT: G3 81 GLN cc_start: 0.9056 (pm20) cc_final: 0.8804 (pm20) REVERT: H3 3 ILE cc_start: 0.7996 (tp) cc_final: 0.7756 (tp) REVERT: I3 49 TYR cc_start: 0.7702 (p90) cc_final: 0.7216 (p90) REVERT: I3 88 LEU cc_start: 0.8970 (tt) cc_final: 0.8765 (tt) REVERT: J3 81 GLN cc_start: 0.9185 (pm20) cc_final: 0.8960 (pm20) REVERT: J3 95 SER cc_start: 0.8547 (m) cc_final: 0.8330 (m) REVERT: K3 41 TYR cc_start: 0.8945 (t80) cc_final: 0.8675 (t80) REVERT: M3 120 ASP cc_start: 0.8957 (m-30) cc_final: 0.8725 (m-30) REVERT: N3 31 ARG cc_start: 0.8129 (ptt90) cc_final: 0.7815 (ptt90) REVERT: N3 55 GLU cc_start: 0.8621 (pm20) cc_final: 0.8392 (pm20) REVERT: A4 52 ASN cc_start: 0.9134 (m110) cc_final: 0.8666 (m110) REVERT: A4 84 PHE cc_start: 0.8305 (m-80) cc_final: 0.8033 (m-10) REVERT: B4 52 ASN cc_start: 0.9021 (m110) cc_final: 0.8459 (m110) REVERT: D4 6 ARG cc_start: 0.8527 (tpt-90) cc_final: 0.7944 (tpp80) REVERT: E4 57 ASP cc_start: 0.7841 (m-30) cc_final: 0.7508 (m-30) REVERT: F4 84 PHE cc_start: 0.8370 (m-80) cc_final: 0.8164 (m-10) REVERT: F4 92 ASP cc_start: 0.8663 (p0) cc_final: 0.8419 (p0) REVERT: A7 21 GLN cc_start: 0.8271 (mt0) cc_final: 0.8070 (mt0) REVERT: A7 76 ASN cc_start: 0.8659 (t0) cc_final: 0.8418 (t0) REVERT: A7 122 ASN cc_start: 0.8375 (t0) cc_final: 0.8160 (t0) REVERT: B7 83 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6548 (mt-10) REVERT: C7 83 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6643 (mt-10) REVERT: C7 124 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8116 (mm110) REVERT: A6 24 MET cc_start: 0.8922 (tpt) cc_final: 0.8439 (tpt) REVERT: A6 272 TYR cc_start: 0.8345 (m-80) cc_final: 0.7433 (m-80) REVERT: A6 276 ASN cc_start: 0.8033 (t0) cc_final: 0.7718 (t0) REVERT: A6 295 LEU cc_start: 0.8588 (mp) cc_final: 0.8226 (mp) REVERT: A6 329 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8845 (mmtm) REVERT: A6 384 GLU cc_start: 0.8818 (tp30) cc_final: 0.8373 (tp30) REVERT: A6 418 CYS cc_start: 0.9287 (m) cc_final: 0.8736 (m) REVERT: A6 441 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.7225 (mmm-85) REVERT: A6 491 ILE cc_start: 0.3953 (OUTLIER) cc_final: 0.3480 (tp) REVERT: B6 88 TRP cc_start: 0.8435 (p-90) cc_final: 0.8176 (p-90) REVERT: B6 272 TYR cc_start: 0.8256 (m-80) cc_final: 0.7410 (m-80) REVERT: B6 342 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: B6 384 GLU cc_start: 0.8811 (tp30) cc_final: 0.8402 (tp30) REVERT: B6 491 ILE cc_start: 0.3719 (OUTLIER) cc_final: 0.3263 (tp) REVERT: C6 126 ILE cc_start: 0.7874 (tp) cc_final: 0.7569 (tp) REVERT: C6 295 LEU cc_start: 0.8684 (mp) cc_final: 0.8454 (mp) REVERT: C6 312 MET cc_start: 0.7839 (tpt) cc_final: 0.7629 (tpt) REVERT: C6 324 ILE cc_start: 0.8207 (pt) cc_final: 0.7915 (pt) REVERT: C6 330 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C6 372 CYS cc_start: 0.7471 (m) cc_final: 0.6971 (m) REVERT: C6 400 ILE cc_start: 0.8915 (tp) cc_final: 0.8642 (tp) REVERT: C6 491 ILE cc_start: 0.3670 (OUTLIER) cc_final: 0.2863 (tt) REVERT: D6 24 MET cc_start: 0.8916 (tpt) cc_final: 0.8681 (tpp) REVERT: D6 90 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8633 (m) REVERT: D6 272 TYR cc_start: 0.8193 (m-80) cc_final: 0.7808 (m-80) REVERT: D6 294 CYS cc_start: 0.7903 (m) cc_final: 0.7467 (m) REVERT: D6 295 LEU cc_start: 0.8614 (mp) cc_final: 0.8111 (mp) REVERT: D6 324 ILE cc_start: 0.9182 (pt) cc_final: 0.8802 (pt) REVERT: D6 330 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8027 (mt-10) REVERT: D6 342 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: D6 351 LEU cc_start: 0.8873 (mt) cc_final: 0.8655 (mt) REVERT: D6 393 LEU cc_start: 0.8517 (tp) cc_final: 0.8304 (tp) REVERT: D6 424 ASN cc_start: 0.9067 (t0) cc_final: 0.8826 (t0) REVERT: D6 491 ILE cc_start: 0.3267 (OUTLIER) cc_final: 0.2728 (tp) REVERT: E6 24 MET cc_start: 0.8774 (tpt) cc_final: 0.8375 (tpt) REVERT: E6 83 LEU cc_start: 0.8997 (tt) cc_final: 0.8784 (tt) REVERT: E6 88 TRP cc_start: 0.8510 (p-90) cc_final: 0.8095 (p-90) REVERT: E6 272 TYR cc_start: 0.8201 (m-80) cc_final: 0.7893 (m-80) REVERT: E6 276 ASN cc_start: 0.7841 (t0) cc_final: 0.7637 (t0) REVERT: E6 294 CYS cc_start: 0.7475 (m) cc_final: 0.7109 (m) REVERT: E6 342 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: E6 363 LEU cc_start: 0.9162 (tp) cc_final: 0.8959 (tt) REVERT: E6 384 GLU cc_start: 0.8843 (tp30) cc_final: 0.8431 (tp30) REVERT: E6 491 ILE cc_start: 0.3946 (OUTLIER) cc_final: 0.3376 (tp) REVERT: F6 294 CYS cc_start: 0.7467 (m) cc_final: 0.6790 (m) REVERT: F6 330 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8053 (mt-10) REVERT: F6 342 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: F6 384 GLU cc_start: 0.8763 (tp30) cc_final: 0.8349 (tp30) REVERT: F6 454 TYR cc_start: 0.8845 (t80) cc_final: 0.8619 (t80) REVERT: F6 491 ILE cc_start: 0.3782 (OUTLIER) cc_final: 0.3225 (tp) outliers start: 96 outliers final: 44 residues processed: 2419 average time/residue: 0.5230 time to fit residues: 2193.6137 Evaluate side-chains 2051 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1996 time to evaluate : 5.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 20 GLU Chi-restraints excluded: chain B5 residue 20 GLU Chi-restraints excluded: chain C5 residue 20 GLU Chi-restraints excluded: chain C5 residue 97 GLN Chi-restraints excluded: chain D5 residue 20 GLU Chi-restraints excluded: chain E5 residue 20 GLU Chi-restraints excluded: chain E5 residue 97 GLN Chi-restraints excluded: chain F5 residue 20 GLU Chi-restraints excluded: chain F5 residue 97 GLN Chi-restraints excluded: chain A4 residue 40 ARG Chi-restraints excluded: chain B4 residue 40 ARG Chi-restraints excluded: chain C4 residue 40 ARG Chi-restraints excluded: chain D4 residue 40 ARG Chi-restraints excluded: chain E4 residue 25 ARG Chi-restraints excluded: chain E4 residue 40 ARG Chi-restraints excluded: chain F4 residue 25 ARG Chi-restraints excluded: chain F4 residue 40 ARG Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 108 SER Chi-restraints excluded: chain A6 residue 491 ILE Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 108 SER Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 349 VAL Chi-restraints excluded: chain B6 residue 364 LEU Chi-restraints excluded: chain B6 residue 414 THR Chi-restraints excluded: chain B6 residue 491 ILE Chi-restraints excluded: chain C6 residue 60 SER Chi-restraints excluded: chain C6 residue 108 SER Chi-restraints excluded: chain C6 residue 360 GLU Chi-restraints excluded: chain C6 residue 364 LEU Chi-restraints excluded: chain C6 residue 491 ILE Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 90 SER Chi-restraints excluded: chain D6 residue 108 SER Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 349 VAL Chi-restraints excluded: chain D6 residue 364 LEU Chi-restraints excluded: chain D6 residue 491 ILE Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 108 SER Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 349 VAL Chi-restraints excluded: chain E6 residue 364 LEU Chi-restraints excluded: chain E6 residue 414 THR Chi-restraints excluded: chain E6 residue 491 ILE Chi-restraints excluded: chain F6 residue 60 SER Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 108 SER Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 349 VAL Chi-restraints excluded: chain F6 residue 364 LEU Chi-restraints excluded: chain F6 residue 414 THR Chi-restraints excluded: chain F6 residue 491 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.5980 chunk 568 optimal weight: 7.9990 chunk 315 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 383 optimal weight: 0.9990 chunk 303 optimal weight: 3.9990 chunk 587 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 437 optimal weight: 1.9990 chunk 681 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN B5 31 GLN C5 29 ASN E5 29 ASN E5 31 GLN ** E5 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN F5 31 GLN B3 58 HIS C3 32 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 58 HIS F3 124 GLN ** G3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3 58 HIS K3 54 ASN L3 32 ASN ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3 124 GLN N3 90 ASN O3 32 ASN Q3 54 ASN ** R3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4 52 ASN D4 52 ASN ** A7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 320 GLN A6 345 ASN A6 389 ASN ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 442 GLN ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 320 GLN B6 389 ASN ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 442 GLN ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 345 ASN ** C6 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 424 ASN C6 443 GLN ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 320 GLN D6 389 ASN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 442 GLN ** E6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E6 320 GLN E6 345 ASN E6 389 ASN ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 134 GLN ** F6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN F6 389 ASN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 59988 Z= 0.244 Angle : 0.676 11.852 81510 Z= 0.355 Chirality : 0.047 0.199 9684 Planarity : 0.004 0.075 10548 Dihedral : 6.500 79.110 8398 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.09 % Allowed : 16.08 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.09), residues: 7656 helix: 0.31 (0.12), residues: 1896 sheet: -1.97 (0.11), residues: 2106 loop : -2.44 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRPE4 64 HIS 0.006 0.001 HISQ3 58 PHE 0.035 0.002 PHEB3 51 TYR 0.025 0.002 TYRC5 39 ARG 0.015 0.001 ARGB3 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2589 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 2319 time to evaluate : 7.619 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: A5 65 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A5 82 ASP cc_start: 0.8471 (p0) cc_final: 0.7615 (p0) REVERT: B5 56 SER cc_start: 0.8954 (m) cc_final: 0.8301 (m) REVERT: B5 82 ASP cc_start: 0.8522 (p0) cc_final: 0.7500 (p0) REVERT: D5 56 SER cc_start: 0.8905 (m) cc_final: 0.8501 (m) REVERT: D5 65 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8261 (tm-30) REVERT: E5 82 ASP cc_start: 0.8623 (p0) cc_final: 0.7912 (p0) REVERT: E5 85 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8453 (mm-30) REVERT: E5 86 ASN cc_start: 0.8690 (m110) cc_final: 0.8365 (m-40) REVERT: F5 20 GLU cc_start: 0.7734 (mp0) cc_final: 0.7197 (mp0) REVERT: F5 65 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7901 (tm-30) REVERT: F5 82 ASP cc_start: 0.8487 (p0) cc_final: 0.7623 (p0) REVERT: A3 89 ILE cc_start: 0.8181 (mm) cc_final: 0.7854 (tp) REVERT: D3 31 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8356 (ptt-90) REVERT: D3 81 GLN cc_start: 0.8811 (pm20) cc_final: 0.8274 (pm20) REVERT: D3 89 ILE cc_start: 0.8289 (mm) cc_final: 0.8054 (tp) REVERT: E3 109 ASP cc_start: 0.8463 (m-30) cc_final: 0.8225 (m-30) REVERT: F3 4 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7375 (tm-30) REVERT: G3 23 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7804 (ttp80) REVERT: G3 62 ILE cc_start: 0.8122 (mp) cc_final: 0.7744 (mm) REVERT: H3 3 ILE cc_start: 0.8121 (tp) cc_final: 0.7846 (tp) REVERT: I3 49 TYR cc_start: 0.7782 (p90) cc_final: 0.7235 (p90) REVERT: I3 88 LEU cc_start: 0.8994 (tt) cc_final: 0.8781 (tt) REVERT: J3 89 ILE cc_start: 0.8263 (mm) cc_final: 0.7983 (tp) REVERT: K3 27 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8243 (mmtt) REVERT: K3 59 LYS cc_start: 0.8755 (mttm) cc_final: 0.8504 (mttm) REVERT: N3 116 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8364 (mm-40) REVERT: Q3 23 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7690 (ttm-80) REVERT: Q3 27 LYS cc_start: 0.8849 (tptt) cc_final: 0.8617 (tptt) REVERT: Q3 41 TYR cc_start: 0.8866 (t80) cc_final: 0.8591 (t80) REVERT: R3 4 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A4 44 GLN cc_start: 0.6409 (mt0) cc_final: 0.6005 (mt0) REVERT: A4 52 ASN cc_start: 0.9094 (m-40) cc_final: 0.8880 (m-40) REVERT: B4 6 ARG cc_start: 0.8196 (tpt-90) cc_final: 0.7981 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9011 (m110) cc_final: 0.8491 (m110) REVERT: B4 92 ASP cc_start: 0.8375 (p0) cc_final: 0.8092 (p0) REVERT: C4 57 ASP cc_start: 0.7959 (m-30) cc_final: 0.7693 (m-30) REVERT: E4 44 GLN cc_start: 0.6143 (mt0) cc_final: 0.5665 (mt0) REVERT: E4 57 ASP cc_start: 0.7726 (m-30) cc_final: 0.7412 (m-30) REVERT: E4 104 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: F4 6 ARG cc_start: 0.8226 (tpt-90) cc_final: 0.7871 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7916 (m-30) cc_final: 0.7441 (m-30) REVERT: F4 92 ASP cc_start: 0.8509 (p0) cc_final: 0.8217 (p0) REVERT: A7 73 LYS cc_start: 0.8936 (tptp) cc_final: 0.8728 (tptp) REVERT: C7 73 LYS cc_start: 0.9162 (tptp) cc_final: 0.8600 (tppt) REVERT: C7 83 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6556 (mt-10) REVERT: D7 73 LYS cc_start: 0.9206 (tptp) cc_final: 0.8830 (tppt) REVERT: E7 133 VAL cc_start: 0.8962 (t) cc_final: 0.8634 (p) REVERT: F7 91 MET cc_start: 0.8343 (ttm) cc_final: 0.8109 (ttt) REVERT: F7 133 VAL cc_start: 0.9023 (t) cc_final: 0.8627 (p) REVERT: A6 272 TYR cc_start: 0.8452 (m-80) cc_final: 0.7547 (m-80) REVERT: A6 276 ASN cc_start: 0.8007 (t0) cc_final: 0.7724 (t0) REVERT: A6 295 LEU cc_start: 0.8695 (mp) cc_final: 0.8241 (mp) REVERT: A6 369 ASN cc_start: 0.8741 (t0) cc_final: 0.8488 (t0) REVERT: A6 384 GLU cc_start: 0.8877 (tp30) cc_final: 0.8653 (tp30) REVERT: A6 418 CYS cc_start: 0.9238 (m) cc_final: 0.8622 (m) REVERT: B6 88 TRP cc_start: 0.8269 (p-90) cc_final: 0.7901 (p-90) REVERT: B6 265 TYR cc_start: 0.8871 (m-80) cc_final: 0.8589 (m-80) REVERT: B6 272 TYR cc_start: 0.8372 (m-80) cc_final: 0.7584 (m-80) REVERT: B6 308 TYR cc_start: 0.8443 (t80) cc_final: 0.8176 (t80) REVERT: B6 342 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: B6 384 GLU cc_start: 0.8836 (tp30) cc_final: 0.8588 (tp30) REVERT: C6 67 ASN cc_start: 0.7995 (m-40) cc_final: 0.7757 (m-40) REVERT: C6 312 MET cc_start: 0.8144 (tpt) cc_final: 0.7937 (tpt) REVERT: C6 330 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7578 (mt-10) REVERT: C6 491 ILE cc_start: 0.3285 (tp) cc_final: 0.2932 (tp) REVERT: D6 24 MET cc_start: 0.9047 (tpt) cc_final: 0.8743 (tpp) REVERT: D6 88 TRP cc_start: 0.8489 (p-90) cc_final: 0.8065 (p-90) REVERT: D6 272 TYR cc_start: 0.8275 (m-80) cc_final: 0.8045 (m-80) REVERT: D6 295 LEU cc_start: 0.8630 (mp) cc_final: 0.8129 (mp) REVERT: D6 326 MET cc_start: 0.8152 (mtp) cc_final: 0.7931 (mmm) REVERT: D6 330 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7985 (mt-10) REVERT: D6 342 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: E6 9 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7701 (mtm110) REVERT: E6 24 MET cc_start: 0.8931 (tpt) cc_final: 0.8416 (tpt) REVERT: E6 342 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: E6 376 TYR cc_start: 0.8933 (t80) cc_final: 0.8732 (t80) REVERT: E6 384 GLU cc_start: 0.8929 (tp30) cc_final: 0.8541 (tp30) REVERT: E6 421 TYR cc_start: 0.8969 (m-80) cc_final: 0.8533 (m-10) REVERT: F6 272 TYR cc_start: 0.8455 (m-80) cc_final: 0.7453 (m-80) REVERT: F6 276 ASN cc_start: 0.8111 (t0) cc_final: 0.7811 (t0) REVERT: F6 295 LEU cc_start: 0.8891 (mt) cc_final: 0.8684 (mt) REVERT: F6 330 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7991 (mt-10) REVERT: F6 342 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: F6 384 GLU cc_start: 0.8721 (tp30) cc_final: 0.8226 (tp30) outliers start: 270 outliers final: 201 residues processed: 2400 average time/residue: 0.5153 time to fit residues: 2150.8116 Evaluate side-chains 2262 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 2056 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 64 MET Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 148 LEU Chi-restraints excluded: chain B5 residue 49 ASN Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain B5 residue 122 LEU Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 122 LEU Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 120 LYS Chi-restraints excluded: chain D5 residue 122 LEU Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 65 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 148 LEU Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 67 SER Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 122 LEU Chi-restraints excluded: chain F5 residue 148 LEU Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 44 THR Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 101 VAL Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain B3 residue 110 GLU Chi-restraints excluded: chain C3 residue 44 THR Chi-restraints excluded: chain C3 residue 100 LEU Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 28 ILE Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 55 GLU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 101 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 33 THR Chi-restraints excluded: chain E3 residue 89 ILE Chi-restraints excluded: chain E3 residue 92 LEU Chi-restraints excluded: chain F3 residue 20 ILE Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 44 THR Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 101 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain H3 residue 89 ILE Chi-restraints excluded: chain I3 residue 20 ILE Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 64 TYR Chi-restraints excluded: chain I3 residue 104 LEU Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 101 VAL Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 54 ASN Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 20 ILE Chi-restraints excluded: chain L3 residue 44 THR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain L3 residue 104 LEU Chi-restraints excluded: chain M3 residue 8 ILE Chi-restraints excluded: chain M3 residue 13 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 101 VAL Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain O3 residue 42 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 8 ILE Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 101 VAL Chi-restraints excluded: chain Q3 residue 3 ILE Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 54 ASN Chi-restraints excluded: chain Q3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 110 GLU Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain R3 residue 69 SER Chi-restraints excluded: chain R3 residue 100 LEU Chi-restraints excluded: chain R3 residue 104 LEU Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 113 SER Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 86 LEU Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 16 ASN Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 16 ASN Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 16 ASN Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 49 SER Chi-restraints excluded: chain F7 residue 55 ASP Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 108 SER Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 355 THR Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain B6 residue 4 ILE Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 108 SER Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 414 THR Chi-restraints excluded: chain B6 residue 462 ASP Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 60 SER Chi-restraints excluded: chain C6 residue 108 SER Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 253 ILE Chi-restraints excluded: chain C6 residue 270 THR Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 19 ILE Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 108 SER Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 414 THR Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain E6 residue 25 ASN Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 108 SER Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 364 LEU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 413 ASP Chi-restraints excluded: chain E6 residue 414 THR Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 489 GLU Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 60 SER Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 108 SER Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 414 THR Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 460 LEU Chi-restraints excluded: chain F6 residue 475 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 566 optimal weight: 3.9990 chunk 463 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 682 optimal weight: 2.9990 chunk 737 optimal weight: 9.9990 chunk 607 optimal weight: 5.9990 chunk 676 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 547 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN ** A5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 31 GLN B5 48 GLN C5 29 ASN E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** F5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 32 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 32 ASN ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 32 ASN R3 54 ASN ** R3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 320 GLN ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 442 GLN ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 320 GLN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 442 GLN ** E6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E6 320 GLN ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 59988 Z= 0.336 Angle : 0.682 9.513 81510 Z= 0.358 Chirality : 0.047 0.196 9684 Planarity : 0.004 0.068 10548 Dihedral : 5.965 80.163 8311 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 6.23 % Allowed : 20.77 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.09), residues: 7656 helix: 0.44 (0.12), residues: 1914 sheet: -1.86 (0.11), residues: 2142 loop : -2.42 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRPD4 64 HIS 0.005 0.001 HISG3 58 PHE 0.030 0.002 PHEB4 84 TYR 0.023 0.002 TYRD6 46 ARG 0.009 0.001 ARGA4 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2633 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 2222 time to evaluate : 5.203 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: A5 82 ASP cc_start: 0.8570 (p0) cc_final: 0.7741 (p0) REVERT: A5 137 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7296 (tt) REVERT: B5 64 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7670 (ttm) REVERT: B5 82 ASP cc_start: 0.8596 (p0) cc_final: 0.7815 (p0) REVERT: B5 100 LYS cc_start: 0.8939 (mttp) cc_final: 0.8690 (mttm) REVERT: C5 70 GLU cc_start: 0.8826 (pt0) cc_final: 0.8597 (pt0) REVERT: C5 82 ASP cc_start: 0.8546 (p0) cc_final: 0.7756 (p0) REVERT: C5 160 ASP cc_start: 0.8069 (p0) cc_final: 0.7861 (p0) REVERT: D5 20 GLU cc_start: 0.8190 (mp0) cc_final: 0.7852 (mp0) REVERT: D5 65 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D5 76 LEU cc_start: 0.8855 (mt) cc_final: 0.8650 (mp) REVERT: D5 137 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7448 (tt) REVERT: E5 82 ASP cc_start: 0.8700 (p0) cc_final: 0.8077 (p0) REVERT: E5 102 VAL cc_start: 0.9200 (p) cc_final: 0.8854 (p) REVERT: E5 156 GLU cc_start: 0.8450 (pp20) cc_final: 0.7461 (pp20) REVERT: F5 65 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F5 82 ASP cc_start: 0.8576 (p0) cc_final: 0.7786 (p0) REVERT: F5 100 LYS cc_start: 0.8782 (mttp) cc_final: 0.8557 (mttm) REVERT: F5 137 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7424 (tt) REVERT: A3 89 ILE cc_start: 0.8456 (mm) cc_final: 0.8237 (tp) REVERT: B3 65 ARG cc_start: 0.7654 (ttm170) cc_final: 0.5846 (ttp80) REVERT: D3 81 GLN cc_start: 0.8791 (pm20) cc_final: 0.8383 (pm20) REVERT: E3 39 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7356 (tm-30) REVERT: F3 4 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G3 81 GLN cc_start: 0.8893 (pm20) cc_final: 0.8644 (pm20) REVERT: H3 100 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7935 (tp) REVERT: I3 49 TYR cc_start: 0.7846 (p90) cc_final: 0.7316 (p90) REVERT: I3 88 LEU cc_start: 0.9022 (tt) cc_final: 0.8798 (tt) REVERT: K3 27 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8350 (mmtt) REVERT: K3 59 LYS cc_start: 0.8769 (mttm) cc_final: 0.8488 (mttm) REVERT: L3 100 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8562 (pp) REVERT: M3 81 GLN cc_start: 0.9040 (pm20) cc_final: 0.8759 (pm20) REVERT: N3 39 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7621 (tm-30) REVERT: N3 65 ARG cc_start: 0.7457 (ttm170) cc_final: 0.5960 (ttp80) REVERT: N3 116 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8392 (mm-40) REVERT: P3 88 LEU cc_start: 0.9010 (tt) cc_final: 0.8808 (tp) REVERT: P3 89 ILE cc_start: 0.8672 (mm) cc_final: 0.8465 (tp) REVERT: Q3 65 ARG cc_start: 0.7491 (ttm170) cc_final: 0.5870 (ttp80) REVERT: R3 4 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A4 44 GLN cc_start: 0.6619 (mt0) cc_final: 0.6153 (mt0) REVERT: B4 6 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7855 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9015 (m110) cc_final: 0.8510 (m110) REVERT: B4 58 TRP cc_start: 0.9192 (p-90) cc_final: 0.8965 (p-90) REVERT: B4 92 ASP cc_start: 0.8490 (p0) cc_final: 0.8191 (p0) REVERT: D4 6 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8503 (mmm-85) REVERT: E4 6 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8380 (mmm-85) REVERT: E4 40 ARG cc_start: 0.8365 (mmt180) cc_final: 0.8131 (mmt180) REVERT: E4 44 GLN cc_start: 0.6038 (mt0) cc_final: 0.5583 (mt0) REVERT: E4 47 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7995 (t0) REVERT: E4 57 ASP cc_start: 0.7840 (m-30) cc_final: 0.7496 (m-30) REVERT: E4 104 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: F4 6 ARG cc_start: 0.8209 (tpt-90) cc_final: 0.7759 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7955 (m-30) cc_final: 0.7491 (m-30) REVERT: F4 92 ASP cc_start: 0.8554 (p0) cc_final: 0.8242 (p0) REVERT: A7 135 GLU cc_start: 0.8640 (pp20) cc_final: 0.7957 (pp20) REVERT: B7 25 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B7 135 GLU cc_start: 0.8681 (pp20) cc_final: 0.8139 (pp20) REVERT: C7 91 MET cc_start: 0.8276 (ttm) cc_final: 0.8015 (ttt) REVERT: D7 40 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7661 (ptp-170) REVERT: E7 133 VAL cc_start: 0.9032 (t) cc_final: 0.8679 (p) REVERT: E7 135 GLU cc_start: 0.8735 (pp20) cc_final: 0.8203 (pp20) REVERT: A6 276 ASN cc_start: 0.8036 (t0) cc_final: 0.7738 (t0) REVERT: A6 342 GLU cc_start: 0.8446 (pm20) cc_final: 0.8038 (pm20) REVERT: A6 384 GLU cc_start: 0.8991 (tp30) cc_final: 0.8692 (tp30) REVERT: A6 417 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (p) REVERT: A6 418 CYS cc_start: 0.9264 (m) cc_final: 0.8680 (m) REVERT: B6 25 ASN cc_start: 0.8532 (p0) cc_final: 0.8241 (p0) REVERT: B6 88 TRP cc_start: 0.8317 (p-90) cc_final: 0.7858 (p-90) REVERT: B6 265 TYR cc_start: 0.8921 (m-80) cc_final: 0.8706 (m-80) REVERT: B6 342 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: C6 67 ASN cc_start: 0.8000 (m-40) cc_final: 0.7752 (m110) REVERT: C6 88 TRP cc_start: 0.8398 (p-90) cc_final: 0.8172 (p-90) REVERT: C6 167 ASN cc_start: 0.8854 (t0) cc_final: 0.8491 (t0) REVERT: C6 329 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8462 (mmtp) REVERT: C6 330 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C6 342 GLU cc_start: 0.7858 (pm20) cc_final: 0.7615 (pm20) REVERT: D6 88 TRP cc_start: 0.8497 (p-90) cc_final: 0.8080 (p-90) REVERT: D6 295 LEU cc_start: 0.8698 (mp) cc_final: 0.8373 (mp) REVERT: D6 326 MET cc_start: 0.8391 (mtp) cc_final: 0.7965 (mmm) REVERT: D6 330 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D6 342 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: D6 424 ASN cc_start: 0.8874 (t0) cc_final: 0.8620 (t0) REVERT: D6 462 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: E6 24 MET cc_start: 0.9113 (tpt) cc_final: 0.8875 (tpt) REVERT: E6 308 TYR cc_start: 0.8673 (t80) cc_final: 0.8459 (t80) REVERT: E6 342 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: E6 376 TYR cc_start: 0.9108 (t80) cc_final: 0.8743 (t80) REVERT: E6 384 GLU cc_start: 0.9052 (tp30) cc_final: 0.8622 (tp30) REVERT: E6 393 LEU cc_start: 0.8551 (tp) cc_final: 0.8343 (tp) REVERT: E6 421 TYR cc_start: 0.8986 (m-80) cc_final: 0.8711 (m-10) REVERT: F6 24 MET cc_start: 0.8824 (tpt) cc_final: 0.8562 (tpp) REVERT: F6 276 ASN cc_start: 0.8149 (t0) cc_final: 0.7860 (t0) REVERT: F6 295 LEU cc_start: 0.8956 (mt) cc_final: 0.8745 (mt) REVERT: F6 330 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F6 342 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: F6 384 GLU cc_start: 0.8893 (tp30) cc_final: 0.8266 (tp30) outliers start: 411 outliers final: 295 residues processed: 2368 average time/residue: 0.5184 time to fit residues: 2128.2819 Evaluate side-chains 2363 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 2054 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 49 ASN Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 64 MET Chi-restraints excluded: chain A5 residue 74 ILE Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 148 LEU Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 49 ASN Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 64 MET Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 74 ILE Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain B5 residue 122 LEU Chi-restraints excluded: chain C5 residue 49 ASN Chi-restraints excluded: chain C5 residue 55 SER Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 65 GLU Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 74 ILE Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 55 SER Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 71 SER Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 122 LEU Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 65 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 148 LEU Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 67 SER Chi-restraints excluded: chain F5 residue 74 ILE Chi-restraints excluded: chain F5 residue 89 LEU Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 122 LEU Chi-restraints excluded: chain F5 residue 137 ILE Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 148 LEU Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 28 ILE Chi-restraints excluded: chain A3 residue 36 LEU Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 101 VAL Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 33 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 44 THR Chi-restraints excluded: chain D3 residue 13 LEU Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 28 ILE Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 92 LEU Chi-restraints excluded: chain D3 residue 101 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 33 THR Chi-restraints excluded: chain E3 residue 92 LEU Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 15 THR Chi-restraints excluded: chain F3 residue 20 ILE Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 64 TYR Chi-restraints excluded: chain G3 residue 13 LEU Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 28 ILE Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 92 LEU Chi-restraints excluded: chain G3 residue 101 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain H3 residue 100 LEU Chi-restraints excluded: chain H3 residue 126 THR Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 20 ILE Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain I3 residue 64 TYR Chi-restraints excluded: chain J3 residue 13 LEU Chi-restraints excluded: chain J3 residue 15 THR Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 101 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 33 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 15 THR Chi-restraints excluded: chain L3 residue 20 ILE Chi-restraints excluded: chain L3 residue 44 THR Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 101 VAL Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 33 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 100 LEU Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain O3 residue 15 THR Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 42 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 8 ILE Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 55 GLU Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain P3 residue 101 VAL Chi-restraints excluded: chain Q3 residue 3 ILE Chi-restraints excluded: chain Q3 residue 15 THR Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain Q3 residue 126 THR Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 20 SER Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 73 ILE Chi-restraints excluded: chain D4 residue 113 SER Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 47 ASP Chi-restraints excluded: chain E4 residue 70 LYS Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 69 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain A7 residue 110 THR Chi-restraints excluded: chain B7 residue 3 VAL Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 43 SER Chi-restraints excluded: chain B7 residue 44 ILE Chi-restraints excluded: chain B7 residue 81 SER Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain B7 residue 110 THR Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 110 THR Chi-restraints excluded: chain D7 residue 3 VAL Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 44 ILE Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain D7 residue 110 THR Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 43 SER Chi-restraints excluded: chain E7 residue 44 ILE Chi-restraints excluded: chain E7 residue 81 SER Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain E7 residue 110 THR Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 55 ASP Chi-restraints excluded: chain F7 residue 81 SER Chi-restraints excluded: chain F7 residue 110 THR Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 36 VAL Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 108 SER Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 208 VAL Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 253 ILE Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 269 ASP Chi-restraints excluded: chain A6 residue 332 SER Chi-restraints excluded: chain A6 residue 334 THR Chi-restraints excluded: chain A6 residue 341 THR Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 372 CYS Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 417 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 475 VAL Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 19 ILE Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 108 SER Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 208 VAL Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 332 SER Chi-restraints excluded: chain B6 residue 334 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 414 THR Chi-restraints excluded: chain B6 residue 462 ASP Chi-restraints excluded: chain B6 residue 465 THR Chi-restraints excluded: chain B6 residue 475 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 10 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 60 SER Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 108 SER Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 263 LEU Chi-restraints excluded: chain C6 residue 269 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 398 THR Chi-restraints excluded: chain C6 residue 409 THR Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 475 VAL Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 19 ILE Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 60 SER Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 108 SER Chi-restraints excluded: chain D6 residue 208 VAL Chi-restraints excluded: chain D6 residue 210 THR Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 414 THR Chi-restraints excluded: chain D6 residue 434 ARG Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 68 THR Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 108 SER Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 208 VAL Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 489 GLU Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 10 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 108 SER Chi-restraints excluded: chain F6 residue 208 VAL Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 334 THR Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 356 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 414 THR Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 460 LEU Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 0.0970 chunk 512 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 458 optimal weight: 0.9990 chunk 684 optimal weight: 7.9990 chunk 724 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 648 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN C5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** A3 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 58 HIS G3 58 HIS ** H3 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 54 ASN R3 32 ASN R3 54 ASN ** R3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4 66 HIS B4 66 HIS ** A7 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 320 GLN ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 320 GLN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 59988 Z= 0.275 Angle : 0.649 8.755 81510 Z= 0.338 Chirality : 0.046 0.288 9684 Planarity : 0.004 0.069 10548 Dihedral : 5.706 76.312 8306 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.86 % Allowed : 23.30 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.09), residues: 7656 helix: 0.61 (0.12), residues: 1878 sheet: -1.71 (0.11), residues: 2112 loop : -2.28 (0.10), residues: 3666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPD4 64 HIS 0.010 0.001 HISB4 66 PHE 0.026 0.002 PHEE4 84 TYR 0.039 0.002 TYRA3 34 ARG 0.010 0.001 ARGB3 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2689 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 453 poor density : 2236 time to evaluate : 5.154 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: A5 82 ASP cc_start: 0.8530 (p0) cc_final: 0.7818 (p0) REVERT: A5 137 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7316 (tt) REVERT: B5 64 MET cc_start: 0.8136 (ttm) cc_final: 0.7758 (ttm) REVERT: B5 82 ASP cc_start: 0.8567 (p0) cc_final: 0.7831 (p0) REVERT: B5 100 LYS cc_start: 0.8868 (mttp) cc_final: 0.8630 (mttm) REVERT: B5 156 GLU cc_start: 0.8261 (pp20) cc_final: 0.7263 (pp20) REVERT: C5 68 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8559 (tttt) REVERT: C5 70 GLU cc_start: 0.8825 (pt0) cc_final: 0.8609 (pt0) REVERT: D5 56 SER cc_start: 0.8974 (m) cc_final: 0.8466 (m) REVERT: D5 65 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8206 (tm-30) REVERT: D5 76 LEU cc_start: 0.8817 (mt) cc_final: 0.8607 (mp) REVERT: D5 137 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7388 (tt) REVERT: E5 82 ASP cc_start: 0.8700 (p0) cc_final: 0.8098 (p0) REVERT: E5 156 GLU cc_start: 0.8338 (pp20) cc_final: 0.7444 (pp20) REVERT: F5 65 GLU cc_start: 0.8758 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F5 82 ASP cc_start: 0.8568 (p0) cc_final: 0.7810 (p0) REVERT: B3 27 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8302 (mmtt) REVERT: B3 30 TYR cc_start: 0.7861 (t80) cc_final: 0.7552 (t80) REVERT: B3 65 ARG cc_start: 0.7583 (ttm170) cc_final: 0.5815 (ttp80) REVERT: C3 49 TYR cc_start: 0.8105 (p90) cc_final: 0.7694 (p90) REVERT: C3 68 SER cc_start: 0.9035 (m) cc_final: 0.8818 (p) REVERT: E3 39 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E3 41 TYR cc_start: 0.8923 (t80) cc_final: 0.8653 (t80) REVERT: F3 4 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7462 (tm-30) REVERT: F3 64 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: H3 39 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7579 (tm-30) REVERT: I3 49 TYR cc_start: 0.7889 (p90) cc_final: 0.7373 (p90) REVERT: I3 88 LEU cc_start: 0.9011 (tt) cc_final: 0.8759 (tt) REVERT: K3 27 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8380 (mmtt) REVERT: K3 39 GLU cc_start: 0.8579 (tp30) cc_final: 0.7709 (tm-30) REVERT: K3 59 LYS cc_start: 0.8745 (mttm) cc_final: 0.8450 (mttm) REVERT: L3 107 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8132 (pt) REVERT: N3 23 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7825 (ttm-80) REVERT: N3 27 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8483 (mmtt) REVERT: N3 41 TYR cc_start: 0.9016 (t80) cc_final: 0.8702 (t80) REVERT: N3 65 ARG cc_start: 0.7444 (ttm170) cc_final: 0.5909 (ttp80) REVERT: P3 88 LEU cc_start: 0.9022 (tt) cc_final: 0.8793 (tp) REVERT: Q3 59 LYS cc_start: 0.8779 (mttp) cc_final: 0.8563 (mttp) REVERT: Q3 65 ARG cc_start: 0.7519 (ttm170) cc_final: 0.5874 (ttp80) REVERT: A4 6 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: B4 6 ARG cc_start: 0.8184 (tpt-90) cc_final: 0.7844 (mmm-85) REVERT: B4 52 ASN cc_start: 0.8985 (m110) cc_final: 0.8466 (m110) REVERT: B4 58 TRP cc_start: 0.9186 (p-90) cc_final: 0.8970 (p-90) REVERT: B4 92 ASP cc_start: 0.8498 (p0) cc_final: 0.8266 (p0) REVERT: E4 6 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5916 (mt0) cc_final: 0.5467 (mt0) REVERT: E4 47 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (t0) REVERT: E4 57 ASP cc_start: 0.7809 (m-30) cc_final: 0.7497 (m-30) REVERT: E4 104 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: F4 6 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7794 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7852 (m-30) cc_final: 0.7423 (m-30) REVERT: F4 92 ASP cc_start: 0.8495 (p0) cc_final: 0.8192 (p0) REVERT: A7 14 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (t) REVERT: B7 25 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C7 14 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8903 (t) REVERT: C7 42 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7531 (p0) REVERT: C7 91 MET cc_start: 0.8282 (ttm) cc_final: 0.8069 (ttt) REVERT: D7 83 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6366 (mt-10) REVERT: E7 42 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7783 (p0) REVERT: E7 133 VAL cc_start: 0.9045 (t) cc_final: 0.8692 (p) REVERT: A6 276 ASN cc_start: 0.7996 (t0) cc_final: 0.7713 (t0) REVERT: A6 312 MET cc_start: 0.9019 (tpt) cc_final: 0.8486 (tpt) REVERT: A6 339 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7265 (p) REVERT: A6 342 GLU cc_start: 0.8407 (pm20) cc_final: 0.7904 (pm20) REVERT: A6 418 CYS cc_start: 0.9275 (m) cc_final: 0.8686 (m) REVERT: A6 424 ASN cc_start: 0.8725 (t0) cc_final: 0.8430 (t0) REVERT: B6 24 MET cc_start: 0.8911 (tpt) cc_final: 0.8520 (tpp) REVERT: B6 25 ASN cc_start: 0.8242 (p0) cc_final: 0.7837 (p0) REVERT: B6 88 TRP cc_start: 0.8240 (p-90) cc_final: 0.7616 (p-90) REVERT: B6 265 TYR cc_start: 0.8860 (m-80) cc_final: 0.8644 (m-10) REVERT: B6 342 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: B6 384 GLU cc_start: 0.8989 (tp30) cc_final: 0.8576 (tp30) REVERT: B6 424 ASN cc_start: 0.8774 (t0) cc_final: 0.8490 (t0) REVERT: C6 167 ASN cc_start: 0.8952 (t0) cc_final: 0.8587 (t0) REVERT: C6 276 ASN cc_start: 0.8156 (t0) cc_final: 0.7888 (t0) REVERT: C6 330 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C6 342 GLU cc_start: 0.7909 (pm20) cc_final: 0.7629 (pm20) REVERT: C6 491 ILE cc_start: 0.3391 (tp) cc_final: 0.2913 (tp) REVERT: D6 46 TYR cc_start: 0.8331 (m-10) cc_final: 0.7989 (m-10) REVERT: D6 88 TRP cc_start: 0.8368 (p-90) cc_final: 0.8023 (p-90) REVERT: D6 272 TYR cc_start: 0.8169 (m-80) cc_final: 0.7323 (m-80) REVERT: D6 326 MET cc_start: 0.8348 (mtp) cc_final: 0.7982 (mmm) REVERT: D6 330 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D6 342 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: D6 424 ASN cc_start: 0.8794 (t0) cc_final: 0.8503 (t0) REVERT: D6 462 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: E6 88 TRP cc_start: 0.8213 (p-90) cc_final: 0.7797 (p-90) REVERT: E6 342 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: E6 393 LEU cc_start: 0.8600 (tp) cc_final: 0.8359 (tp) REVERT: E6 421 TYR cc_start: 0.8960 (m-80) cc_final: 0.8688 (m-10) REVERT: F6 24 MET cc_start: 0.8932 (tpt) cc_final: 0.8640 (tpp) REVERT: F6 276 ASN cc_start: 0.8164 (t0) cc_final: 0.7915 (t0) REVERT: F6 308 TYR cc_start: 0.8449 (t80) cc_final: 0.8061 (t80) REVERT: F6 330 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7895 (mt-10) REVERT: F6 424 ASN cc_start: 0.8701 (t0) cc_final: 0.8479 (t0) outliers start: 453 outliers final: 325 residues processed: 2400 average time/residue: 0.5083 time to fit residues: 2123.3758 Evaluate side-chains 2418 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 2076 time to evaluate : 5.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 65 GLU Chi-restraints excluded: chain A5 residue 67 SER Chi-restraints excluded: chain A5 residue 74 ILE Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 33 SER Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain B5 residue 133 VAL Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 55 SER Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 122 LEU Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 49 ASN Chi-restraints excluded: chain D5 residue 55 SER Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 122 LEU Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 49 ASN Chi-restraints excluded: chain E5 residue 65 GLU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 148 LEU Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 49 ASN Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 67 SER Chi-restraints excluded: chain F5 residue 74 ILE Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 122 LEU Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 28 ILE Chi-restraints excluded: chain A3 residue 36 LEU Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 27 LYS Chi-restraints excluded: chain B3 residue 28 ILE Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 44 THR Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 13 LEU Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 28 ILE Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 101 VAL Chi-restraints excluded: chain D3 residue 102 VAL Chi-restraints excluded: chain E3 residue 15 THR Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 92 LEU Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 15 THR Chi-restraints excluded: chain F3 residue 20 ILE Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 64 TYR Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 15 THR Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 28 ILE Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 92 LEU Chi-restraints excluded: chain G3 residue 125 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain H3 residue 92 LEU Chi-restraints excluded: chain H3 residue 126 THR Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 20 ILE Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain I3 residue 64 TYR Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 101 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 33 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain K3 residue 126 THR Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 15 THR Chi-restraints excluded: chain L3 residue 20 ILE Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 44 THR Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 29 SER Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 101 VAL Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 15 THR Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 23 ARG Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 100 LEU Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain O3 residue 15 THR Chi-restraints excluded: chain O3 residue 42 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 64 TYR Chi-restraints excluded: chain O3 residue 69 SER Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 8 ILE Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 55 GLU Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain P3 residue 101 VAL Chi-restraints excluded: chain P3 residue 102 VAL Chi-restraints excluded: chain Q3 residue 15 THR Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain Q3 residue 126 THR Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 83 ASP Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 20 SER Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 113 SER Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 47 ASP Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 73 ILE Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 5 VAL Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 69 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 16 ASN Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 43 SER Chi-restraints excluded: chain B7 residue 44 ILE Chi-restraints excluded: chain B7 residue 69 SER Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 16 ASN Chi-restraints excluded: chain C7 residue 30 VAL Chi-restraints excluded: chain C7 residue 42 ASN Chi-restraints excluded: chain C7 residue 44 ILE Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain C7 residue 110 THR Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 43 SER Chi-restraints excluded: chain D7 residue 44 ILE Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 16 ASN Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 42 ASN Chi-restraints excluded: chain E7 residue 43 SER Chi-restraints excluded: chain E7 residue 69 SER Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 44 ILE Chi-restraints excluded: chain F7 residue 69 SER Chi-restraints excluded: chain F7 residue 81 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain F7 residue 110 THR Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 27 VAL Chi-restraints excluded: chain A6 residue 36 VAL Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 109 GLU Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 208 VAL Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 253 ILE Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 334 THR Chi-restraints excluded: chain A6 residue 339 THR Chi-restraints excluded: chain A6 residue 341 THR Chi-restraints excluded: chain A6 residue 355 THR Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 372 CYS Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 19 ILE Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 109 GLU Chi-restraints excluded: chain B6 residue 129 ASP Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 208 VAL Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 269 ASP Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 341 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 465 THR Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 29 ILE Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 60 SER Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 108 SER Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 263 LEU Chi-restraints excluded: chain C6 residue 269 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 398 THR Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 19 ILE Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 92 SER Chi-restraints excluded: chain D6 residue 109 GLU Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 208 VAL Chi-restraints excluded: chain D6 residue 210 THR Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 434 ARG Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 19 ILE Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 129 ASP Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 208 VAL Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 341 THR Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain E6 residue 489 GLU Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 60 SER Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 109 GLU Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 208 VAL Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 0.4980 chunk 411 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 539 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 618 optimal weight: 0.9980 chunk 501 optimal weight: 0.0000 chunk 0 optimal weight: 7.9990 chunk 370 optimal weight: 2.9990 chunk 650 optimal weight: 0.3980 chunk 182 optimal weight: 7.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN C5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN A3 81 GLN C3 58 HIS F3 58 HIS H3 4 GLN L3 58 HIS O3 54 ASN R3 58 HIS ** A7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 155 ASN A6 320 GLN ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 155 ASN ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 320 GLN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E6 155 ASN ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 155 ASN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 442 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59988 Z= 0.180 Angle : 0.624 9.129 81510 Z= 0.320 Chirality : 0.045 0.196 9684 Planarity : 0.004 0.067 10548 Dihedral : 5.359 66.291 8299 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.17 % Allowed : 26.17 % Favored : 67.67 % 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: -1.90 (0.10), residues: 7656 helix: 0.69 (0.12), residues: 1926 sheet: -1.54 (0.11), residues: 2118 loop : -2.18 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRPF6 88 HIS 0.007 0.001 HISA3 58 PHE 0.046 0.002 PHEN3 51 TYR 0.029 0.002 TYRC5 57 ARG 0.008 0.001 ARGF6 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2625 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 2218 time to evaluate : 5.129 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: A5 108 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A5 137 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7147 (tt) REVERT: B5 64 MET cc_start: 0.8023 (ttm) cc_final: 0.7762 (ttm) REVERT: C5 57 TYR cc_start: 0.6273 (t80) cc_final: 0.5867 (t80) REVERT: C5 58 ASP cc_start: 0.8527 (t0) cc_final: 0.8298 (t0) REVERT: C5 100 LYS cc_start: 0.8480 (mttp) cc_final: 0.8063 (mttm) REVERT: D5 56 SER cc_start: 0.8830 (m) cc_final: 0.8321 (m) REVERT: D5 65 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D5 100 LYS cc_start: 0.8315 (mttp) cc_final: 0.7843 (mttm) REVERT: D5 137 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7365 (tp) REVERT: E5 82 ASP cc_start: 0.8632 (p0) cc_final: 0.8002 (p0) REVERT: F5 56 SER cc_start: 0.8738 (m) cc_final: 0.8205 (m) REVERT: F5 65 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7943 (tm-30) REVERT: F5 82 ASP cc_start: 0.8430 (p0) cc_final: 0.7698 (p0) REVERT: B3 30 TYR cc_start: 0.8105 (t80) cc_final: 0.7175 (t80) REVERT: B3 39 GLU cc_start: 0.8336 (tp30) cc_final: 0.7605 (tm-30) REVERT: B3 59 LYS cc_start: 0.8676 (mttp) cc_final: 0.8400 (mttp) REVERT: C3 49 TYR cc_start: 0.7972 (p90) cc_final: 0.7668 (p90) REVERT: C3 68 SER cc_start: 0.9023 (m) cc_final: 0.8803 (p) REVERT: D3 55 GLU cc_start: 0.8466 (pm20) cc_final: 0.7975 (mp0) REVERT: E3 23 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7701 (ttm-80) REVERT: E3 41 TYR cc_start: 0.8890 (t80) cc_final: 0.8677 (t80) REVERT: F3 4 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7595 (tm-30) REVERT: F3 49 TYR cc_start: 0.7771 (p90) cc_final: 0.7465 (p90) REVERT: F3 64 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: H3 27 LYS cc_start: 0.8557 (tptt) cc_final: 0.8160 (tppt) REVERT: H3 59 LYS cc_start: 0.8806 (mttm) cc_final: 0.8062 (mttm) REVERT: I3 4 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7582 (tm-30) REVERT: I3 49 TYR cc_start: 0.7790 (p90) cc_final: 0.7278 (p90) REVERT: I3 88 LEU cc_start: 0.8969 (tt) cc_final: 0.8721 (tt) REVERT: I3 121 ASP cc_start: 0.8061 (t0) cc_final: 0.7848 (t0) REVERT: J3 20 ILE cc_start: 0.8400 (mm) cc_final: 0.8117 (tp) REVERT: J3 62 ILE cc_start: 0.8696 (mm) cc_final: 0.8451 (mp) REVERT: K3 39 GLU cc_start: 0.8476 (tp30) cc_final: 0.7731 (tm-30) REVERT: K3 59 LYS cc_start: 0.8716 (mttm) cc_final: 0.8432 (mttp) REVERT: L3 4 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7608 (tm-30) REVERT: L3 107 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8129 (pt) REVERT: M3 20 ILE cc_start: 0.8361 (mm) cc_final: 0.8139 (tp) REVERT: M3 54 ASN cc_start: 0.7280 (t0) cc_final: 0.6919 (t0) REVERT: N3 39 GLU cc_start: 0.8327 (tp30) cc_final: 0.7452 (tm-30) REVERT: N3 41 TYR cc_start: 0.8917 (t80) cc_final: 0.8674 (t80) REVERT: P3 62 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8290 (mp) REVERT: Q3 23 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7424 (ttm-80) REVERT: Q3 39 GLU cc_start: 0.8264 (tp30) cc_final: 0.7756 (tm-30) REVERT: Q3 49 TYR cc_start: 0.8252 (p90) cc_final: 0.7927 (p90) REVERT: Q3 59 LYS cc_start: 0.8741 (mttp) cc_final: 0.8391 (mttp) REVERT: R3 121 ASP cc_start: 0.8121 (t0) cc_final: 0.7884 (t0) REVERT: A4 6 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.7767 (mmm-85) REVERT: A4 44 GLN cc_start: 0.6097 (mt0) cc_final: 0.5662 (mt0) REVERT: A4 52 ASN cc_start: 0.9001 (m-40) cc_final: 0.8726 (m110) REVERT: B4 52 ASN cc_start: 0.9018 (m110) cc_final: 0.8570 (m110) REVERT: B4 57 ASP cc_start: 0.7903 (m-30) cc_final: 0.7519 (m-30) REVERT: C4 6 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: C4 52 ASN cc_start: 0.8765 (m110) cc_final: 0.8438 (m110) REVERT: C4 57 ASP cc_start: 0.7919 (m-30) cc_final: 0.7618 (m-30) REVERT: D4 6 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.7762 (mmm-85) REVERT: D4 57 ASP cc_start: 0.7989 (m-30) cc_final: 0.7643 (m-30) REVERT: E4 44 GLN cc_start: 0.5967 (mt0) cc_final: 0.5626 (mt0) REVERT: E4 57 ASP cc_start: 0.7632 (m-30) cc_final: 0.7364 (m-30) REVERT: E4 104 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: F4 57 ASP cc_start: 0.7645 (m-30) cc_final: 0.7316 (m-30) REVERT: F4 75 GLN cc_start: 0.8199 (mt0) cc_final: 0.7972 (mt0) REVERT: F4 92 ASP cc_start: 0.8480 (p0) cc_final: 0.8279 (p0) REVERT: A7 25 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8415 (tm-30) REVERT: A7 119 LYS cc_start: 0.8224 (mttp) cc_final: 0.7863 (mttm) REVERT: B7 73 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8347 (tppt) REVERT: C7 14 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8871 (t) REVERT: C7 73 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8376 (tppt) REVERT: D7 73 LYS cc_start: 0.9029 (tptp) cc_final: 0.8508 (tppt) REVERT: D7 83 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6271 (mt-10) REVERT: E7 73 LYS cc_start: 0.8926 (tptp) cc_final: 0.8640 (tptp) REVERT: A6 44 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7676 (ttm-80) REVERT: A6 339 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.6991 (p) REVERT: A6 342 GLU cc_start: 0.8397 (pm20) cc_final: 0.7970 (pm20) REVERT: A6 384 GLU cc_start: 0.9009 (tp30) cc_final: 0.8501 (tp30) REVERT: A6 418 CYS cc_start: 0.9289 (m) cc_final: 0.8812 (m) REVERT: A6 424 ASN cc_start: 0.8514 (t0) cc_final: 0.8259 (t0) REVERT: B6 24 MET cc_start: 0.8938 (tpt) cc_final: 0.8634 (tpp) REVERT: B6 88 TRP cc_start: 0.8115 (p-90) cc_final: 0.7465 (p-90) REVERT: B6 272 TYR cc_start: 0.8243 (m-80) cc_final: 0.7419 (m-80) REVERT: B6 308 TYR cc_start: 0.8112 (t80) cc_final: 0.7768 (t80) REVERT: B6 342 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: B6 424 ASN cc_start: 0.8586 (t0) cc_final: 0.8334 (t0) REVERT: C6 67 ASN cc_start: 0.7811 (m-40) cc_final: 0.7517 (m110) REVERT: C6 167 ASN cc_start: 0.8882 (t0) cc_final: 0.8633 (t0) REVERT: C6 276 ASN cc_start: 0.8116 (t0) cc_final: 0.7913 (t0) REVERT: C6 330 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7437 (mt-10) REVERT: C6 388 ASN cc_start: 0.8540 (m110) cc_final: 0.8320 (m-40) REVERT: C6 491 ILE cc_start: 0.3439 (tp) cc_final: 0.2975 (tp) REVERT: D6 46 TYR cc_start: 0.8257 (m-10) cc_final: 0.8045 (m-10) REVERT: D6 88 TRP cc_start: 0.8228 (p-90) cc_final: 0.7972 (p-90) REVERT: D6 320 GLN cc_start: 0.8122 (tp40) cc_final: 0.7570 (mt0) REVERT: D6 326 MET cc_start: 0.8230 (mtp) cc_final: 0.7767 (mtp) REVERT: D6 330 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7941 (mt-10) REVERT: D6 342 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: D6 462 ASP cc_start: 0.7789 (t70) cc_final: 0.7497 (m-30) REVERT: E6 342 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: E6 421 TYR cc_start: 0.8808 (m-80) cc_final: 0.8572 (m-10) REVERT: F6 9 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7793 (mtm110) REVERT: F6 330 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F6 342 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: F6 424 ASN cc_start: 0.8512 (t0) cc_final: 0.8245 (t0) REVERT: F6 460 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8353 (mm) outliers start: 407 outliers final: 268 residues processed: 2383 average time/residue: 0.5189 time to fit residues: 2150.9956 Evaluate side-chains 2345 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 2061 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 29 ASN Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 33 SER Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain B5 residue 133 VAL Chi-restraints excluded: chain B5 residue 148 LEU Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 4 SER Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 63 ILE Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 148 LEU Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 67 SER Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 28 ILE Chi-restraints excluded: chain A3 residue 36 LEU Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 28 ILE Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 44 THR Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain E3 residue 15 THR Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 92 LEU Chi-restraints excluded: chain F3 residue 20 ILE Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 64 TYR Chi-restraints excluded: chain G3 residue 5 VAL Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain G3 residue 125 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain H3 residue 100 LEU Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 20 ILE Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain I3 residue 100 LEU Chi-restraints excluded: chain I3 residue 104 LEU Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain K3 residue 126 THR Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 100 LEU Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain O3 residue 104 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 62 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain P3 residue 102 VAL Chi-restraints excluded: chain Q3 residue 15 THR Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 32 ILE Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 99 ASN Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 20 SER Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 20 SER Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 5 VAL Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 3 VAL Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 14 THR Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 16 ASN Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 14 THR Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 16 ASN Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 43 SER Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain E7 residue 110 THR Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 36 VAL Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 339 THR Chi-restraints excluded: chain A6 residue 355 THR Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain A6 residue 492 ILE Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 25 ASN Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 294 CYS Chi-restraints excluded: chain B6 residue 332 SER Chi-restraints excluded: chain B6 residue 334 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 385 ILE Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 29 ILE Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 109 GLU Chi-restraints excluded: chain C6 residue 129 ASP Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 253 ILE Chi-restraints excluded: chain C6 residue 269 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 334 THR Chi-restraints excluded: chain C6 residue 372 CYS Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 60 SER Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 109 GLU Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 353 LEU Chi-restraints excluded: chain D6 residue 355 THR Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 385 ILE Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 25 ASN Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 330 GLU Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain E6 residue 489 GLU Chi-restraints excluded: chain F6 residue 6 GLU Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 60 SER Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 334 THR Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 460 LEU Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 5.9990 chunk 652 optimal weight: 0.3980 chunk 143 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 725 optimal weight: 6.9990 chunk 602 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 240 optimal weight: 0.8980 chunk 380 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 124 GLN ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N3 52 GLN ** R3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4 52 ASN ** B7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 59988 Z= 0.258 Angle : 0.648 10.029 81510 Z= 0.333 Chirality : 0.046 0.273 9684 Planarity : 0.004 0.068 10548 Dihedral : 5.310 55.993 8297 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.27 % Allowed : 27.39 % Favored : 66.33 % 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: -1.85 (0.10), residues: 7656 helix: 0.69 (0.12), residues: 1938 sheet: -1.45 (0.11), residues: 2130 loop : -2.17 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPC4 64 HIS 0.009 0.001 HISB4 66 PHE 0.033 0.002 PHEE3 51 TYR 0.028 0.002 TYRD6 308 ARG 0.013 0.001 ARGD4 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2545 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 2131 time to evaluate : 5.110 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: A5 108 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8981 (tt) REVERT: A5 137 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7252 (tt) REVERT: B5 64 MET cc_start: 0.8123 (ttm) cc_final: 0.7818 (ttm) REVERT: B5 82 ASP cc_start: 0.8506 (p0) cc_final: 0.7821 (p0) REVERT: C5 57 TYR cc_start: 0.6555 (t80) cc_final: 0.6262 (t80) REVERT: D5 65 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8286 (tm-30) REVERT: D5 137 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7338 (tt) REVERT: E5 64 MET cc_start: 0.8737 (tpt) cc_final: 0.8471 (tpt) REVERT: E5 82 ASP cc_start: 0.8716 (p0) cc_final: 0.8035 (p0) REVERT: F5 65 GLU cc_start: 0.8675 (tm-30) cc_final: 0.7942 (tm-30) REVERT: F5 82 ASP cc_start: 0.8482 (p0) cc_final: 0.7751 (p0) REVERT: A3 62 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B3 30 TYR cc_start: 0.7854 (t80) cc_final: 0.7278 (t80) REVERT: B3 59 LYS cc_start: 0.8643 (mttp) cc_final: 0.8275 (mttp) REVERT: C3 49 TYR cc_start: 0.8015 (p90) cc_final: 0.7713 (p90) REVERT: C3 68 SER cc_start: 0.9004 (m) cc_final: 0.8759 (p) REVERT: E3 39 GLU cc_start: 0.8394 (tp30) cc_final: 0.7381 (tm-30) REVERT: E3 55 GLU cc_start: 0.8806 (pm20) cc_final: 0.8577 (pm20) REVERT: F3 4 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7639 (tm-30) REVERT: F3 49 TYR cc_start: 0.7816 (p90) cc_final: 0.7596 (p90) REVERT: F3 64 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: H3 27 LYS cc_start: 0.8711 (tptt) cc_final: 0.8371 (tptt) REVERT: I3 4 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7718 (tm-30) REVERT: I3 49 TYR cc_start: 0.7811 (p90) cc_final: 0.7308 (p90) REVERT: I3 88 LEU cc_start: 0.9019 (tt) cc_final: 0.8757 (tt) REVERT: J3 62 ILE cc_start: 0.8730 (mm) cc_final: 0.8461 (mp) REVERT: J3 72 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8393 (ttmt) REVERT: K3 27 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8349 (mmtt) REVERT: K3 39 GLU cc_start: 0.8616 (tp30) cc_final: 0.7664 (tm-30) REVERT: K3 59 LYS cc_start: 0.8705 (mttm) cc_final: 0.8335 (mttp) REVERT: L3 4 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7674 (tm-30) REVERT: L3 107 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8094 (pt) REVERT: M3 54 ASN cc_start: 0.7324 (t0) cc_final: 0.6920 (t0) REVERT: M3 106 GLU cc_start: 0.6996 (tp30) cc_final: 0.6370 (tp30) REVERT: N3 1 MET cc_start: 0.7059 (tpt) cc_final: 0.6816 (tpt) REVERT: N3 39 GLU cc_start: 0.8487 (tp30) cc_final: 0.7468 (tm-30) REVERT: N3 59 LYS cc_start: 0.8823 (mttp) cc_final: 0.8584 (mttp) REVERT: N3 65 ARG cc_start: 0.7385 (ttm170) cc_final: 0.5798 (ttp80) REVERT: O3 2 SER cc_start: 0.7807 (m) cc_final: 0.7239 (p) REVERT: O3 4 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7955 (tm-30) REVERT: P3 55 GLU cc_start: 0.8466 (pm20) cc_final: 0.8234 (mp0) REVERT: P3 62 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8292 (mp) REVERT: Q3 23 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7682 (ttm-80) REVERT: Q3 39 GLU cc_start: 0.8388 (tp30) cc_final: 0.7795 (tm-30) REVERT: Q3 49 TYR cc_start: 0.8380 (p90) cc_final: 0.7859 (p90) REVERT: Q3 59 LYS cc_start: 0.8703 (mttp) cc_final: 0.8332 (mttp) REVERT: Q3 65 ARG cc_start: 0.7548 (ttm170) cc_final: 0.5901 (ttp80) REVERT: R3 2 SER cc_start: 0.7879 (m) cc_final: 0.7306 (p) REVERT: B4 6 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9030 (m110) cc_final: 0.8428 (m110) REVERT: C4 6 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: C4 52 ASN cc_start: 0.8818 (m110) cc_final: 0.8329 (m110) REVERT: D4 6 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.7817 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5831 (mt0) cc_final: 0.5499 (mt0) REVERT: E4 57 ASP cc_start: 0.7691 (m-30) cc_final: 0.7416 (m-30) REVERT: E4 92 ASP cc_start: 0.8588 (p0) cc_final: 0.8131 (p0) REVERT: F4 6 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8026 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7690 (m-30) cc_final: 0.7310 (m-30) REVERT: F4 75 GLN cc_start: 0.8303 (mt0) cc_final: 0.7983 (mt0) REVERT: F4 92 ASP cc_start: 0.8526 (p0) cc_final: 0.8266 (p0) REVERT: A7 14 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8943 (t) REVERT: A7 135 GLU cc_start: 0.8585 (pp20) cc_final: 0.8322 (pp20) REVERT: B7 135 GLU cc_start: 0.8658 (pp20) cc_final: 0.8365 (pp20) REVERT: C7 14 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8870 (t) REVERT: C7 42 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C7 73 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8390 (tppt) REVERT: C7 133 VAL cc_start: 0.9004 (t) cc_final: 0.8680 (p) REVERT: D7 14 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9009 (t) REVERT: D7 25 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D7 83 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6083 (mt-10) REVERT: E7 135 GLU cc_start: 0.9031 (pp20) cc_final: 0.8401 (pp20) REVERT: A6 342 GLU cc_start: 0.8416 (pm20) cc_final: 0.7889 (pm20) REVERT: A6 384 GLU cc_start: 0.9046 (tp30) cc_final: 0.8510 (tp30) REVERT: A6 418 CYS cc_start: 0.9313 (m) cc_final: 0.8864 (m) REVERT: B6 88 TRP cc_start: 0.8189 (p-90) cc_final: 0.7472 (p-90) REVERT: B6 272 TYR cc_start: 0.8251 (m-80) cc_final: 0.7399 (m-80) REVERT: B6 309 MET cc_start: 0.8764 (ttm) cc_final: 0.8366 (ttm) REVERT: B6 342 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: B6 424 ASN cc_start: 0.8636 (t0) cc_final: 0.8391 (t0) REVERT: C6 167 ASN cc_start: 0.8902 (t0) cc_final: 0.8632 (t0) REVERT: C6 276 ASN cc_start: 0.8164 (t0) cc_final: 0.7940 (t0) REVERT: C6 388 ASN cc_start: 0.8566 (m110) cc_final: 0.8299 (m-40) REVERT: D6 320 GLN cc_start: 0.8092 (tp40) cc_final: 0.7491 (mt0) REVERT: D6 330 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7801 (mt-10) REVERT: D6 462 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: E6 326 MET cc_start: 0.7942 (mtp) cc_final: 0.7569 (mmm) REVERT: E6 376 TYR cc_start: 0.9125 (t80) cc_final: 0.8890 (t80) REVERT: E6 421 TYR cc_start: 0.8795 (m-80) cc_final: 0.8585 (m-10) REVERT: F6 9 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7652 (mtm110) REVERT: F6 24 MET cc_start: 0.8980 (tpt) cc_final: 0.8755 (tpp) REVERT: F6 330 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F6 424 ASN cc_start: 0.8557 (t0) cc_final: 0.8257 (t0) REVERT: F6 460 LEU cc_start: 0.8692 (mm) cc_final: 0.8489 (mm) outliers start: 414 outliers final: 324 residues processed: 2302 average time/residue: 0.5032 time to fit residues: 2022.1676 Evaluate side-chains 2397 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 2058 time to evaluate : 5.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 19 ASP Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 65 GLU Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 113 VAL Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 31 GLN Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 49 ASN Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 108 LEU Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 75 THR Chi-restraints excluded: chain C5 residue 108 LEU Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 4 SER Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 49 ASN Chi-restraints excluded: chain E5 residue 55 SER Chi-restraints excluded: chain E5 residue 63 ILE Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 49 ASN Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 150 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 28 ILE Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 62 ILE Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain B3 residue 100 LEU Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 44 THR Chi-restraints excluded: chain C3 residue 54 ASN Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 13 LEU Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 44 THR Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 92 LEU Chi-restraints excluded: chain D3 residue 102 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 73 LEU Chi-restraints excluded: chain E3 residue 92 LEU Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 64 TYR Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 28 ILE Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 92 LEU Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain G3 residue 125 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain H3 residue 100 LEU Chi-restraints excluded: chain I3 residue 2 SER Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 42 VAL Chi-restraints excluded: chain J3 residue 72 LYS Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 102 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 28 ILE Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 44 THR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 55 GLU Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 3 ILE Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 28 ILE Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 100 LEU Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 75 ASP Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 42 VAL Chi-restraints excluded: chain P3 residue 62 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain P3 residue 102 VAL Chi-restraints excluded: chain Q3 residue 15 THR Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 73 LEU Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 10 GLU Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 100 LEU Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 32 ILE Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 70 LYS Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 9 LEU Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 19 LYS Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 70 LYS Chi-restraints excluded: chain B4 residue 83 ASP Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 65 VAL Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 9 LEU Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 20 SER Chi-restraints excluded: chain D4 residue 24 ILE Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 9 LEU Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 20 SER Chi-restraints excluded: chain F4 residue 32 ILE Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 5 VAL Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain A7 residue 110 THR Chi-restraints excluded: chain B7 residue 3 VAL Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 16 ASN Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 42 ASN Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 14 THR Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 42 ASN Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain E7 residue 110 THR Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 36 VAL Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 253 ILE Chi-restraints excluded: chain A6 residue 267 VAL Chi-restraints excluded: chain A6 residue 269 ASP Chi-restraints excluded: chain A6 residue 315 VAL Chi-restraints excluded: chain A6 residue 330 GLU Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 109 GLU Chi-restraints excluded: chain B6 residue 129 ASP Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 253 ILE Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 269 ASP Chi-restraints excluded: chain B6 residue 294 CYS Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 334 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 465 THR Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain B6 residue 492 ILE Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 19 ILE Chi-restraints excluded: chain C6 residue 29 ILE Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 253 ILE Chi-restraints excluded: chain C6 residue 269 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 365 THR Chi-restraints excluded: chain C6 residue 372 CYS Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 475 VAL Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 60 SER Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 109 GLU Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain D6 residue 492 ILE Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 60 SER Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 208 VAL Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 269 ASP Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 330 GLU Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 410 ILE Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 475 VAL Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 73 THR Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 208 VAL Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 334 THR Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 409 THR Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 699 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 413 optimal weight: 1.9990 chunk 529 optimal weight: 4.9990 chunk 410 optimal weight: 0.8980 chunk 610 optimal weight: 0.1980 chunk 405 optimal weight: 1.9990 chunk 722 optimal weight: 0.1980 chunk 452 optimal weight: 10.0000 chunk 440 optimal weight: 0.7980 chunk 333 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 58 HIS ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R3 32 ASN R3 58 HIS ** B4 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 155 ASN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59988 Z= 0.199 Angle : 0.643 12.762 81510 Z= 0.326 Chirality : 0.045 0.198 9684 Planarity : 0.004 0.067 10548 Dihedral : 5.239 55.207 8297 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.24 % Allowed : 28.27 % Favored : 65.48 % 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: -1.71 (0.10), residues: 7656 helix: 0.79 (0.12), residues: 1926 sheet: -1.32 (0.11), residues: 2094 loop : -2.10 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRPF6 88 HIS 0.007 0.001 HISB4 66 PHE 0.035 0.002 PHEG3 57 TYR 0.033 0.002 TYRD5 57 ARG 0.007 0.001 ARGN3 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2544 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 2132 time to evaluate : 7.183 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: A5 96 SER cc_start: 0.8592 (p) cc_final: 0.8237 (p) REVERT: A5 108 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A5 137 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7191 (tt) REVERT: B5 20 GLU cc_start: 0.7952 (mp0) cc_final: 0.7507 (mp0) REVERT: B5 64 MET cc_start: 0.8119 (ttm) cc_final: 0.7863 (ttm) REVERT: B5 85 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8384 (mm-30) REVERT: C5 57 TYR cc_start: 0.6478 (t80) cc_final: 0.6219 (t80) REVERT: D5 65 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D5 137 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7281 (tt) REVERT: E5 82 ASP cc_start: 0.8654 (p0) cc_final: 0.8026 (p0) REVERT: F5 82 ASP cc_start: 0.8435 (p0) cc_final: 0.7750 (p0) REVERT: F5 100 LYS cc_start: 0.8765 (mttm) cc_final: 0.8549 (mttm) REVERT: A3 62 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B3 30 TYR cc_start: 0.7901 (t80) cc_final: 0.7255 (t80) REVERT: B3 39 GLU cc_start: 0.8487 (tp30) cc_final: 0.7629 (tm-30) REVERT: C3 49 TYR cc_start: 0.8022 (p90) cc_final: 0.7754 (p90) REVERT: C3 68 SER cc_start: 0.8993 (m) cc_final: 0.8762 (p) REVERT: E3 39 GLU cc_start: 0.8297 (tp30) cc_final: 0.7325 (tm-30) REVERT: E3 41 TYR cc_start: 0.8870 (t80) cc_final: 0.8655 (t80) REVERT: E3 55 GLU cc_start: 0.8778 (pm20) cc_final: 0.8577 (pm20) REVERT: F3 4 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F3 64 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.7338 (m-10) REVERT: I3 4 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7652 (tm-30) REVERT: I3 49 TYR cc_start: 0.7800 (p90) cc_final: 0.7325 (p90) REVERT: I3 88 LEU cc_start: 0.8992 (tt) cc_final: 0.8720 (tt) REVERT: J3 62 ILE cc_start: 0.8728 (mm) cc_final: 0.8466 (mp) REVERT: K3 27 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8332 (mmtt) REVERT: K3 39 GLU cc_start: 0.8586 (tp30) cc_final: 0.7704 (tm-30) REVERT: K3 59 LYS cc_start: 0.8692 (mttm) cc_final: 0.8334 (mttp) REVERT: L3 4 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7652 (tm-30) REVERT: L3 107 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8087 (pt) REVERT: M3 20 ILE cc_start: 0.8374 (mm) cc_final: 0.8146 (tp) REVERT: M3 54 ASN cc_start: 0.7404 (t0) cc_final: 0.6929 (t0) REVERT: M3 55 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: M3 106 GLU cc_start: 0.6920 (tp30) cc_final: 0.6281 (tp30) REVERT: N3 27 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8394 (mmtt) REVERT: N3 39 GLU cc_start: 0.8474 (tp30) cc_final: 0.7547 (tm-30) REVERT: N3 59 LYS cc_start: 0.8750 (mttp) cc_final: 0.8287 (mttp) REVERT: N3 65 ARG cc_start: 0.7382 (ttm170) cc_final: 0.5787 (ttp80) REVERT: O3 2 SER cc_start: 0.7880 (m) cc_final: 0.7293 (p) REVERT: O3 4 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7981 (tm-30) REVERT: P3 30 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7528 (t80) REVERT: P3 55 GLU cc_start: 0.8319 (pm20) cc_final: 0.8081 (mp0) REVERT: P3 62 ILE cc_start: 0.8618 (mm) cc_final: 0.8363 (mp) REVERT: Q3 23 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7724 (ttm-80) REVERT: Q3 49 TYR cc_start: 0.8352 (p90) cc_final: 0.7852 (p90) REVERT: Q3 59 LYS cc_start: 0.8582 (mttp) cc_final: 0.8245 (mttp) REVERT: Q3 65 ARG cc_start: 0.7570 (ttm170) cc_final: 0.5910 (ttp80) REVERT: R3 2 SER cc_start: 0.7843 (m) cc_final: 0.7270 (p) REVERT: R3 4 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7368 (tm-30) REVERT: R3 121 ASP cc_start: 0.8069 (t0) cc_final: 0.7774 (t0) REVERT: A4 57 ASP cc_start: 0.7878 (m-30) cc_final: 0.7617 (m-30) REVERT: B4 6 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9026 (m110) cc_final: 0.8563 (m110) REVERT: B4 57 ASP cc_start: 0.7894 (m-30) cc_final: 0.7609 (m-30) REVERT: B4 99 ASN cc_start: 0.8794 (p0) cc_final: 0.8592 (p0) REVERT: C4 6 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: C4 52 ASN cc_start: 0.8824 (m110) cc_final: 0.8511 (m110) REVERT: C4 57 ASP cc_start: 0.7920 (m-30) cc_final: 0.7598 (m-30) REVERT: C4 75 GLN cc_start: 0.8130 (mt0) cc_final: 0.7509 (mt0) REVERT: D4 6 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: D4 57 ASP cc_start: 0.7732 (m-30) cc_final: 0.7376 (m-30) REVERT: D4 71 MET cc_start: 0.8407 (mtp) cc_final: 0.8147 (mtm) REVERT: E4 6 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5763 (mt0) cc_final: 0.5449 (mt0) REVERT: E4 57 ASP cc_start: 0.7666 (m-30) cc_final: 0.7413 (m-30) REVERT: E4 83 ASP cc_start: 0.7581 (p0) cc_final: 0.7354 (p0) REVERT: F4 6 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7751 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7588 (m-30) cc_final: 0.7262 (m-30) REVERT: F4 75 GLN cc_start: 0.8269 (mt0) cc_final: 0.7944 (mt0) REVERT: A7 14 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8744 (t) REVERT: A7 135 GLU cc_start: 0.8461 (pp20) cc_final: 0.8254 (pp20) REVERT: B7 14 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8841 (t) REVERT: B7 73 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8324 (tppt) REVERT: C7 14 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8640 (t) REVERT: C7 42 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7750 (p0) REVERT: C7 73 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8343 (tppt) REVERT: D7 73 LYS cc_start: 0.8992 (tptp) cc_final: 0.8399 (tppt) REVERT: D7 83 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6056 (mt-10) REVERT: E7 14 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8716 (t) REVERT: E7 73 LYS cc_start: 0.8893 (tptp) cc_final: 0.8575 (tptp) REVERT: E7 135 GLU cc_start: 0.9005 (pp20) cc_final: 0.8506 (pp20) REVERT: A6 55 ASP cc_start: 0.7909 (t0) cc_final: 0.7630 (t0) REVERT: A6 342 GLU cc_start: 0.8484 (pm20) cc_final: 0.8059 (pm20) REVERT: A6 384 GLU cc_start: 0.9068 (tp30) cc_final: 0.8502 (tp30) REVERT: B6 88 TRP cc_start: 0.8111 (p-90) cc_final: 0.7383 (p-90) REVERT: B6 266 GLU cc_start: 0.8321 (tp30) cc_final: 0.8020 (tp30) REVERT: B6 272 TYR cc_start: 0.8265 (m-80) cc_final: 0.7452 (m-80) REVERT: B6 342 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: B6 388 ASN cc_start: 0.8921 (m110) cc_final: 0.8640 (m-40) REVERT: B6 424 ASN cc_start: 0.8531 (t0) cc_final: 0.8313 (t0) REVERT: C6 44 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7834 (mtm-85) REVERT: C6 167 ASN cc_start: 0.8895 (t0) cc_final: 0.8646 (t0) REVERT: C6 376 TYR cc_start: 0.8605 (t80) cc_final: 0.8293 (t80) REVERT: C6 378 LEU cc_start: 0.8410 (tt) cc_final: 0.8163 (tp) REVERT: C6 491 ILE cc_start: 0.3703 (tp) cc_final: 0.3185 (tp) REVERT: D6 266 GLU cc_start: 0.8413 (tp30) cc_final: 0.8173 (tp30) REVERT: D6 320 GLN cc_start: 0.8015 (tp40) cc_final: 0.7447 (mt0) REVERT: D6 330 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7727 (mt-10) REVERT: D6 342 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: D6 384 GLU cc_start: 0.8750 (tp30) cc_final: 0.8537 (tp30) REVERT: E6 290 SER cc_start: 0.9364 (p) cc_final: 0.8921 (t) REVERT: E6 320 GLN cc_start: 0.8188 (tp40) cc_final: 0.7406 (mt0) REVERT: E6 326 MET cc_start: 0.7862 (mtp) cc_final: 0.7571 (mmm) REVERT: E6 342 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: E6 384 GLU cc_start: 0.8997 (tp30) cc_final: 0.8687 (tp30) REVERT: F6 330 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7726 (mt-10) REVERT: F6 424 ASN cc_start: 0.8418 (t0) cc_final: 0.8129 (t0) outliers start: 412 outliers final: 318 residues processed: 2300 average time/residue: 0.5057 time to fit residues: 2028.0796 Evaluate side-chains 2390 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 2053 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 19 ASP Chi-restraints excluded: chain A5 residue 29 ASN Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 67 SER Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 113 VAL Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 29 ASN Chi-restraints excluded: chain B5 residue 31 GLN Chi-restraints excluded: chain B5 residue 33 SER Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 108 LEU Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 76 LEU Chi-restraints excluded: chain C5 residue 108 LEU Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 55 SER Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 108 LEU Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 142 SER Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 29 ASN Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 108 LEU Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 150 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 62 ILE Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 54 ASN Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain E3 residue 13 LEU Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 73 LEU Chi-restraints excluded: chain E3 residue 89 ILE Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 64 TYR Chi-restraints excluded: chain F3 residue 80 ASP Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 5 VAL Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 72 LYS Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain G3 residue 125 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain I3 residue 100 LEU Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 42 VAL Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 102 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 33 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 21 THR Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 61 LEU Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 75 ASP Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 45 THR Chi-restraints excluded: chain M3 residue 55 GLU Chi-restraints excluded: chain M3 residue 72 LYS Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 15 THR Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 27 LYS Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 110 GLU Chi-restraints excluded: chain N3 residue 126 THR Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 54 ASN Chi-restraints excluded: chain O3 residue 75 ASP Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain O3 residue 101 VAL Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 30 TYR Chi-restraints excluded: chain P3 residue 42 VAL Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 15 THR Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 73 LEU Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 10 GLU Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 32 ILE Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 70 LYS Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 19 LYS Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 83 ASP Chi-restraints excluded: chain C4 residue 99 ASN Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 20 SER Chi-restraints excluded: chain D4 residue 24 ILE Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 73 ILE Chi-restraints excluded: chain D4 residue 91 ASP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 32 ILE Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 9 LEU Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 20 SER Chi-restraints excluded: chain F4 residue 32 ILE Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 14 THR Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 43 SER Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain B7 residue 121 ASP Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 30 VAL Chi-restraints excluded: chain C7 residue 42 ASN Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain C7 residue 91 MET Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 42 ASN Chi-restraints excluded: chain D7 residue 43 SER Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 14 THR Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 55 ASP Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 36 VAL Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 109 GLU Chi-restraints excluded: chain A6 residue 129 ASP Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 218 LEU Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 269 ASP Chi-restraints excluded: chain A6 residue 315 VAL Chi-restraints excluded: chain A6 residue 330 GLU Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 475 VAL Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain A6 residue 492 ILE Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 109 GLU Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 330 GLU Chi-restraints excluded: chain B6 residue 334 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain B6 residue 492 ILE Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 129 ASP Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 269 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 365 THR Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 411 GLU Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 457 ILE Chi-restraints excluded: chain C6 residue 475 VAL Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 25 ASN Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 109 GLU Chi-restraints excluded: chain D6 residue 111 VAL Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 353 LEU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain D6 residue 492 ILE Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 6 GLU Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 60 SER Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 109 GLU Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 330 GLU Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 73 THR Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 109 GLU Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 334 THR Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 409 THR Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 447 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 431 optimal weight: 0.0070 chunk 217 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 459 optimal weight: 0.8980 chunk 492 optimal weight: 7.9990 chunk 357 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 568 optimal weight: 8.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 29 ASN ** E5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R3 124 GLN B4 66 HIS ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN F6 377 ASN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 59988 Z= 0.235 Angle : 0.657 10.878 81510 Z= 0.335 Chirality : 0.046 0.192 9684 Planarity : 0.004 0.066 10548 Dihedral : 5.216 57.897 8297 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 6.14 % Allowed : 28.74 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 7656 helix: 0.77 (0.12), residues: 1944 sheet: -1.28 (0.11), residues: 2100 loop : -2.14 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRPD4 64 HIS 0.006 0.001 HISG3 58 PHE 0.036 0.002 PHEG3 57 TYR 0.028 0.002 TYRD5 57 ARG 0.008 0.001 ARGF6 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2516 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 2111 time to evaluate : 5.505 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: A5 108 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9005 (tt) REVERT: A5 137 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7232 (tt) REVERT: B5 64 MET cc_start: 0.8142 (ttm) cc_final: 0.7849 (ttm) REVERT: B5 82 ASP cc_start: 0.8440 (p0) cc_final: 0.7837 (p0) REVERT: B5 85 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8451 (mm-30) REVERT: D5 65 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D5 137 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7298 (tt) REVERT: E5 82 ASP cc_start: 0.8689 (p0) cc_final: 0.8061 (p0) REVERT: F5 82 ASP cc_start: 0.8466 (p0) cc_final: 0.7737 (p0) REVERT: F5 100 LYS cc_start: 0.8773 (mttm) cc_final: 0.8558 (mttm) REVERT: A3 62 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B3 27 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8442 (mmtt) REVERT: B3 30 TYR cc_start: 0.7903 (t80) cc_final: 0.7220 (t80) REVERT: C3 49 TYR cc_start: 0.8042 (p90) cc_final: 0.7779 (p90) REVERT: C3 68 SER cc_start: 0.8971 (m) cc_final: 0.8767 (p) REVERT: D3 106 GLU cc_start: 0.6305 (tp30) cc_final: 0.6003 (tp30) REVERT: E3 27 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8497 (mmtt) REVERT: E3 39 GLU cc_start: 0.8386 (tp30) cc_final: 0.7387 (tm-30) REVERT: E3 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8643 (t80) REVERT: F3 4 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G3 55 GLU cc_start: 0.8394 (pm20) cc_final: 0.7965 (mp0) REVERT: G3 62 ILE cc_start: 0.8189 (mp) cc_final: 0.7828 (mm) REVERT: G3 113 GLU cc_start: 0.8410 (tt0) cc_final: 0.7877 (tp30) REVERT: H3 27 LYS cc_start: 0.8672 (tptt) cc_final: 0.8286 (mptt) REVERT: I3 4 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7662 (tm-30) REVERT: I3 49 TYR cc_start: 0.7803 (p90) cc_final: 0.7342 (p90) REVERT: J3 62 ILE cc_start: 0.8750 (mm) cc_final: 0.8505 (mp) REVERT: K3 27 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8397 (mmtt) REVERT: K3 39 GLU cc_start: 0.8635 (tp30) cc_final: 0.7786 (tm-30) REVERT: L3 4 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7678 (tm-30) REVERT: L3 107 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8058 (pt) REVERT: M3 20 ILE cc_start: 0.8434 (mm) cc_final: 0.8200 (tp) REVERT: M3 54 ASN cc_start: 0.7407 (t0) cc_final: 0.6925 (t0) REVERT: M3 55 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: M3 106 GLU cc_start: 0.6966 (tp30) cc_final: 0.6291 (tp30) REVERT: N3 27 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (mmtt) REVERT: N3 65 ARG cc_start: 0.7438 (ttm170) cc_final: 0.5841 (ttp80) REVERT: O3 2 SER cc_start: 0.8002 (m) cc_final: 0.7401 (p) REVERT: O3 4 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7939 (tm-30) REVERT: O3 68 SER cc_start: 0.8957 (m) cc_final: 0.8606 (p) REVERT: P3 30 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7552 (t80) REVERT: P3 62 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8366 (mp) REVERT: Q3 49 TYR cc_start: 0.8426 (p90) cc_final: 0.7922 (p90) REVERT: Q3 59 LYS cc_start: 0.8547 (mttp) cc_final: 0.8212 (mttp) REVERT: Q3 65 ARG cc_start: 0.7593 (ttm170) cc_final: 0.5940 (ttp80) REVERT: R3 2 SER cc_start: 0.7948 (m) cc_final: 0.7386 (p) REVERT: R3 4 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7383 (tm-30) REVERT: A4 44 GLN cc_start: 0.6214 (mt0) cc_final: 0.5879 (mt0) REVERT: A4 57 ASP cc_start: 0.7873 (m-30) cc_final: 0.7507 (m-30) REVERT: B4 6 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9029 (m110) cc_final: 0.8399 (m110) REVERT: C4 6 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: C4 52 ASN cc_start: 0.8835 (m110) cc_final: 0.8600 (m110) REVERT: C4 57 ASP cc_start: 0.7928 (m-30) cc_final: 0.7638 (m-30) REVERT: D4 6 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: D4 57 ASP cc_start: 0.7757 (m-30) cc_final: 0.7389 (m-30) REVERT: D4 75 GLN cc_start: 0.8379 (mt0) cc_final: 0.8056 (mt0) REVERT: E4 6 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7918 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5923 (mt0) cc_final: 0.5578 (mt0) REVERT: E4 57 ASP cc_start: 0.7706 (m-30) cc_final: 0.7416 (m-30) REVERT: E4 83 ASP cc_start: 0.7652 (p0) cc_final: 0.7432 (p0) REVERT: F4 6 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7797 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7599 (m-30) cc_final: 0.7268 (m-30) REVERT: F4 75 GLN cc_start: 0.8294 (mt0) cc_final: 0.7997 (mt0) REVERT: A7 14 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8767 (t) REVERT: B7 14 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (t) REVERT: B7 73 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8352 (tppt) REVERT: C7 14 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8681 (t) REVERT: C7 42 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7704 (p0) REVERT: C7 73 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8349 (tppt) REVERT: D7 14 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8944 (t) REVERT: D7 24 TYR cc_start: 0.9188 (t80) cc_final: 0.8923 (t80) REVERT: D7 83 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6047 (mt-10) REVERT: D7 97 GLU cc_start: 0.8248 (tp30) cc_final: 0.7680 (tp30) REVERT: E7 14 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8722 (t) REVERT: E7 135 GLU cc_start: 0.8982 (pp20) cc_final: 0.8764 (pp20) REVERT: A6 44 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7501 (ttm-80) REVERT: A6 55 ASP cc_start: 0.7995 (t0) cc_final: 0.7630 (t0) REVERT: A6 266 GLU cc_start: 0.8337 (tp30) cc_final: 0.8058 (tp30) REVERT: A6 326 MET cc_start: 0.7825 (mtp) cc_final: 0.6844 (mmm) REVERT: A6 342 GLU cc_start: 0.8455 (pm20) cc_final: 0.8009 (pm20) REVERT: A6 384 GLU cc_start: 0.9085 (tp30) cc_final: 0.8842 (tp30) REVERT: B6 88 TRP cc_start: 0.8118 (p-90) cc_final: 0.7612 (p-90) REVERT: B6 266 GLU cc_start: 0.8251 (tp30) cc_final: 0.7722 (tp30) REVERT: B6 272 TYR cc_start: 0.8254 (m-80) cc_final: 0.7430 (m-80) REVERT: B6 326 MET cc_start: 0.8183 (mmm) cc_final: 0.7247 (mmm) REVERT: B6 342 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B6 384 GLU cc_start: 0.9034 (tp30) cc_final: 0.8498 (tp30) REVERT: B6 424 ASN cc_start: 0.8572 (t0) cc_final: 0.8344 (t0) REVERT: C6 44 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7720 (mtm-85) REVERT: C6 88 TRP cc_start: 0.8567 (p-90) cc_final: 0.8129 (p-90) REVERT: C6 167 ASN cc_start: 0.8940 (t0) cc_final: 0.8701 (t0) REVERT: C6 376 TYR cc_start: 0.8625 (t80) cc_final: 0.8315 (t80) REVERT: D6 55 ASP cc_start: 0.7593 (t0) cc_final: 0.7364 (t0) REVERT: D6 88 TRP cc_start: 0.8207 (p-90) cc_final: 0.7911 (p-90) REVERT: D6 266 GLU cc_start: 0.8400 (tp30) cc_final: 0.8182 (tp30) REVERT: D6 320 GLN cc_start: 0.8007 (tp40) cc_final: 0.7416 (mt0) REVERT: D6 330 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D6 342 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: D6 423 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7936 (mtm110) REVERT: E6 320 GLN cc_start: 0.8212 (tp40) cc_final: 0.7452 (mt0) REVERT: E6 326 MET cc_start: 0.7970 (mtp) cc_final: 0.7717 (mmm) REVERT: E6 342 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: E6 384 GLU cc_start: 0.9021 (tp30) cc_final: 0.8756 (tp30) REVERT: F6 44 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7741 (ttm-80) REVERT: F6 55 ASP cc_start: 0.8266 (t0) cc_final: 0.7998 (t0) REVERT: F6 293 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8208 (mmm-85) REVERT: F6 312 MET cc_start: 0.9400 (tpp) cc_final: 0.9141 (tpt) REVERT: F6 330 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F6 408 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8349 (t0) REVERT: F6 424 ASN cc_start: 0.8405 (t0) cc_final: 0.8136 (t0) outliers start: 405 outliers final: 336 residues processed: 2275 average time/residue: 0.5048 time to fit residues: 1997.9981 Evaluate side-chains 2421 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 2063 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 19 ASP Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 49 ASN Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 67 SER Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 113 VAL Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 49 ASN Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 108 LEU Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 76 LEU Chi-restraints excluded: chain C5 residue 108 LEU Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 55 SER Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 108 LEU Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 63 ILE Chi-restraints excluded: chain E5 residue 108 LEU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 142 SER Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 64 MET Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 150 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 62 ILE Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 27 LYS Chi-restraints excluded: chain B3 residue 28 ILE Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 54 ASN Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 102 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 28 ILE Chi-restraints excluded: chain E3 residue 73 LEU Chi-restraints excluded: chain E3 residue 88 LEU Chi-restraints excluded: chain E3 residue 89 ILE Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 15 THR Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 80 ASP Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 5 VAL Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 42 VAL Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 72 LYS Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain G3 residue 125 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 42 VAL Chi-restraints excluded: chain J3 residue 72 LYS Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 102 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 28 ILE Chi-restraints excluded: chain K3 residue 33 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 44 THR Chi-restraints excluded: chain L3 residue 54 ASN Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 75 ASP Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 55 GLU Chi-restraints excluded: chain M3 residue 58 HIS Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 15 THR Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 27 LYS Chi-restraints excluded: chain N3 residue 28 ILE Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 110 GLU Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 54 ASN Chi-restraints excluded: chain O3 residue 75 ASP Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 30 TYR Chi-restraints excluded: chain P3 residue 42 VAL Chi-restraints excluded: chain P3 residue 62 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 73 LEU Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 10 GLU Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 32 ILE Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 113 SER Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 99 ASN Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 9 LEU Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 24 ILE Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 73 ILE Chi-restraints excluded: chain D4 residue 91 ASP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 9 LEU Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 20 SER Chi-restraints excluded: chain F4 residue 32 ILE Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 5 VAL Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 14 THR Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain B7 residue 121 ASP Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 30 VAL Chi-restraints excluded: chain C7 residue 42 ASN Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 44 ILE Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain C7 residue 91 MET Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 14 THR Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 42 ASN Chi-restraints excluded: chain D7 residue 43 SER Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 14 THR Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 55 ASP Chi-restraints excluded: chain E7 residue 69 SER Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 81 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 6 GLU Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 109 GLU Chi-restraints excluded: chain A6 residue 111 VAL Chi-restraints excluded: chain A6 residue 129 ASP Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 218 LEU Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 253 ILE Chi-restraints excluded: chain A6 residue 269 ASP Chi-restraints excluded: chain A6 residue 315 VAL Chi-restraints excluded: chain A6 residue 330 GLU Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 475 VAL Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 7 VAL Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 109 GLU Chi-restraints excluded: chain B6 residue 129 ASP Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 269 ASP Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 330 GLU Chi-restraints excluded: chain B6 residue 334 THR Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 465 THR Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain B6 residue 492 ILE Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 129 ASP Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 334 THR Chi-restraints excluded: chain C6 residue 365 THR Chi-restraints excluded: chain C6 residue 372 CYS Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 411 GLU Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 109 GLU Chi-restraints excluded: chain D6 residue 111 VAL Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 353 LEU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain D6 residue 492 ILE Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 6 GLU Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 60 SER Chi-restraints excluded: chain E6 residue 73 THR Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 109 GLU Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 269 ASP Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 475 VAL Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain F6 residue 4 ILE Chi-restraints excluded: chain F6 residue 6 GLU Chi-restraints excluded: chain F6 residue 7 VAL Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 73 THR Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 109 GLU Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 263 LEU Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 334 THR Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 408 ASP Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 434 ARG Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 5.9990 chunk 692 optimal weight: 3.9990 chunk 631 optimal weight: 0.0170 chunk 673 optimal weight: 9.9990 chunk 405 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 528 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 chunk 608 optimal weight: 0.5980 chunk 637 optimal weight: 0.7980 chunk 671 optimal weight: 9.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN B5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 86 ASN E5 29 ASN ** E5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 58 HIS ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 59988 Z= 0.204 Angle : 0.659 12.545 81510 Z= 0.332 Chirality : 0.046 0.201 9684 Planarity : 0.004 0.067 10548 Dihedral : 5.146 59.121 8297 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.82 % Allowed : 29.62 % Favored : 64.56 % 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: -1.66 (0.10), residues: 7656 helix: 0.82 (0.12), residues: 1938 sheet: -1.17 (0.11), residues: 2076 loop : -2.16 (0.10), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPF6 88 HIS 0.007 0.001 HISG3 58 PHE 0.035 0.002 PHEG3 57 TYR 0.026 0.002 TYRC6 308 ARG 0.007 0.001 ARGG3 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2500 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 2116 time to evaluate : 5.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A5 108 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8964 (tt) REVERT: A5 137 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7170 (tt) REVERT: B5 39 TYR cc_start: 0.8737 (m-80) cc_final: 0.8112 (m-80) REVERT: B5 85 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8409 (mm-30) REVERT: C5 64 MET cc_start: 0.8398 (tpt) cc_final: 0.7942 (tpt) REVERT: D5 64 MET cc_start: 0.8510 (tpt) cc_final: 0.8155 (tpt) REVERT: D5 65 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8292 (tm-30) REVERT: D5 137 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7246 (tt) REVERT: E5 82 ASP cc_start: 0.8651 (p0) cc_final: 0.8062 (p0) REVERT: F5 82 ASP cc_start: 0.8424 (p0) cc_final: 0.7788 (p0) REVERT: A3 62 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B3 30 TYR cc_start: 0.7930 (t80) cc_final: 0.7311 (t80) REVERT: B3 39 GLU cc_start: 0.8484 (tp30) cc_final: 0.7562 (tm-30) REVERT: C3 4 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C3 49 TYR cc_start: 0.7960 (p90) cc_final: 0.7704 (p90) REVERT: C3 68 SER cc_start: 0.8973 (m) cc_final: 0.8764 (p) REVERT: E3 27 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8524 (mmtt) REVERT: E3 39 GLU cc_start: 0.8399 (tp30) cc_final: 0.7354 (tm-30) REVERT: E3 41 TYR cc_start: 0.8877 (t80) cc_final: 0.8662 (t80) REVERT: F3 4 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7720 (tm-30) REVERT: G3 55 GLU cc_start: 0.8349 (pm20) cc_final: 0.7990 (mp0) REVERT: G3 62 ILE cc_start: 0.8171 (mp) cc_final: 0.7836 (mm) REVERT: G3 113 GLU cc_start: 0.8417 (tt0) cc_final: 0.7881 (tp30) REVERT: H3 27 LYS cc_start: 0.8660 (tptt) cc_final: 0.8319 (mptt) REVERT: I3 4 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7680 (tm-30) REVERT: I3 49 TYR cc_start: 0.7783 (p90) cc_final: 0.7358 (p90) REVERT: I3 88 LEU cc_start: 0.8988 (tt) cc_final: 0.8728 (tt) REVERT: J3 62 ILE cc_start: 0.8743 (mm) cc_final: 0.8497 (mp) REVERT: K3 27 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8372 (mmtt) REVERT: K3 34 TYR cc_start: 0.8143 (m-80) cc_final: 0.7423 (m-80) REVERT: K3 39 GLU cc_start: 0.8595 (tp30) cc_final: 0.7718 (tm-30) REVERT: L3 4 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7693 (tm-30) REVERT: L3 107 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8085 (pt) REVERT: M3 20 ILE cc_start: 0.8363 (mm) cc_final: 0.8153 (tp) REVERT: M3 54 ASN cc_start: 0.7500 (t0) cc_final: 0.7011 (t0) REVERT: M3 55 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: M3 106 GLU cc_start: 0.6975 (tp30) cc_final: 0.6289 (tp30) REVERT: N3 27 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8518 (mmtt) REVERT: N3 39 GLU cc_start: 0.8534 (tp30) cc_final: 0.7675 (tm-30) REVERT: N3 65 ARG cc_start: 0.7433 (ttm170) cc_final: 0.5853 (ttp80) REVERT: O3 2 SER cc_start: 0.7959 (m) cc_final: 0.7380 (p) REVERT: O3 4 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7964 (tm-30) REVERT: O3 68 SER cc_start: 0.8948 (m) cc_final: 0.8619 (p) REVERT: P3 30 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7636 (t80) REVERT: P3 62 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8375 (mp) REVERT: Q3 39 GLU cc_start: 0.8326 (tp30) cc_final: 0.8082 (tp30) REVERT: Q3 49 TYR cc_start: 0.8336 (p90) cc_final: 0.8021 (p90) REVERT: Q3 59 LYS cc_start: 0.8589 (mttp) cc_final: 0.8272 (mttp) REVERT: Q3 65 ARG cc_start: 0.7589 (ttm170) cc_final: 0.5985 (ttp80) REVERT: R3 2 SER cc_start: 0.7929 (m) cc_final: 0.7372 (p) REVERT: R3 4 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A4 44 GLN cc_start: 0.6125 (mt0) cc_final: 0.5805 (mt0) REVERT: A4 57 ASP cc_start: 0.7780 (m-30) cc_final: 0.7555 (m-30) REVERT: A4 75 GLN cc_start: 0.8039 (mt0) cc_final: 0.7761 (mt0) REVERT: B4 6 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: B4 52 ASN cc_start: 0.9031 (m110) cc_final: 0.8609 (m110) REVERT: B4 57 ASP cc_start: 0.7825 (m-30) cc_final: 0.7559 (m-30) REVERT: C4 6 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8054 (mmm-85) REVERT: C4 52 ASN cc_start: 0.8882 (m110) cc_final: 0.8614 (m110) REVERT: C4 57 ASP cc_start: 0.7870 (m-30) cc_final: 0.7526 (m-30) REVERT: D4 6 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.7866 (mmm-85) REVERT: D4 57 ASP cc_start: 0.7693 (m-30) cc_final: 0.7341 (m-30) REVERT: D4 75 GLN cc_start: 0.8359 (mt0) cc_final: 0.8073 (mt0) REVERT: E4 6 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5849 (mt0) cc_final: 0.5503 (mt0) REVERT: E4 57 ASP cc_start: 0.7639 (m-30) cc_final: 0.7309 (m-30) REVERT: E4 75 GLN cc_start: 0.8153 (mt0) cc_final: 0.7795 (mt0) REVERT: E4 83 ASP cc_start: 0.7557 (p0) cc_final: 0.7343 (p0) REVERT: F4 6 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7814 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7583 (m-30) cc_final: 0.7272 (m-30) REVERT: A7 14 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8783 (t) REVERT: A7 135 GLU cc_start: 0.8501 (pp20) cc_final: 0.8043 (pp20) REVERT: B7 14 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8880 (t) REVERT: B7 73 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8315 (tppt) REVERT: C7 14 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8654 (t) REVERT: C7 73 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8309 (tppt) REVERT: D7 14 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8844 (t) REVERT: D7 73 LYS cc_start: 0.8941 (tptp) cc_final: 0.8338 (tppt) REVERT: D7 83 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6054 (mt-10) REVERT: D7 97 GLU cc_start: 0.8172 (tp30) cc_final: 0.7675 (tp30) REVERT: E7 73 LYS cc_start: 0.8837 (tptp) cc_final: 0.8516 (tptp) REVERT: E7 135 GLU cc_start: 0.8928 (pp20) cc_final: 0.8714 (pp20) REVERT: A6 44 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7595 (ttm-80) REVERT: A6 55 ASP cc_start: 0.7990 (t0) cc_final: 0.7595 (t0) REVERT: A6 320 GLN cc_start: 0.7905 (tp40) cc_final: 0.7371 (mt0) REVERT: A6 326 MET cc_start: 0.7823 (mtp) cc_final: 0.6854 (mmm) REVERT: A6 342 GLU cc_start: 0.8457 (pm20) cc_final: 0.8001 (pm20) REVERT: B6 88 TRP cc_start: 0.8089 (p-90) cc_final: 0.7597 (p-90) REVERT: B6 93 GLU cc_start: 0.7866 (tp30) cc_final: 0.7649 (tp30) REVERT: B6 266 GLU cc_start: 0.8177 (tp30) cc_final: 0.7896 (tp30) REVERT: B6 272 TYR cc_start: 0.8265 (m-80) cc_final: 0.7450 (m-80) REVERT: B6 309 MET cc_start: 0.8608 (ttm) cc_final: 0.8285 (tmm) REVERT: B6 342 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B6 388 ASN cc_start: 0.8922 (m110) cc_final: 0.8637 (m-40) REVERT: B6 424 ASN cc_start: 0.8468 (t0) cc_final: 0.8263 (t0) REVERT: C6 55 ASP cc_start: 0.8332 (t0) cc_final: 0.7640 (t0) REVERT: C6 88 TRP cc_start: 0.8418 (p-90) cc_final: 0.8206 (p-90) REVERT: C6 167 ASN cc_start: 0.8969 (t0) cc_final: 0.8758 (t0) REVERT: C6 312 MET cc_start: 0.8849 (tpt) cc_final: 0.8535 (tpt) REVERT: C6 378 LEU cc_start: 0.8270 (tt) cc_final: 0.8009 (tp) REVERT: D6 55 ASP cc_start: 0.7705 (t0) cc_final: 0.7231 (t0) REVERT: D6 88 TRP cc_start: 0.8177 (p-90) cc_final: 0.7911 (p-90) REVERT: D6 266 GLU cc_start: 0.8311 (tp30) cc_final: 0.8108 (tp30) REVERT: D6 320 GLN cc_start: 0.7944 (tp40) cc_final: 0.7389 (mt0) REVERT: D6 330 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7606 (mt-10) REVERT: D6 342 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: D6 423 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7926 (mtm110) REVERT: E6 290 SER cc_start: 0.9366 (p) cc_final: 0.8866 (t) REVERT: E6 320 GLN cc_start: 0.8106 (tp40) cc_final: 0.7489 (mt0) REVERT: E6 326 MET cc_start: 0.7974 (mtp) cc_final: 0.7718 (mmm) REVERT: E6 342 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: E6 384 GLU cc_start: 0.9011 (tp30) cc_final: 0.8754 (tp30) REVERT: F6 312 MET cc_start: 0.9431 (tpp) cc_final: 0.9108 (tpt) REVERT: F6 330 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7706 (mt-10) REVERT: F6 408 ASP cc_start: 0.8713 (t0) cc_final: 0.8475 (t0) REVERT: F6 424 ASN cc_start: 0.8357 (t0) cc_final: 0.8072 (t0) outliers start: 384 outliers final: 324 residues processed: 2275 average time/residue: 0.5238 time to fit residues: 2085.5257 Evaluate side-chains 2400 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 2058 time to evaluate : 5.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 19 ASP Chi-restraints excluded: chain A5 residue 29 ASN Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 65 GLU Chi-restraints excluded: chain A5 residue 67 SER Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 113 VAL Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 122 LEU Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 108 LEU Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 63 ILE Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 75 THR Chi-restraints excluded: chain C5 residue 76 LEU Chi-restraints excluded: chain C5 residue 108 LEU Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 18 TYR Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 29 ASN Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 108 LEU Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 63 ILE Chi-restraints excluded: chain E5 residue 108 LEU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 142 SER Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 29 ASN Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 64 MET Chi-restraints excluded: chain F5 residue 108 LEU Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 150 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 62 ILE Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 10 GLU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 54 ASN Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 102 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 73 LEU Chi-restraints excluded: chain E3 residue 89 ILE Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 15 THR Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 61 LEU Chi-restraints excluded: chain F3 residue 80 ASP Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 5 VAL Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 42 VAL Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 72 LYS Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 42 VAL Chi-restraints excluded: chain J3 residue 72 LYS Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 102 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 89 ILE Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 10 GLU Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 54 ASN Chi-restraints excluded: chain L3 residue 61 LEU Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 100 LEU Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 45 THR Chi-restraints excluded: chain M3 residue 55 GLU Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 15 THR Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 27 LYS Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 71 THR Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 54 ASN Chi-restraints excluded: chain O3 residue 75 ASP Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 30 TYR Chi-restraints excluded: chain P3 residue 42 VAL Chi-restraints excluded: chain P3 residue 62 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 10 GLU Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 32 ILE Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 70 LYS Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 19 LYS Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 32 ILE Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain B4 residue 83 ASP Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 99 ASN Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 24 ILE Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 73 ILE Chi-restraints excluded: chain D4 residue 91 ASP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 32 ILE Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 20 SER Chi-restraints excluded: chain F4 residue 32 ILE Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 42 ASN Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 14 THR Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 43 SER Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 30 VAL Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain C7 residue 91 MET Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 14 THR Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 42 ASN Chi-restraints excluded: chain D7 residue 43 SER Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain D7 residue 135 GLU Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 55 ASP Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 42 ASN Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 109 GLU Chi-restraints excluded: chain A6 residue 129 ASP Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 315 VAL Chi-restraints excluded: chain A6 residue 330 GLU Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 411 GLU Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain A6 residue 492 ILE Chi-restraints excluded: chain B6 residue 6 GLU Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 129 ASP Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 269 ASP Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 330 GLU Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 411 GLU Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain B6 residue 492 ILE Chi-restraints excluded: chain C6 residue 6 GLU Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 129 ASP Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 334 THR Chi-restraints excluded: chain C6 residue 365 THR Chi-restraints excluded: chain C6 residue 372 CYS Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 411 GLU Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 457 ILE Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 210 THR Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 353 LEU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain D6 residue 492 ILE Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 60 SER Chi-restraints excluded: chain E6 residue 73 THR Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 109 GLU Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 269 ASP Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 330 GLU Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 411 GLU Chi-restraints excluded: chain E6 residue 434 ARG Chi-restraints excluded: chain E6 residue 475 VAL Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain F6 residue 4 ILE Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 73 THR Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 109 GLU Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 198 VAL Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 263 LEU Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 353 LEU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 385 ILE Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Chi-restraints excluded: chain F6 residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 5.9990 chunk 712 optimal weight: 2.9990 chunk 434 optimal weight: 3.9990 chunk 337 optimal weight: 0.7980 chunk 495 optimal weight: 4.9990 chunk 747 optimal weight: 3.9990 chunk 687 optimal weight: 8.9990 chunk 594 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 459 optimal weight: 0.9990 chunk 364 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN E5 29 ASN ** E5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN A3 32 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 54 ASN ** F3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3 124 GLN ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M3 58 HIS ** A7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 134 GLN ** D6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 59988 Z= 0.273 Angle : 0.693 12.573 81510 Z= 0.351 Chirality : 0.046 0.238 9684 Planarity : 0.004 0.066 10548 Dihedral : 5.209 56.247 8297 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.53 % Allowed : 30.21 % Favored : 64.26 % 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: -1.70 (0.10), residues: 7656 helix: 0.82 (0.12), residues: 1932 sheet: -1.23 (0.11), residues: 2112 loop : -2.17 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRPE6 432 HIS 0.007 0.001 HISG3 58 PHE 0.037 0.002 PHEG3 57 TYR 0.031 0.002 TYRC6 308 ARG 0.017 0.001 ARGQ3 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15312 Ramachandran restraints generated. 7656 Oldfield, 0 Emsley, 7656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2468 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 2103 time to evaluate : 5.119 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: A5 82 ASP cc_start: 0.8526 (p0) cc_final: 0.7931 (p0) REVERT: A5 108 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9047 (tt) REVERT: A5 137 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B5 65 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: B5 82 ASP cc_start: 0.8511 (p0) cc_final: 0.7897 (p0) REVERT: B5 85 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8484 (mm-30) REVERT: C5 64 MET cc_start: 0.8493 (tpt) cc_final: 0.7948 (tpt) REVERT: D5 64 MET cc_start: 0.8463 (tpt) cc_final: 0.8081 (tpt) REVERT: D5 65 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8311 (tm-30) REVERT: D5 82 ASP cc_start: 0.8697 (p0) cc_final: 0.8376 (p0) REVERT: D5 137 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7309 (tt) REVERT: E5 82 ASP cc_start: 0.8745 (p0) cc_final: 0.8113 (p0) REVERT: F5 82 ASP cc_start: 0.8521 (p0) cc_final: 0.7851 (p0) REVERT: F5 100 LYS cc_start: 0.8671 (mttp) cc_final: 0.8355 (mttm) REVERT: A3 62 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B3 27 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8214 (mmtt) REVERT: B3 30 TYR cc_start: 0.8033 (t80) cc_final: 0.7314 (t80) REVERT: B3 39 GLU cc_start: 0.8535 (tp30) cc_final: 0.7631 (tm-30) REVERT: B3 65 ARG cc_start: 0.7594 (ttm170) cc_final: 0.5822 (ttp80) REVERT: C3 4 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C3 49 TYR cc_start: 0.8058 (p90) cc_final: 0.7846 (p90) REVERT: C3 68 SER cc_start: 0.8985 (m) cc_final: 0.8763 (p) REVERT: E3 27 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8514 (mmtt) REVERT: E3 39 GLU cc_start: 0.8456 (tp30) cc_final: 0.7381 (tm-30) REVERT: E3 41 TYR cc_start: 0.8943 (t80) cc_final: 0.8593 (t80) REVERT: E3 109 ASP cc_start: 0.8622 (m-30) cc_final: 0.8306 (t0) REVERT: F3 4 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7715 (tm-30) REVERT: G3 55 GLU cc_start: 0.8313 (pm20) cc_final: 0.7977 (mp0) REVERT: G3 62 ILE cc_start: 0.8199 (mp) cc_final: 0.7846 (mm) REVERT: G3 113 GLU cc_start: 0.8426 (tt0) cc_final: 0.7826 (tt0) REVERT: H3 27 LYS cc_start: 0.8694 (tptt) cc_final: 0.8341 (tptt) REVERT: H3 35 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8530 (ttp80) REVERT: I3 4 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7707 (tm-30) REVERT: I3 49 TYR cc_start: 0.7899 (p90) cc_final: 0.7509 (p90) REVERT: I3 88 LEU cc_start: 0.8973 (tt) cc_final: 0.8742 (tt) REVERT: J3 62 ILE cc_start: 0.8774 (mm) cc_final: 0.8524 (mp) REVERT: K3 27 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8398 (mmtt) REVERT: K3 39 GLU cc_start: 0.8664 (tp30) cc_final: 0.8454 (tp30) REVERT: L3 4 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7676 (tm-30) REVERT: L3 107 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8139 (pt) REVERT: M3 13 LEU cc_start: 0.9149 (mm) cc_final: 0.8909 (mm) REVERT: M3 54 ASN cc_start: 0.7439 (t0) cc_final: 0.6923 (t0) REVERT: M3 55 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: M3 106 GLU cc_start: 0.7063 (tp30) cc_final: 0.6315 (tp30) REVERT: N3 39 GLU cc_start: 0.8583 (tp30) cc_final: 0.7791 (tm-30) REVERT: N3 65 ARG cc_start: 0.7516 (ttm170) cc_final: 0.5882 (ttp80) REVERT: O3 2 SER cc_start: 0.8076 (m) cc_final: 0.7516 (p) REVERT: O3 4 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7913 (tm-30) REVERT: O3 68 SER cc_start: 0.8976 (m) cc_final: 0.8658 (p) REVERT: P3 30 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7639 (t80) REVERT: P3 62 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (mp) REVERT: Q3 39 GLU cc_start: 0.8304 (tp30) cc_final: 0.7955 (tm-30) REVERT: Q3 49 TYR cc_start: 0.8474 (p90) cc_final: 0.8050 (p90) REVERT: Q3 59 LYS cc_start: 0.8575 (mttp) cc_final: 0.8273 (mttp) REVERT: Q3 65 ARG cc_start: 0.7626 (ttm170) cc_final: 0.6025 (ttp80) REVERT: R3 2 SER cc_start: 0.8014 (m) cc_final: 0.7499 (p) REVERT: R3 4 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7432 (tm-30) REVERT: R3 81 GLN cc_start: 0.8136 (pt0) cc_final: 0.7777 (pt0) REVERT: A4 44 GLN cc_start: 0.6252 (mt0) cc_final: 0.5944 (mt0) REVERT: A4 57 ASP cc_start: 0.7854 (m-30) cc_final: 0.7576 (m-30) REVERT: A4 75 GLN cc_start: 0.8168 (mt0) cc_final: 0.7546 (mt0) REVERT: B4 6 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: B4 52 ASN cc_start: 0.8997 (m110) cc_final: 0.8429 (m110) REVERT: C4 6 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8095 (mmm-85) REVERT: C4 57 ASP cc_start: 0.7955 (m-30) cc_final: 0.7654 (m-30) REVERT: D4 6 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.7877 (mmm-85) REVERT: D4 57 ASP cc_start: 0.7846 (m-30) cc_final: 0.7425 (m-30) REVERT: D4 66 HIS cc_start: 0.8601 (m-70) cc_final: 0.8281 (m-70) REVERT: D4 92 ASP cc_start: 0.8558 (p0) cc_final: 0.8132 (p0) REVERT: E4 6 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: E4 44 GLN cc_start: 0.5638 (mt0) cc_final: 0.5245 (mt0) REVERT: E4 57 ASP cc_start: 0.7705 (m-30) cc_final: 0.7428 (m-30) REVERT: E4 83 ASP cc_start: 0.7764 (p0) cc_final: 0.7549 (p0) REVERT: E4 92 ASP cc_start: 0.8628 (p0) cc_final: 0.8084 (p0) REVERT: F4 6 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7826 (mmm-85) REVERT: F4 57 ASP cc_start: 0.7663 (m-30) cc_final: 0.7339 (m-30) REVERT: F4 75 GLN cc_start: 0.8314 (mt0) cc_final: 0.8003 (mt0) REVERT: A7 14 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8798 (t) REVERT: A7 135 GLU cc_start: 0.8492 (pp20) cc_final: 0.8015 (pp20) REVERT: B7 14 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (t) REVERT: B7 73 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8346 (tppt) REVERT: C7 14 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8687 (t) REVERT: C7 73 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8370 (tppt) REVERT: D7 14 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8937 (t) REVERT: D7 83 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6118 (mt-10) REVERT: E7 14 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8713 (t) REVERT: E7 135 GLU cc_start: 0.8914 (pp20) cc_final: 0.8644 (pp20) REVERT: A6 44 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7683 (ttm-80) REVERT: A6 55 ASP cc_start: 0.8042 (t0) cc_final: 0.7673 (t0) REVERT: A6 308 TYR cc_start: 0.8372 (t80) cc_final: 0.8136 (t80) REVERT: A6 320 GLN cc_start: 0.7963 (tp40) cc_final: 0.7513 (mt0) REVERT: A6 342 GLU cc_start: 0.8420 (pm20) cc_final: 0.8040 (pm20) REVERT: B6 88 TRP cc_start: 0.8149 (p-90) cc_final: 0.7685 (p-90) REVERT: B6 93 GLU cc_start: 0.7946 (tp30) cc_final: 0.7745 (tp30) REVERT: B6 266 GLU cc_start: 0.8145 (tp30) cc_final: 0.7856 (tp30) REVERT: B6 272 TYR cc_start: 0.8236 (m-80) cc_final: 0.7425 (m-80) REVERT: B6 308 TYR cc_start: 0.8239 (t80) cc_final: 0.7933 (t80) REVERT: B6 342 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: B6 384 GLU cc_start: 0.9035 (tp30) cc_final: 0.8499 (tp30) REVERT: B6 424 ASN cc_start: 0.8551 (t0) cc_final: 0.8333 (t0) REVERT: C6 167 ASN cc_start: 0.8996 (t0) cc_final: 0.8786 (t0) REVERT: C6 342 GLU cc_start: 0.8148 (pm20) cc_final: 0.7767 (pm20) REVERT: C6 384 GLU cc_start: 0.8788 (tp30) cc_final: 0.8175 (mm-30) REVERT: D6 88 TRP cc_start: 0.8197 (p-90) cc_final: 0.7889 (p-90) REVERT: D6 266 GLU cc_start: 0.8307 (tp30) cc_final: 0.8104 (tp30) REVERT: D6 320 GLN cc_start: 0.7928 (tp40) cc_final: 0.7383 (mt0) REVERT: D6 330 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D6 342 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: D6 423 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7927 (mtm110) REVERT: D6 462 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: E6 320 GLN cc_start: 0.8116 (tp40) cc_final: 0.7404 (mt0) REVERT: E6 326 MET cc_start: 0.8129 (mtp) cc_final: 0.7776 (mmm) REVERT: E6 342 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: E6 384 GLU cc_start: 0.9019 (tp30) cc_final: 0.8767 (tp30) REVERT: F6 293 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8215 (mmm-85) REVERT: F6 312 MET cc_start: 0.9443 (tpp) cc_final: 0.9036 (tpt) REVERT: F6 330 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7781 (mt-10) REVERT: F6 342 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: F6 408 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (t0) REVERT: F6 424 ASN cc_start: 0.8431 (t0) cc_final: 0.8141 (t0) outliers start: 365 outliers final: 316 residues processed: 2257 average time/residue: 0.5039 time to fit residues: 1985.5616 Evaluate side-chains 2400 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 2062 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A5 residue 19 ASP Chi-restraints excluded: chain A5 residue 29 ASN Chi-restraints excluded: chain A5 residue 47 VAL Chi-restraints excluded: chain A5 residue 55 SER Chi-restraints excluded: chain A5 residue 63 ILE Chi-restraints excluded: chain A5 residue 65 GLU Chi-restraints excluded: chain A5 residue 67 SER Chi-restraints excluded: chain A5 residue 108 LEU Chi-restraints excluded: chain A5 residue 113 VAL Chi-restraints excluded: chain A5 residue 119 VAL Chi-restraints excluded: chain A5 residue 137 ILE Chi-restraints excluded: chain A5 residue 142 SER Chi-restraints excluded: chain B5 residue 19 ASP Chi-restraints excluded: chain B5 residue 47 VAL Chi-restraints excluded: chain B5 residue 55 SER Chi-restraints excluded: chain B5 residue 63 ILE Chi-restraints excluded: chain B5 residue 65 GLU Chi-restraints excluded: chain B5 residue 67 SER Chi-restraints excluded: chain B5 residue 108 LEU Chi-restraints excluded: chain B5 residue 119 VAL Chi-restraints excluded: chain C5 residue 19 ASP Chi-restraints excluded: chain C5 residue 47 VAL Chi-restraints excluded: chain C5 residue 65 GLU Chi-restraints excluded: chain C5 residue 67 SER Chi-restraints excluded: chain C5 residue 75 THR Chi-restraints excluded: chain C5 residue 76 LEU Chi-restraints excluded: chain C5 residue 108 LEU Chi-restraints excluded: chain C5 residue 119 VAL Chi-restraints excluded: chain C5 residue 142 SER Chi-restraints excluded: chain D5 residue 18 TYR Chi-restraints excluded: chain D5 residue 19 ASP Chi-restraints excluded: chain D5 residue 47 VAL Chi-restraints excluded: chain D5 residue 63 ILE Chi-restraints excluded: chain D5 residue 67 SER Chi-restraints excluded: chain D5 residue 108 LEU Chi-restraints excluded: chain D5 residue 119 VAL Chi-restraints excluded: chain D5 residue 137 ILE Chi-restraints excluded: chain E5 residue 19 ASP Chi-restraints excluded: chain E5 residue 47 VAL Chi-restraints excluded: chain E5 residue 63 ILE Chi-restraints excluded: chain E5 residue 108 LEU Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 142 SER Chi-restraints excluded: chain F5 residue 19 ASP Chi-restraints excluded: chain F5 residue 29 ASN Chi-restraints excluded: chain F5 residue 47 VAL Chi-restraints excluded: chain F5 residue 55 SER Chi-restraints excluded: chain F5 residue 63 ILE Chi-restraints excluded: chain F5 residue 64 MET Chi-restraints excluded: chain F5 residue 108 LEU Chi-restraints excluded: chain F5 residue 119 VAL Chi-restraints excluded: chain F5 residue 142 SER Chi-restraints excluded: chain F5 residue 150 VAL Chi-restraints excluded: chain A3 residue 5 VAL Chi-restraints excluded: chain A3 residue 21 THR Chi-restraints excluded: chain A3 residue 42 VAL Chi-restraints excluded: chain A3 residue 62 ILE Chi-restraints excluded: chain A3 residue 75 ASP Chi-restraints excluded: chain A3 residue 92 LEU Chi-restraints excluded: chain A3 residue 102 VAL Chi-restraints excluded: chain B3 residue 15 THR Chi-restraints excluded: chain B3 residue 21 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 92 LEU Chi-restraints excluded: chain C3 residue 10 GLU Chi-restraints excluded: chain C3 residue 15 THR Chi-restraints excluded: chain C3 residue 25 VAL Chi-restraints excluded: chain C3 residue 54 ASN Chi-restraints excluded: chain C3 residue 80 ASP Chi-restraints excluded: chain D3 residue 21 THR Chi-restraints excluded: chain D3 residue 42 VAL Chi-restraints excluded: chain D3 residue 53 LEU Chi-restraints excluded: chain D3 residue 75 ASP Chi-restraints excluded: chain D3 residue 102 VAL Chi-restraints excluded: chain E3 residue 21 THR Chi-restraints excluded: chain E3 residue 73 LEU Chi-restraints excluded: chain E3 residue 89 ILE Chi-restraints excluded: chain E3 residue 100 LEU Chi-restraints excluded: chain F3 residue 15 THR Chi-restraints excluded: chain F3 residue 21 THR Chi-restraints excluded: chain F3 residue 42 VAL Chi-restraints excluded: chain F3 residue 44 THR Chi-restraints excluded: chain F3 residue 54 ASN Chi-restraints excluded: chain F3 residue 89 ILE Chi-restraints excluded: chain G3 residue 5 VAL Chi-restraints excluded: chain G3 residue 21 THR Chi-restraints excluded: chain G3 residue 42 VAL Chi-restraints excluded: chain G3 residue 53 LEU Chi-restraints excluded: chain G3 residue 72 LYS Chi-restraints excluded: chain G3 residue 75 ASP Chi-restraints excluded: chain G3 residue 102 VAL Chi-restraints excluded: chain H3 residue 15 THR Chi-restraints excluded: chain H3 residue 21 THR Chi-restraints excluded: chain I3 residue 10 GLU Chi-restraints excluded: chain I3 residue 15 THR Chi-restraints excluded: chain I3 residue 44 THR Chi-restraints excluded: chain I3 residue 54 ASN Chi-restraints excluded: chain J3 residue 5 VAL Chi-restraints excluded: chain J3 residue 21 THR Chi-restraints excluded: chain J3 residue 42 VAL Chi-restraints excluded: chain J3 residue 72 LYS Chi-restraints excluded: chain J3 residue 75 ASP Chi-restraints excluded: chain J3 residue 92 LEU Chi-restraints excluded: chain J3 residue 102 VAL Chi-restraints excluded: chain K3 residue 15 THR Chi-restraints excluded: chain K3 residue 21 THR Chi-restraints excluded: chain K3 residue 33 THR Chi-restraints excluded: chain K3 residue 92 LEU Chi-restraints excluded: chain L3 residue 25 VAL Chi-restraints excluded: chain L3 residue 54 ASN Chi-restraints excluded: chain L3 residue 64 TYR Chi-restraints excluded: chain L3 residue 80 ASP Chi-restraints excluded: chain L3 residue 89 ILE Chi-restraints excluded: chain L3 residue 107 LEU Chi-restraints excluded: chain M3 residue 28 ILE Chi-restraints excluded: chain M3 residue 42 VAL Chi-restraints excluded: chain M3 residue 45 THR Chi-restraints excluded: chain M3 residue 55 GLU Chi-restraints excluded: chain M3 residue 58 HIS Chi-restraints excluded: chain M3 residue 72 LYS Chi-restraints excluded: chain M3 residue 75 ASP Chi-restraints excluded: chain M3 residue 92 LEU Chi-restraints excluded: chain M3 residue 102 VAL Chi-restraints excluded: chain N3 residue 21 THR Chi-restraints excluded: chain N3 residue 57 PHE Chi-restraints excluded: chain N3 residue 92 LEU Chi-restraints excluded: chain N3 residue 110 GLU Chi-restraints excluded: chain O3 residue 15 THR Chi-restraints excluded: chain O3 residue 25 VAL Chi-restraints excluded: chain O3 residue 44 THR Chi-restraints excluded: chain O3 residue 54 ASN Chi-restraints excluded: chain O3 residue 75 ASP Chi-restraints excluded: chain O3 residue 80 ASP Chi-restraints excluded: chain O3 residue 100 LEU Chi-restraints excluded: chain P3 residue 5 VAL Chi-restraints excluded: chain P3 residue 15 THR Chi-restraints excluded: chain P3 residue 21 THR Chi-restraints excluded: chain P3 residue 28 ILE Chi-restraints excluded: chain P3 residue 30 TYR Chi-restraints excluded: chain P3 residue 42 VAL Chi-restraints excluded: chain P3 residue 62 ILE Chi-restraints excluded: chain P3 residue 75 ASP Chi-restraints excluded: chain P3 residue 92 LEU Chi-restraints excluded: chain Q3 residue 21 THR Chi-restraints excluded: chain Q3 residue 33 THR Chi-restraints excluded: chain Q3 residue 71 THR Chi-restraints excluded: chain Q3 residue 73 LEU Chi-restraints excluded: chain Q3 residue 100 LEU Chi-restraints excluded: chain R3 residue 10 GLU Chi-restraints excluded: chain R3 residue 15 THR Chi-restraints excluded: chain R3 residue 22 ILE Chi-restraints excluded: chain R3 residue 44 THR Chi-restraints excluded: chain R3 residue 54 ASN Chi-restraints excluded: chain R3 residue 64 TYR Chi-restraints excluded: chain A4 residue 16 VAL Chi-restraints excluded: chain A4 residue 64 TRP Chi-restraints excluded: chain A4 residue 70 LYS Chi-restraints excluded: chain A4 residue 113 SER Chi-restraints excluded: chain B4 residue 16 VAL Chi-restraints excluded: chain B4 residue 23 THR Chi-restraints excluded: chain B4 residue 47 ASP Chi-restraints excluded: chain B4 residue 64 TRP Chi-restraints excluded: chain C4 residue 9 LEU Chi-restraints excluded: chain C4 residue 16 VAL Chi-restraints excluded: chain C4 residue 64 TRP Chi-restraints excluded: chain C4 residue 99 ASN Chi-restraints excluded: chain C4 residue 112 VAL Chi-restraints excluded: chain C4 residue 113 SER Chi-restraints excluded: chain D4 residue 16 VAL Chi-restraints excluded: chain D4 residue 24 ILE Chi-restraints excluded: chain D4 residue 32 ILE Chi-restraints excluded: chain D4 residue 64 TRP Chi-restraints excluded: chain D4 residue 73 ILE Chi-restraints excluded: chain D4 residue 91 ASP Chi-restraints excluded: chain D4 residue 112 VAL Chi-restraints excluded: chain D4 residue 113 SER Chi-restraints excluded: chain E4 residue 16 VAL Chi-restraints excluded: chain E4 residue 32 ILE Chi-restraints excluded: chain E4 residue 73 ILE Chi-restraints excluded: chain E4 residue 91 ASP Chi-restraints excluded: chain E4 residue 104 GLU Chi-restraints excluded: chain E4 residue 113 SER Chi-restraints excluded: chain F4 residue 9 LEU Chi-restraints excluded: chain F4 residue 16 VAL Chi-restraints excluded: chain F4 residue 64 TRP Chi-restraints excluded: chain F4 residue 91 ASP Chi-restraints excluded: chain F4 residue 113 SER Chi-restraints excluded: chain A7 residue 13 LEU Chi-restraints excluded: chain A7 residue 14 THR Chi-restraints excluded: chain A7 residue 16 ASN Chi-restraints excluded: chain A7 residue 30 VAL Chi-restraints excluded: chain A7 residue 42 ASN Chi-restraints excluded: chain A7 residue 43 SER Chi-restraints excluded: chain A7 residue 91 MET Chi-restraints excluded: chain B7 residue 13 LEU Chi-restraints excluded: chain B7 residue 14 THR Chi-restraints excluded: chain B7 residue 30 VAL Chi-restraints excluded: chain B7 residue 43 SER Chi-restraints excluded: chain B7 residue 73 LYS Chi-restraints excluded: chain B7 residue 91 MET Chi-restraints excluded: chain C7 residue 13 LEU Chi-restraints excluded: chain C7 residue 14 THR Chi-restraints excluded: chain C7 residue 30 VAL Chi-restraints excluded: chain C7 residue 43 SER Chi-restraints excluded: chain C7 residue 73 LYS Chi-restraints excluded: chain D7 residue 3 VAL Chi-restraints excluded: chain D7 residue 13 LEU Chi-restraints excluded: chain D7 residue 14 THR Chi-restraints excluded: chain D7 residue 16 ASN Chi-restraints excluded: chain D7 residue 30 VAL Chi-restraints excluded: chain D7 residue 42 ASN Chi-restraints excluded: chain D7 residue 43 SER Chi-restraints excluded: chain D7 residue 91 MET Chi-restraints excluded: chain D7 residue 135 GLU Chi-restraints excluded: chain E7 residue 3 VAL Chi-restraints excluded: chain E7 residue 5 VAL Chi-restraints excluded: chain E7 residue 13 LEU Chi-restraints excluded: chain E7 residue 14 THR Chi-restraints excluded: chain E7 residue 30 VAL Chi-restraints excluded: chain E7 residue 44 ILE Chi-restraints excluded: chain E7 residue 55 ASP Chi-restraints excluded: chain E7 residue 91 MET Chi-restraints excluded: chain F7 residue 3 VAL Chi-restraints excluded: chain F7 residue 13 LEU Chi-restraints excluded: chain F7 residue 30 VAL Chi-restraints excluded: chain F7 residue 42 ASN Chi-restraints excluded: chain F7 residue 43 SER Chi-restraints excluded: chain F7 residue 91 MET Chi-restraints excluded: chain A6 residue 37 LEU Chi-restraints excluded: chain A6 residue 41 ASP Chi-restraints excluded: chain A6 residue 60 SER Chi-restraints excluded: chain A6 residue 84 VAL Chi-restraints excluded: chain A6 residue 109 GLU Chi-restraints excluded: chain A6 residue 129 ASP Chi-restraints excluded: chain A6 residue 195 ILE Chi-restraints excluded: chain A6 residue 210 THR Chi-restraints excluded: chain A6 residue 218 LEU Chi-restraints excluded: chain A6 residue 243 ASP Chi-restraints excluded: chain A6 residue 263 LEU Chi-restraints excluded: chain A6 residue 315 VAL Chi-restraints excluded: chain A6 residue 365 THR Chi-restraints excluded: chain A6 residue 396 THR Chi-restraints excluded: chain A6 residue 462 ASP Chi-restraints excluded: chain A6 residue 475 VAL Chi-restraints excluded: chain A6 residue 486 VAL Chi-restraints excluded: chain A6 residue 492 ILE Chi-restraints excluded: chain B6 residue 41 ASP Chi-restraints excluded: chain B6 residue 60 SER Chi-restraints excluded: chain B6 residue 84 VAL Chi-restraints excluded: chain B6 residue 129 ASP Chi-restraints excluded: chain B6 residue 195 ILE Chi-restraints excluded: chain B6 residue 210 THR Chi-restraints excluded: chain B6 residue 243 ASP Chi-restraints excluded: chain B6 residue 263 LEU Chi-restraints excluded: chain B6 residue 269 ASP Chi-restraints excluded: chain B6 residue 315 VAL Chi-restraints excluded: chain B6 residue 330 GLU Chi-restraints excluded: chain B6 residue 342 GLU Chi-restraints excluded: chain B6 residue 365 THR Chi-restraints excluded: chain B6 residue 411 GLU Chi-restraints excluded: chain B6 residue 465 THR Chi-restraints excluded: chain B6 residue 486 VAL Chi-restraints excluded: chain B6 residue 489 GLU Chi-restraints excluded: chain B6 residue 492 ILE Chi-restraints excluded: chain C6 residue 4 ILE Chi-restraints excluded: chain C6 residue 7 VAL Chi-restraints excluded: chain C6 residue 41 ASP Chi-restraints excluded: chain C6 residue 84 VAL Chi-restraints excluded: chain C6 residue 129 ASP Chi-restraints excluded: chain C6 residue 173 THR Chi-restraints excluded: chain C6 residue 243 ASP Chi-restraints excluded: chain C6 residue 315 VAL Chi-restraints excluded: chain C6 residue 332 SER Chi-restraints excluded: chain C6 residue 365 THR Chi-restraints excluded: chain C6 residue 372 CYS Chi-restraints excluded: chain C6 residue 392 LEU Chi-restraints excluded: chain C6 residue 396 THR Chi-restraints excluded: chain C6 residue 411 GLU Chi-restraints excluded: chain C6 residue 443 GLN Chi-restraints excluded: chain C6 residue 486 VAL Chi-restraints excluded: chain D6 residue 7 VAL Chi-restraints excluded: chain D6 residue 41 ASP Chi-restraints excluded: chain D6 residue 84 VAL Chi-restraints excluded: chain D6 residue 195 ILE Chi-restraints excluded: chain D6 residue 210 THR Chi-restraints excluded: chain D6 residue 218 LEU Chi-restraints excluded: chain D6 residue 243 ASP Chi-restraints excluded: chain D6 residue 263 LEU Chi-restraints excluded: chain D6 residue 294 CYS Chi-restraints excluded: chain D6 residue 315 VAL Chi-restraints excluded: chain D6 residue 342 GLU Chi-restraints excluded: chain D6 residue 353 LEU Chi-restraints excluded: chain D6 residue 365 THR Chi-restraints excluded: chain D6 residue 396 THR Chi-restraints excluded: chain D6 residue 443 GLN Chi-restraints excluded: chain D6 residue 462 ASP Chi-restraints excluded: chain D6 residue 486 VAL Chi-restraints excluded: chain D6 residue 492 ILE Chi-restraints excluded: chain E6 residue 4 ILE Chi-restraints excluded: chain E6 residue 41 ASP Chi-restraints excluded: chain E6 residue 60 SER Chi-restraints excluded: chain E6 residue 73 THR Chi-restraints excluded: chain E6 residue 84 VAL Chi-restraints excluded: chain E6 residue 109 GLU Chi-restraints excluded: chain E6 residue 195 ILE Chi-restraints excluded: chain E6 residue 210 THR Chi-restraints excluded: chain E6 residue 243 ASP Chi-restraints excluded: chain E6 residue 263 LEU Chi-restraints excluded: chain E6 residue 269 ASP Chi-restraints excluded: chain E6 residue 315 VAL Chi-restraints excluded: chain E6 residue 330 GLU Chi-restraints excluded: chain E6 residue 342 GLU Chi-restraints excluded: chain E6 residue 365 THR Chi-restraints excluded: chain E6 residue 396 THR Chi-restraints excluded: chain E6 residue 475 VAL Chi-restraints excluded: chain E6 residue 486 VAL Chi-restraints excluded: chain F6 residue 4 ILE Chi-restraints excluded: chain F6 residue 41 ASP Chi-restraints excluded: chain F6 residue 73 THR Chi-restraints excluded: chain F6 residue 84 VAL Chi-restraints excluded: chain F6 residue 109 GLU Chi-restraints excluded: chain F6 residue 129 ASP Chi-restraints excluded: chain F6 residue 195 ILE Chi-restraints excluded: chain F6 residue 198 VAL Chi-restraints excluded: chain F6 residue 210 THR Chi-restraints excluded: chain F6 residue 243 ASP Chi-restraints excluded: chain F6 residue 263 LEU Chi-restraints excluded: chain F6 residue 315 VAL Chi-restraints excluded: chain F6 residue 342 GLU Chi-restraints excluded: chain F6 residue 355 THR Chi-restraints excluded: chain F6 residue 365 THR Chi-restraints excluded: chain F6 residue 408 ASP Chi-restraints excluded: chain F6 residue 411 GLU Chi-restraints excluded: chain F6 residue 465 THR Chi-restraints excluded: chain F6 residue 475 VAL Chi-restraints excluded: chain F6 residue 486 VAL Chi-restraints excluded: chain F6 residue 489 GLU Chi-restraints excluded: chain F6 residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 9.9990 chunk 633 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 548 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 595 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 611 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5 29 ASN ** C5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 29 ASN E5 29 ASN ** E5 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 29 ASN B3 90 ASN ** C3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3 54 ASN F3 58 HIS ** L3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R3 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4 66 HIS ** A7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 374 ASN ** C6 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 320 GLN ** F6 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131943 restraints weight = 107574.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135636 restraints weight = 49700.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138018 restraints weight = 27398.970| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59988 Z= 0.215 Angle : 0.687 13.579 81510 Z= 0.345 Chirality : 0.046 0.423 9684 Planarity : 0.004 0.067 10548 Dihedral : 5.185 58.555 8297 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.53 % Allowed : 30.41 % Favored : 64.06 % 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: -1.66 (0.10), residues: 7656 helix: 0.86 (0.12), residues: 1932 sheet: -1.22 (0.11), residues: 2112 loop : -2.15 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRPC6 88 HIS 0.037 0.001 HISM3 58 PHE 0.035 0.002 PHEG3 57 TYR 0.030 0.002 TYRC6 308 ARG 0.009 0.001 ARGK3 23 =============================================================================== Job complete usr+sys time: 25738.49 seconds wall clock time: 447 minutes 18.94 seconds (26838.94 seconds total)