Starting phenix.real_space_refine on Sun Mar 24 06:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mue_24006/03_2024/7mue_24006.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 90 5.16 5 C 25470 2.51 5 N 6948 2.21 5 O 7758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XH GLU 125": "OE1" <-> "OE2" Residue "XH PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XH ASP 198": "OD1" <-> "OD2" Residue "BF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YH GLU 135": "OE1" <-> "OE2" Residue "YH ASP 249": "OD1" <-> "OD2" Residue "YH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZH GLU 138": "OE1" <-> "OE2" Residue "ZH ASP 195": "OD1" <-> "OD2" Residue "ZH ASP 198": "OD1" <-> "OD2" Residue "ZH ASP 253": "OD1" <-> "OD2" Residue "ZH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IG ASP 800": "OD1" <-> "OD2" Residue "GF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "XF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZF TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZF PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ASP 811": "OD1" <-> "OD2" Residue "CG ASP 800": "OD1" <-> "OD2" Residue "CG ASP 811": "OD1" <-> "OD2" Residue "DG ASP 800": "OD1" <-> "OD2" Residue "EG ASP 811": "OD1" <-> "OD2" Residue "FG ASP 800": "OD1" <-> "OD2" Residue "GG ASP 800": "OD1" <-> "OD2" Residue "GG ASP 811": "OD1" <-> "OD2" Residue "HG ASP 811": "OD1" <-> "OD2" Residue "HG GLU 822": "OE1" <-> "OE2" Residue "KG ASP 800": "OD1" <-> "OD2" Residue "KG GLU 822": "OE1" <-> "OE2" Residue "LG ASP 800": "OD1" <-> "OD2" Residue "LG ASP 811": "OD1" <-> "OD2" Residue "MG ASP 811": "OD1" <-> "OD2" Residue "VG ASP 800": "OD1" <-> "OD2" Residue "VG ASP 811": "OD1" <-> "OD2" Residue "WG ASP 811": "OD1" <-> "OD2" Residue "WG GLU 822": "OE1" <-> "OE2" Residue "YG ASP 800": "OD1" <-> "OD2" Residue "AH GLU 138": "OE1" <-> "OE2" Residue "AH ASP 198": "OD1" <-> "OD2" Residue "AH ASP 253": "OD1" <-> "OD2" Residue "BH GLU 125": "OE1" <-> "OE2" Residue "BH PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH ASP 198": "OD1" <-> "OD2" Residue "BH ASP 253": "OD1" <-> "OD2" Residue "CH ASP 114": "OD1" <-> "OD2" Residue "CH GLU 135": "OE1" <-> "OE2" Residue "CH GLU 138": "OE1" <-> "OE2" Residue "CH ASP 198": "OD1" <-> "OD2" Residue "CH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DH ASP 114": "OD1" <-> "OD2" Residue "DH GLU 135": "OE1" <-> "OE2" Residue "DH ASP 198": "OD1" <-> "OD2" Residue "DH ASP 253": "OD1" <-> "OD2" Residue "DH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EH GLU 138": "OE1" <-> "OE2" Residue "EH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FH ASP 114": "OD1" <-> "OD2" Residue "FH GLU 125": "OE1" <-> "OE2" Residue "FH PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FH ASP 198": "OD1" <-> "OD2" Residue "FH ASP 253": "OD1" <-> "OD2" Residue "GH ASP 195": "OD1" <-> "OD2" Residue "GH ASP 198": "OD1" <-> "OD2" Residue "GH ASP 253": "OD1" <-> "OD2" Residue "GH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HH GLU 138": "OE1" <-> "OE2" Residue "HH ASP 198": "OD1" <-> "OD2" Residue "HH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IH ASP 114": "OD1" <-> "OD2" Residue "IH GLU 125": "OE1" <-> "OE2" Residue "IH ASP 198": "OD1" <-> "OD2" Residue "IH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JH GLU 135": "OE1" <-> "OE2" Residue "JH GLU 138": "OE1" <-> "OE2" Residue "JH ASP 198": "OD1" <-> "OD2" Residue "JH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KH ASP 114": "OD1" <-> "OD2" Residue "KH GLU 135": "OE1" <-> "OE2" Residue "KH GLU 138": "OE1" <-> "OE2" Residue "KH ASP 183": "OD1" <-> "OD2" Residue "KH ASP 253": "OD1" <-> "OD2" Residue "KH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 114": "OD1" <-> "OD2" Residue "LH GLU 125": "OE1" <-> "OE2" Residue "LH PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 198": "OD1" <-> "OD2" Residue "LH ASP 249": "OD1" <-> "OD2" Residue "LH ASP 253": "OD1" <-> "OD2" Residue "MH GLU 125": "OE1" <-> "OE2" Residue "MH GLU 138": "OE1" <-> "OE2" Residue "MH ASP 198": "OD1" <-> "OD2" Residue "MH ASP 249": "OD1" <-> "OD2" Residue "MH ASP 253": "OD1" <-> "OD2" Residue "VH GLU 135": "OE1" <-> "OE2" Residue "VH GLU 138": "OE1" <-> "OE2" Residue "VH ASP 198": "OD1" <-> "OD2" Residue "VH ASP 253": "OD1" <-> "OD2" Residue "VH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WH ASP 114": "OD1" <-> "OD2" Residue "WH GLU 125": "OE1" <-> "OE2" Residue "WH ASP 198": "OD1" <-> "OD2" Residue "WH TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40266 Number of models: 1 Model: "" Number of chains: 72 Chain: "AF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "XH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "BF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "YH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "ZH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "AX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "BX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "CX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "DX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "EX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "FX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "GX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "HX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "IX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "JX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "KX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "LX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "MX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "VX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "WX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "XX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "YX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "ZX" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 240 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "CF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "DF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "EF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "FF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "IG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "GF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "HF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "IF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "JF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "KF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "LF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "MF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "VF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "WF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "XF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "YF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "ZF" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "AG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "BG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "CG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "DG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "EG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "FG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "GG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "HG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "JG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "KG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "LG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "MG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "VG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "WG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "XG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "YG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "ZG" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "AH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "BH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "CH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "DH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "EH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "FH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "GH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "HH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "IH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "JH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "KH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "LH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "MH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "VH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "WH" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Time building chain proxies: 20.20, per 1000 atoms: 0.50 Number of scatterers: 40266 At special positions: 0 Unit cell: (216.7, 214.5, 90.2, 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 90 16.00 O 7758 8.00 N 6948 7.00 C 25470 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: 14.08 Conformation dependent library (CDL) restraints added in 6.7 seconds 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10296 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 90 sheets defined 31.5% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'AF' and resid 249 through 252 removed outlier: 3.883A pdb=" N GLYAF 252 " --> pdb=" O SERAF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 249 through 252' Processing helix chain 'XH' and resid 106 through 120 removed outlier: 3.527A pdb=" N LYSXH 110 " --> pdb=" O VALXH 106 " (cutoff:3.500A) Processing helix chain 'XH' and resid 123 through 143 Processing helix chain 'BF' and resid 249 through 252 removed outlier: 3.865A pdb=" N GLYBF 252 " --> pdb=" O SERBF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 249 through 252' Processing helix chain 'YH' and resid 106 through 120 Processing helix chain 'YH' and resid 123 through 143 removed outlier: 3.502A pdb=" N LYSYH 129 " --> pdb=" O GLUYH 125 " (cutoff:3.500A) Processing helix chain 'ZH' and resid 106 through 120 Processing helix chain 'ZH' and resid 123 through 143 Processing helix chain 'AX' and resid 3 through 15 removed outlier: 3.540A pdb=" N UNKAX 7 " --> pdb=" O UNKAX 3 " (cutoff:3.500A) Processing helix chain 'AX' and resid 73 through 77 Processing helix chain 'BX' and resid 3 through 15 removed outlier: 3.519A pdb=" N UNKBX 7 " --> pdb=" O UNKBX 3 " (cutoff:3.500A) Processing helix chain 'BX' and resid 73 through 77 Processing helix chain 'CX' and resid 3 through 15 removed outlier: 3.583A pdb=" N UNKCX 7 " --> pdb=" O UNKCX 3 " (cutoff:3.500A) Processing helix chain 'CX' and resid 73 through 77 Processing helix chain 'DX' and resid 3 through 15 removed outlier: 3.541A pdb=" N UNKDX 7 " --> pdb=" O UNKDX 3 " (cutoff:3.500A) Processing helix chain 'DX' and resid 73 through 77 Processing helix chain 'EX' and resid 3 through 15 removed outlier: 3.592A pdb=" N UNKEX 7 " --> pdb=" O UNKEX 3 " (cutoff:3.500A) Processing helix chain 'EX' and resid 73 through 77 Processing helix chain 'FX' and resid 3 through 15 removed outlier: 3.581A pdb=" N UNKFX 7 " --> pdb=" O UNKFX 3 " (cutoff:3.500A) Processing helix chain 'FX' and resid 73 through 77 Processing helix chain 'GX' and resid 3 through 15 removed outlier: 3.565A pdb=" N UNKGX 7 " --> pdb=" O UNKGX 3 " (cutoff:3.500A) Processing helix chain 'GX' and resid 73 through 77 Processing helix chain 'HX' and resid 3 through 15 removed outlier: 3.540A pdb=" N UNKHX 7 " --> pdb=" O UNKHX 3 " (cutoff:3.500A) Processing helix chain 'HX' and resid 73 through 77 Processing helix chain 'IX' and resid 3 through 15 removed outlier: 3.579A pdb=" N UNKIX 7 " --> pdb=" O UNKIX 3 " (cutoff:3.500A) Processing helix chain 'IX' and resid 73 through 77 Processing helix chain 'JX' and resid 3 through 15 removed outlier: 3.561A pdb=" N UNKJX 7 " --> pdb=" O UNKJX 3 " (cutoff:3.500A) Processing helix chain 'JX' and resid 73 through 77 Processing helix chain 'KX' and resid 3 through 15 removed outlier: 3.547A pdb=" N UNKKX 7 " --> pdb=" O UNKKX 3 " (cutoff:3.500A) Processing helix chain 'KX' and resid 73 through 77 Processing helix chain 'LX' and resid 3 through 15 removed outlier: 3.581A pdb=" N UNKLX 7 " --> pdb=" O UNKLX 3 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 77 Processing helix chain 'MX' and resid 3 through 15 removed outlier: 3.551A pdb=" N UNKMX 7 " --> pdb=" O UNKMX 3 " (cutoff:3.500A) Processing helix chain 'MX' and resid 73 through 77 Processing helix chain 'VX' and resid 3 through 15 removed outlier: 3.534A pdb=" N UNKVX 7 " --> pdb=" O UNKVX 3 " (cutoff:3.500A) Processing helix chain 'VX' and resid 73 through 77 Processing helix chain 'WX' and resid 3 through 15 removed outlier: 3.570A pdb=" N UNKWX 7 " --> pdb=" O UNKWX 3 " (cutoff:3.500A) Processing helix chain 'WX' and resid 73 through 77 Processing helix chain 'XX' and resid 3 through 15 removed outlier: 3.539A pdb=" N UNKXX 7 " --> pdb=" O UNKXX 3 " (cutoff:3.500A) Processing helix chain 'XX' and resid 73 through 77 Processing helix chain 'YX' and resid 3 through 15 removed outlier: 3.562A pdb=" N UNKYX 7 " --> pdb=" O UNKYX 3 " (cutoff:3.500A) Processing helix chain 'YX' and resid 73 through 77 Processing helix chain 'ZX' and resid 3 through 15 removed outlier: 3.560A pdb=" N UNKZX 7 " --> pdb=" O UNKZX 3 " (cutoff:3.500A) Processing helix chain 'ZX' and resid 73 through 77 Processing helix chain 'CF' and resid 249 through 252 removed outlier: 3.940A pdb=" N GLYCF 252 " --> pdb=" O SERCF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 249 through 252' Processing helix chain 'DF' and resid 249 through 252 removed outlier: 3.859A pdb=" N GLYDF 252 " --> pdb=" O SERDF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'DF' and resid 249 through 252' Processing helix chain 'EF' and resid 249 through 252 removed outlier: 3.902A pdb=" N GLYEF 252 " --> pdb=" O SEREF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'EF' and resid 249 through 252' Processing helix chain 'FF' and resid 249 through 252 removed outlier: 3.879A pdb=" N GLYFF 252 " --> pdb=" O SERFF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'FF' and resid 249 through 252' Processing helix chain 'IG' and resid 792 through 814 removed outlier: 3.504A pdb=" N GLNIG 807 " --> pdb=" O THRIG 803 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLNIG 814 " --> pdb=" O GLNIG 810 " (cutoff:3.500A) Processing helix chain 'GF' and resid 249 through 252 removed outlier: 3.874A pdb=" N GLYGF 252 " --> pdb=" O SERGF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'GF' and resid 249 through 252' Processing helix chain 'HF' and resid 249 through 252 removed outlier: 3.859A pdb=" N GLYHF 252 " --> pdb=" O SERHF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'HF' and resid 249 through 252' Processing helix chain 'IF' and resid 249 through 252 removed outlier: 3.920A pdb=" N GLYIF 252 " --> pdb=" O SERIF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'IF' and resid 249 through 252' Processing helix chain 'JF' and resid 249 through 252 removed outlier: 3.848A pdb=" N GLYJF 252 " --> pdb=" O SERJF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'JF' and resid 249 through 252' Processing helix chain 'KF' and resid 249 through 252 removed outlier: 3.883A pdb=" N GLYKF 252 " --> pdb=" O SERKF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'KF' and resid 249 through 252' Processing helix chain 'LF' and resid 249 through 252 removed outlier: 3.863A pdb=" N GLYLF 252 " --> pdb=" O SERLF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'LF' and resid 249 through 252' Processing helix chain 'MF' and resid 249 through 252 removed outlier: 3.882A pdb=" N GLYMF 252 " --> pdb=" O SERMF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'MF' and resid 249 through 252' Processing helix chain 'VF' and resid 249 through 252 removed outlier: 3.849A pdb=" N GLYVF 252 " --> pdb=" O SERVF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'VF' and resid 249 through 252' Processing helix chain 'WF' and resid 249 through 252 removed outlier: 3.870A pdb=" N GLYWF 252 " --> pdb=" O SERWF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'WF' and resid 249 through 252' Processing helix chain 'XF' and resid 249 through 252 removed outlier: 3.867A pdb=" N GLYXF 252 " --> pdb=" O SERXF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'XF' and resid 249 through 252' Processing helix chain 'YF' and resid 249 through 252 removed outlier: 3.900A pdb=" N GLYYF 252 " --> pdb=" O SERYF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'YF' and resid 249 through 252' Processing helix chain 'ZF' and resid 249 through 252 removed outlier: 3.910A pdb=" N GLYZF 252 " --> pdb=" O SERZF 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'ZF' and resid 249 through 252' Processing helix chain 'AG' and resid 792 through 814 removed outlier: 3.537A pdb=" N GLNAG 807 " --> pdb=" O THRAG 803 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLNAG 814 " --> pdb=" O GLNAG 810 " (cutoff:3.500A) Processing helix chain 'BG' and resid 792 through 814 removed outlier: 3.528A pdb=" N GLNBG 807 " --> pdb=" O THRBG 803 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLNBG 814 " --> pdb=" O GLNBG 810 " (cutoff:3.500A) Processing helix chain 'CG' and resid 792 through 814 removed outlier: 3.550A pdb=" N ASPCG 800 " --> pdb=" O GLNCG 796 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THRCG 803 " --> pdb=" O SERCG 799 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLNCG 807 " --> pdb=" O THRCG 803 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLNCG 814 " --> pdb=" O GLNCG 810 " (cutoff:3.500A) Processing helix chain 'DG' and resid 792 through 814 removed outlier: 3.737A pdb=" N GLNDG 814 " --> pdb=" O GLNDG 810 " (cutoff:3.500A) Processing helix chain 'EG' and resid 792 through 814 removed outlier: 3.516A pdb=" N GLNEG 807 " --> pdb=" O THREG 803 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLNEG 814 " --> pdb=" O GLNEG 810 " (cutoff:3.500A) Processing helix chain 'FG' and resid 792 through 814 removed outlier: 3.589A pdb=" N GLNFG 807 " --> pdb=" O THRFG 803 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLNFG 814 " --> pdb=" O GLNFG 810 " (cutoff:3.500A) Processing helix chain 'GG' and resid 792 through 814 removed outlier: 3.516A pdb=" N GLNGG 807 " --> pdb=" O THRGG 803 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLNGG 814 " --> pdb=" O GLNGG 810 " (cutoff:3.500A) Processing helix chain 'HG' and resid 792 through 814 removed outlier: 3.519A pdb=" N ASPHG 800 " --> pdb=" O GLNHG 796 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLNHG 807 " --> pdb=" O THRHG 803 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLNHG 814 " --> pdb=" O GLNHG 810 " (cutoff:3.500A) Processing helix chain 'JG' and resid 792 through 814 removed outlier: 3.545A pdb=" N GLNJG 807 " --> pdb=" O THRJG 803 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLNJG 814 " --> pdb=" O GLNJG 810 " (cutoff:3.500A) Processing helix chain 'KG' and resid 792 through 814 removed outlier: 3.737A pdb=" N GLNKG 814 " --> pdb=" O GLNKG 810 " (cutoff:3.500A) Processing helix chain 'LG' and resid 792 through 814 removed outlier: 3.514A pdb=" N THRLG 803 " --> pdb=" O SERLG 799 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLNLG 807 " --> pdb=" O THRLG 803 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLNLG 814 " --> pdb=" O GLNLG 810 " (cutoff:3.500A) Processing helix chain 'MG' and resid 792 through 813 removed outlier: 3.559A pdb=" N GLNMG 807 " --> pdb=" O THRMG 803 " (cutoff:3.500A) Processing helix chain 'VG' and resid 792 through 814 removed outlier: 3.540A pdb=" N GLNVG 807 " --> pdb=" O THRVG 803 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLNVG 814 " --> pdb=" O GLNVG 810 " (cutoff:3.500A) Processing helix chain 'WG' and resid 792 through 813 removed outlier: 3.552A pdb=" N GLNWG 807 " --> pdb=" O THRWG 803 " (cutoff:3.500A) Processing helix chain 'XG' and resid 792 through 814 removed outlier: 3.693A pdb=" N GLNXG 796 " --> pdb=" O GLNXG 792 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLNXG 807 " --> pdb=" O THRXG 803 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLNXG 814 " --> pdb=" O GLNXG 810 " (cutoff:3.500A) Processing helix chain 'YG' and resid 792 through 814 removed outlier: 3.539A pdb=" N GLNYG 807 " --> pdb=" O THRYG 803 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLNYG 814 " --> pdb=" O GLNYG 810 " (cutoff:3.500A) Processing helix chain 'ZG' and resid 792 through 814 removed outlier: 3.507A pdb=" N THRZG 803 " --> pdb=" O SERZG 799 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLNZG 807 " --> pdb=" O THRZG 803 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLNZG 814 " --> pdb=" O GLNZG 810 " (cutoff:3.500A) Processing helix chain 'AH' and resid 106 through 120 removed outlier: 3.501A pdb=" N LYSAH 110 " --> pdb=" O VALAH 106 " (cutoff:3.500A) Processing helix chain 'AH' and resid 123 through 143 removed outlier: 3.574A pdb=" N VALAH 128 " --> pdb=" O PROAH 124 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYSAH 129 " --> pdb=" O GLUAH 125 " (cutoff:3.500A) Processing helix chain 'BH' and resid 106 through 120 removed outlier: 3.515A pdb=" N LYSBH 110 " --> pdb=" O VALBH 106 " (cutoff:3.500A) Processing helix chain 'BH' and resid 123 through 143 Processing helix chain 'CH' and resid 106 through 120 removed outlier: 3.507A pdb=" N LYSCH 113 " --> pdb=" O LYSCH 109 " (cutoff:3.500A) Processing helix chain 'CH' and resid 123 through 143 Processing helix chain 'DH' and resid 106 through 120 removed outlier: 3.516A pdb=" N LYSDH 110 " --> pdb=" O VALDH 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASPDH 114 " --> pdb=" O LYSDH 110 " (cutoff:3.500A) Processing helix chain 'DH' and resid 123 through 143 removed outlier: 3.538A pdb=" N VALDH 128 " --> pdb=" O PRODH 124 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSDH 129 " --> pdb=" O GLUDH 125 " (cutoff:3.500A) Processing helix chain 'EH' and resid 106 through 120 removed outlier: 3.516A pdb=" N LYSEH 110 " --> pdb=" O VALEH 106 " (cutoff:3.500A) Processing helix chain 'EH' and resid 123 through 143 Processing helix chain 'FH' and resid 106 through 120 removed outlier: 3.540A pdb=" N LYSFH 113 " --> pdb=" O LYSFH 109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASPFH 114 " --> pdb=" O LYSFH 110 " (cutoff:3.500A) Processing helix chain 'FH' and resid 123 through 143 Processing helix chain 'GH' and resid 106 through 120 removed outlier: 3.535A pdb=" N ASPGH 114 " --> pdb=" O LYSGH 110 " (cutoff:3.500A) Processing helix chain 'GH' and resid 123 through 143 Processing helix chain 'HH' and resid 106 through 120 removed outlier: 3.525A pdb=" N LYSHH 110 " --> pdb=" O VALHH 106 " (cutoff:3.500A) Processing helix chain 'HH' and resid 123 through 143 removed outlier: 3.591A pdb=" N VALHH 128 " --> pdb=" O PROHH 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYSHH 129 " --> pdb=" O GLUHH 125 " (cutoff:3.500A) Processing helix chain 'IH' and resid 106 through 120 removed outlier: 3.504A pdb=" N ASPIH 114 " --> pdb=" O LYSIH 110 " (cutoff:3.500A) Processing helix chain 'IH' and resid 123 through 143 Processing helix chain 'JH' and resid 106 through 120 removed outlier: 3.540A pdb=" N LYSJH 110 " --> pdb=" O VALJH 106 " (cutoff:3.500A) Processing helix chain 'JH' and resid 123 through 143 removed outlier: 3.563A pdb=" N VALJH 128 " --> pdb=" O PROJH 124 " (cutoff:3.500A) Processing helix chain 'KH' and resid 106 through 120 removed outlier: 3.549A pdb=" N LYSKH 113 " --> pdb=" O LYSKH 109 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASPKH 114 " --> pdb=" O LYSKH 110 " (cutoff:3.500A) Processing helix chain 'KH' and resid 123 through 143 removed outlier: 3.543A pdb=" N VALKH 128 " --> pdb=" O PROKH 124 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSKH 129 " --> pdb=" O GLUKH 125 " (cutoff:3.500A) Processing helix chain 'LH' and resid 106 through 120 Processing helix chain 'LH' and resid 123 through 143 Processing helix chain 'MH' and resid 106 through 120 removed outlier: 3.511A pdb=" N ASPMH 114 " --> pdb=" O LYSMH 110 " (cutoff:3.500A) Processing helix chain 'MH' and resid 123 through 143 Processing helix chain 'VH' and resid 106 through 120 removed outlier: 3.539A pdb=" N LYSVH 110 " --> pdb=" O VALVH 106 " (cutoff:3.500A) Processing helix chain 'VH' and resid 123 through 143 removed outlier: 3.563A pdb=" N VALVH 128 " --> pdb=" O PROVH 124 " (cutoff:3.500A) Processing helix chain 'WH' and resid 106 through 120 removed outlier: 3.529A pdb=" N LYSWH 110 " --> pdb=" O VALWH 106 " (cutoff:3.500A) Processing helix chain 'WH' and resid 123 through 143 Processing sheet with id=AA1, first strand: chain 'AF' and resid 210 through 215 removed outlier: 6.669A pdb=" N TRPAF 221 " --> pdb=" O GLNAF 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AF' and resid 237 through 238 removed outlier: 6.489A pdb=" N LEUAF 255 " --> pdb=" O LYSAF 245 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILEAF 247 " --> pdb=" O ARGAF 253 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARGAF 253 " --> pdb=" O ILEAF 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'XH' and resid 150 through 158 removed outlier: 5.777A pdb=" N LYSXH 150 " --> pdb=" O ALAXH 247 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASPXH 249 " --> pdb=" O LYSXH 150 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THRXH 152 " --> pdb=" O ASPXH 249 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARGXH 251 " --> pdb=" O THRXH 152 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N VALXH 176 " --> pdb=" O VALXH 248 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYRXH 250 " --> pdb=" O VALXH 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'XH' and resid 168 through 171 removed outlier: 5.996A pdb=" N ILEXH 169 " --> pdb=" O ILEXH 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BF' and resid 210 through 215 removed outlier: 6.714A pdb=" N TRPBF 221 " --> pdb=" O GLNBF 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BF' and resid 237 through 238 removed outlier: 6.495A pdb=" N LEUBF 255 " --> pdb=" O LYSBF 245 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILEBF 247 " --> pdb=" O ARGBF 253 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ARGBF 253 " --> pdb=" O ILEBF 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'YH' and resid 150 through 158 removed outlier: 5.747A pdb=" N LYSYH 150 " --> pdb=" O ALAYH 247 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASPYH 249 " --> pdb=" O LYSYH 150 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THRYH 152 " --> pdb=" O ASPYH 249 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARGYH 251 " --> pdb=" O THRYH 152 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N VALYH 176 " --> pdb=" O VALYH 248 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYRYH 250 " --> pdb=" O VALYH 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'YH' and resid 168 through 171 removed outlier: 6.016A pdb=" N ILEYH 169 " --> pdb=" O ILEYH 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'ZH' and resid 150 through 158 removed outlier: 5.733A pdb=" N LYSZH 150 " --> pdb=" O ALAZH 247 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASPZH 249 " --> pdb=" O LYSZH 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THRZH 152 " --> pdb=" O ASPZH 249 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARGZH 251 " --> pdb=" O THRZH 152 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N VALZH 176 " --> pdb=" O VALZH 248 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYRZH 250 " --> pdb=" O VALZH 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'ZH' and resid 168 through 171 removed outlier: 6.028A pdb=" N ILEZH 169 " --> pdb=" O ILEZH 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AX' and resid 23 through 25 Processing sheet with id=AB3, first strand: chain 'BX' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'CX' and resid 23 through 25 Processing sheet with id=AB5, first strand: chain 'DX' and resid 23 through 25 Processing sheet with id=AB6, first strand: chain 'EX' and resid 23 through 25 Processing sheet with id=AB7, first strand: chain 'FX' and resid 23 through 25 Processing sheet with id=AB8, first strand: chain 'GX' and resid 23 through 25 Processing sheet with id=AB9, first strand: chain 'HX' and resid 23 through 25 Processing sheet with id=AC1, first strand: chain 'IX' and resid 23 through 25 Processing sheet with id=AC2, first strand: chain 'JX' and resid 23 through 25 Processing sheet with id=AC3, first strand: chain 'KX' and resid 23 through 25 Processing sheet with id=AC4, first strand: chain 'LX' and resid 23 through 25 Processing sheet with id=AC5, first strand: chain 'MX' and resid 23 through 25 Processing sheet with id=AC6, first strand: chain 'VX' and resid 23 through 25 Processing sheet with id=AC7, first strand: chain 'WX' and resid 23 through 25 Processing sheet with id=AC8, first strand: chain 'XX' and resid 23 through 25 Processing sheet with id=AC9, first strand: chain 'YX' and resid 23 through 25 Processing sheet with id=AD1, first strand: chain 'ZX' and resid 23 through 25 Processing sheet with id=AD2, first strand: chain 'CF' and resid 210 through 215 removed outlier: 5.420A pdb=" N ILECF 212 " --> pdb=" O ILECF 223 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILECF 223 " --> pdb=" O ILECF 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'CF' and resid 237 through 238 removed outlier: 6.431A pdb=" N LEUCF 255 " --> pdb=" O LYSCF 245 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILECF 247 " --> pdb=" O ARGCF 253 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ARGCF 253 " --> pdb=" O ILECF 247 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'DF' and resid 210 through 215 removed outlier: 6.670A pdb=" N TRPDF 221 " --> pdb=" O GLNDF 213 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DF' and resid 237 through 238 removed outlier: 6.479A pdb=" N LEUDF 255 " --> pdb=" O LYSDF 245 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILEDF 247 " --> pdb=" O ARGDF 253 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ARGDF 253 " --> pdb=" O ILEDF 247 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'EF' and resid 210 through 215 removed outlier: 6.673A pdb=" N TRPEF 221 " --> pdb=" O GLNEF 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'EF' and resid 237 through 238 removed outlier: 6.454A pdb=" N LEUEF 255 " --> pdb=" O LYSEF 245 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILEEF 247 " --> pdb=" O ARGEF 253 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARGEF 253 " --> pdb=" O ILEEF 247 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'FF' and resid 210 through 215 removed outlier: 5.402A pdb=" N ILEFF 212 " --> pdb=" O ILEFF 223 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILEFF 223 " --> pdb=" O ILEFF 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'FF' and resid 237 through 238 removed outlier: 6.471A pdb=" N LEUFF 255 " --> pdb=" O LYSFF 245 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILEFF 247 " --> pdb=" O ARGFF 253 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARGFF 253 " --> pdb=" O ILEFF 247 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'GF' and resid 210 through 215 removed outlier: 6.722A pdb=" N TRPGF 221 " --> pdb=" O GLNGF 213 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'GF' and resid 237 through 238 removed outlier: 3.634A pdb=" N ARGGF 253 " --> pdb=" O ASPGF 248 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'HF' and resid 210 through 215 removed outlier: 5.434A pdb=" N ILEHF 212 " --> pdb=" O ILEHF 223 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILEHF 223 " --> pdb=" O ILEHF 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'HF' and resid 237 through 238 removed outlier: 6.492A pdb=" N LEUHF 255 " --> pdb=" O LYSHF 245 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILEHF 247 " --> pdb=" O ARGHF 253 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ARGHF 253 " --> pdb=" O ILEHF 247 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'IF' and resid 210 through 215 removed outlier: 5.451A pdb=" N ILEIF 212 " --> pdb=" O ILEIF 223 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILEIF 223 " --> pdb=" O ILEIF 212 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'IF' and resid 237 through 238 removed outlier: 6.515A pdb=" N LEUIF 255 " --> pdb=" O LYSIF 245 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILEIF 247 " --> pdb=" O ARGIF 253 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARGIF 253 " --> pdb=" O ILEIF 247 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'JF' and resid 210 through 215 removed outlier: 5.425A pdb=" N ILEJF 212 " --> pdb=" O ILEJF 223 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILEJF 223 " --> pdb=" O ILEJF 212 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'JF' and resid 237 through 238 removed outlier: 6.506A pdb=" N LEUJF 255 " --> pdb=" O LYSJF 245 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILEJF 247 " --> pdb=" O ARGJF 253 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARGJF 253 " --> pdb=" O ILEJF 247 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'KF' and resid 210 through 215 removed outlier: 6.670A pdb=" N TRPKF 221 " --> pdb=" O GLNKF 213 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'KF' and resid 237 through 238 removed outlier: 6.486A pdb=" N LEUKF 255 " --> pdb=" O LYSKF 245 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILEKF 247 " --> pdb=" O ARGKF 253 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ARGKF 253 " --> pdb=" O ILEKF 247 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LF' and resid 210 through 215 removed outlier: 5.426A pdb=" N ILELF 212 " --> pdb=" O ILELF 223 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILELF 223 " --> pdb=" O ILELF 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LF' and resid 237 through 238 removed outlier: 6.469A pdb=" N LEULF 255 " --> pdb=" O LYSLF 245 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILELF 247 " --> pdb=" O ARGLF 253 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARGLF 253 " --> pdb=" O ILELF 247 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'MF' and resid 210 through 215 removed outlier: 6.674A pdb=" N TRPMF 221 " --> pdb=" O GLNMF 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'MF' and resid 237 through 238 removed outlier: 6.527A pdb=" N LEUMF 255 " --> pdb=" O LYSMF 245 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILEMF 247 " --> pdb=" O ARGMF 253 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARGMF 253 " --> pdb=" O ILEMF 247 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'VF' and resid 210 through 215 removed outlier: 5.418A pdb=" N ILEVF 212 " --> pdb=" O ILEVF 223 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILEVF 223 " --> pdb=" O ILEVF 212 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'VF' and resid 237 through 238 removed outlier: 6.501A pdb=" N LEUVF 255 " --> pdb=" O LYSVF 245 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILEVF 247 " --> pdb=" O ARGVF 253 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ARGVF 253 " --> pdb=" O ILEVF 247 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'WF' and resid 210 through 215 removed outlier: 6.673A pdb=" N TRPWF 221 " --> pdb=" O GLNWF 213 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'WF' and resid 237 through 238 removed outlier: 6.539A pdb=" N LEUWF 255 " --> pdb=" O LYSWF 245 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILEWF 247 " --> pdb=" O ARGWF 253 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ARGWF 253 " --> pdb=" O ILEWF 247 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'XF' and resid 210 through 215 removed outlier: 6.712A pdb=" N TRPXF 221 " --> pdb=" O GLNXF 213 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'XF' and resid 237 through 238 removed outlier: 6.480A pdb=" N LEUXF 255 " --> pdb=" O LYSXF 245 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILEXF 247 " --> pdb=" O ARGXF 253 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ARGXF 253 " --> pdb=" O ILEXF 247 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'YF' and resid 210 through 215 removed outlier: 6.667A pdb=" N TRPYF 221 " --> pdb=" O GLNYF 213 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'YF' and resid 237 through 238 removed outlier: 6.441A pdb=" N LEUYF 255 " --> pdb=" O LYSYF 245 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILEYF 247 " --> pdb=" O ARGYF 253 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARGYF 253 " --> pdb=" O ILEYF 247 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'ZF' and resid 210 through 215 removed outlier: 6.725A pdb=" N TRPZF 221 " --> pdb=" O GLNZF 213 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'ZF' and resid 237 through 238 removed outlier: 3.647A pdb=" N ARGZF 253 " --> pdb=" O ASPZF 248 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'BG' and resid 819 through 822 removed outlier: 6.038A pdb=" N ILEAH 169 " --> pdb=" O ILEAH 242 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'CG' and resid 819 through 822 removed outlier: 5.993A pdb=" N ILEBH 169 " --> pdb=" O ILEBH 242 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'DG' and resid 819 through 822 removed outlier: 6.031A pdb=" N ILEVH 169 " --> pdb=" O ILEVH 242 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'EG' and resid 819 through 822 removed outlier: 6.012A pdb=" N ILEDH 169 " --> pdb=" O ILEDH 242 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'FG' and resid 819 through 822 removed outlier: 6.021A pdb=" N ILEEH 169 " --> pdb=" O ILEEH 242 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'GG' and resid 819 through 822 removed outlier: 5.983A pdb=" N ILEWH 169 " --> pdb=" O ILEWH 242 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'HG' and resid 819 through 822 removed outlier: 6.018A pdb=" N ILEGH 169 " --> pdb=" O ILEGH 242 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'JG' and resid 819 through 822 removed outlier: 5.995A pdb=" N ILEIH 169 " --> pdb=" O ILEIH 242 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'KG' and resid 819 through 822 removed outlier: 6.032A pdb=" N ILEJH 169 " --> pdb=" O ILEJH 242 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'MG' and resid 819 through 822 removed outlier: 6.027A pdb=" N ILELH 169 " --> pdb=" O ILELH 242 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'VG' and resid 819 through 822 removed outlier: 6.008A pdb=" N ILECH 169 " --> pdb=" O ILECH 242 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'WG' and resid 819 through 822 removed outlier: 6.015A pdb=" N ILEFH 169 " --> pdb=" O ILEFH 242 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'XG' and resid 819 through 822 removed outlier: 6.040A pdb=" N ILEHH 169 " --> pdb=" O ILEHH 242 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'YG' and resid 819 through 822 removed outlier: 6.008A pdb=" N ILEKH 169 " --> pdb=" O ILEKH 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'ZG' and resid 819 through 822 Processing sheet with id=AI4, first strand: chain 'AH' and resid 150 through 158 removed outlier: 5.775A pdb=" N LYSAH 150 " --> pdb=" O ALAAH 247 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASPAH 249 " --> pdb=" O LYSAH 150 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THRAH 152 " --> pdb=" O ASPAH 249 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARGAH 251 " --> pdb=" O THRAH 152 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N VALAH 176 " --> pdb=" O VALAH 248 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYRAH 250 " --> pdb=" O VALAH 176 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'BH' and resid 150 through 158 removed outlier: 5.778A pdb=" N LYSBH 150 " --> pdb=" O ALABH 247 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASPBH 249 " --> pdb=" O LYSBH 150 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THRBH 152 " --> pdb=" O ASPBH 249 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARGBH 251 " --> pdb=" O THRBH 152 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N VALBH 176 " --> pdb=" O VALBH 248 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYRBH 250 " --> pdb=" O VALBH 176 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'CH' and resid 150 through 158 removed outlier: 5.783A pdb=" N LYSCH 150 " --> pdb=" O ALACH 247 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASPCH 249 " --> pdb=" O LYSCH 150 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THRCH 152 " --> pdb=" O ASPCH 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARGCH 251 " --> pdb=" O THRCH 152 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N VALCH 176 " --> pdb=" O VALCH 248 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TYRCH 250 " --> pdb=" O VALCH 176 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'DH' and resid 150 through 158 removed outlier: 5.801A pdb=" N LYSDH 150 " --> pdb=" O ALADH 247 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASPDH 249 " --> pdb=" O LYSDH 150 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THRDH 152 " --> pdb=" O ASPDH 249 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARGDH 251 " --> pdb=" O THRDH 152 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N VALDH 176 " --> pdb=" O VALDH 248 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYRDH 250 " --> pdb=" O VALDH 176 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'EH' and resid 150 through 158 removed outlier: 5.747A pdb=" N LYSEH 150 " --> pdb=" O ALAEH 247 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASPEH 249 " --> pdb=" O LYSEH 150 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THREH 152 " --> pdb=" O ASPEH 249 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARGEH 251 " --> pdb=" O THREH 152 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N VALEH 176 " --> pdb=" O VALEH 248 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYREH 250 " --> pdb=" O VALEH 176 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'FH' and resid 150 through 158 removed outlier: 5.803A pdb=" N LYSFH 150 " --> pdb=" O ALAFH 247 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASPFH 249 " --> pdb=" O LYSFH 150 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THRFH 152 " --> pdb=" O ASPFH 249 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARGFH 251 " --> pdb=" O THRFH 152 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N VALFH 176 " --> pdb=" O VALFH 248 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYRFH 250 " --> pdb=" O VALFH 176 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'GH' and resid 150 through 158 removed outlier: 5.755A pdb=" N LYSGH 150 " --> pdb=" O ALAGH 247 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASPGH 249 " --> pdb=" O LYSGH 150 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THRGH 152 " --> pdb=" O ASPGH 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARGGH 251 " --> pdb=" O THRGH 152 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N VALGH 176 " --> pdb=" O VALGH 248 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYRGH 250 " --> pdb=" O VALGH 176 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'HH' and resid 150 through 158 removed outlier: 5.776A pdb=" N LYSHH 150 " --> pdb=" O ALAHH 247 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASPHH 249 " --> pdb=" O LYSHH 150 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THRHH 152 " --> pdb=" O ASPHH 249 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARGHH 251 " --> pdb=" O THRHH 152 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VALHH 176 " --> pdb=" O VALHH 248 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYRHH 250 " --> pdb=" O VALHH 176 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'IH' and resid 150 through 158 removed outlier: 5.784A pdb=" N LYSIH 150 " --> pdb=" O ALAIH 247 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASPIH 249 " --> pdb=" O LYSIH 150 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THRIH 152 " --> pdb=" O ASPIH 249 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGIH 251 " --> pdb=" O THRIH 152 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N VALIH 176 " --> pdb=" O VALIH 248 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYRIH 250 " --> pdb=" O VALIH 176 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'JH' and resid 150 through 158 removed outlier: 5.756A pdb=" N LYSJH 150 " --> pdb=" O ALAJH 247 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASPJH 249 " --> pdb=" O LYSJH 150 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THRJH 152 " --> pdb=" O ASPJH 249 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARGJH 251 " --> pdb=" O THRJH 152 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VALJH 176 " --> pdb=" O VALJH 248 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYRJH 250 " --> pdb=" O VALJH 176 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'KH' and resid 150 through 158 removed outlier: 5.777A pdb=" N LYSKH 150 " --> pdb=" O ALAKH 247 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASPKH 249 " --> pdb=" O LYSKH 150 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THRKH 152 " --> pdb=" O ASPKH 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARGKH 251 " --> pdb=" O THRKH 152 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N VALKH 176 " --> pdb=" O VALKH 248 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYRKH 250 " --> pdb=" O VALKH 176 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'LH' and resid 150 through 158 removed outlier: 5.797A pdb=" N LYSLH 150 " --> pdb=" O ALALH 247 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASPLH 249 " --> pdb=" O LYSLH 150 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THRLH 152 " --> pdb=" O ASPLH 249 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARGLH 251 " --> pdb=" O THRLH 152 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N VALLH 176 " --> pdb=" O VALLH 248 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TYRLH 250 " --> pdb=" O VALLH 176 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'MH' and resid 150 through 158 removed outlier: 5.778A pdb=" N LYSMH 150 " --> pdb=" O ALAMH 247 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASPMH 249 " --> pdb=" O LYSMH 150 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THRMH 152 " --> pdb=" O ASPMH 249 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARGMH 251 " --> pdb=" O THRMH 152 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N VALMH 176 " --> pdb=" O VALMH 248 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYRMH 250 " --> pdb=" O VALMH 176 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'VH' and resid 150 through 158 removed outlier: 5.752A pdb=" N LYSVH 150 " --> pdb=" O ALAVH 247 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASPVH 249 " --> pdb=" O LYSVH 150 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THRVH 152 " --> pdb=" O ASPVH 249 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARGVH 251 " --> pdb=" O THRVH 152 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N VALVH 176 " --> pdb=" O VALVH 248 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYRVH 250 " --> pdb=" O VALVH 176 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'WH' and resid 150 through 158 removed outlier: 5.778A pdb=" N LYSWH 150 " --> pdb=" O ALAWH 247 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASPWH 249 " --> pdb=" O LYSWH 150 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THRWH 152 " --> pdb=" O ASPWH 249 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARGWH 251 " --> pdb=" O THRWH 152 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N VALWH 176 " --> pdb=" O VALWH 248 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYRWH 250 " --> pdb=" O VALWH 176 " (cutoff:3.500A) 1803 hydrogen bonds defined for protein. 5031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.09 Time building geometry restraints manager: 15.21 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: 13279 1.34 - 1.46: 7707 1.46 - 1.58: 19784 1.58 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 40950 Sorted by residual: bond pdb=" CB GLNHG 796 " pdb=" CG GLNHG 796 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" CG GLNHG 796 " pdb=" CD GLNHG 796 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.53e+00 bond pdb=" CB ASPZH 183 " pdb=" CG ASPZH 183 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.06e+00 bond pdb=" CB ASPFH 183 " pdb=" CG ASPFH 183 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CB ASPWH 183 " pdb=" CG ASPWH 183 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.90e+00 ... (remaining 40945 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.63: 1370 106.63 - 113.48: 22397 113.48 - 120.34: 14406 120.34 - 127.19: 17272 127.19 - 134.05: 373 Bond angle restraints: 55818 Sorted by residual: angle pdb=" CB METZH 115 " pdb=" CG METZH 115 " pdb=" SD METZH 115 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CB GLNHG 796 " pdb=" CG GLNHG 796 " pdb=" CD GLNHG 796 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.70e+00 3.46e-01 1.54e+01 angle pdb=" CA METZH 115 " pdb=" CB METZH 115 " pdb=" CG METZH 115 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N GLUBH 105 " pdb=" CA GLUBH 105 " pdb=" C GLUBH 105 " ideal model delta sigma weight residual 114.04 110.02 4.02 1.24e+00 6.50e-01 1.05e+01 angle pdb=" CB GLNXG 796 " pdb=" CG GLNXG 796 " pdb=" CD GLNXG 796 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.70e+00 3.46e-01 1.05e+01 ... (remaining 55813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 22782 17.79 - 35.59: 1588 35.59 - 53.38: 275 53.38 - 71.18: 59 71.18 - 88.97: 82 Dihedral angle restraints: 24786 sinusoidal: 8874 harmonic: 15912 Sorted by residual: dihedral pdb=" CA ASPZH 207 " pdb=" C ASPZH 207 " pdb=" N LYSZH 208 " pdb=" CA LYSZH 208 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASPWH 207 " pdb=" C ASPWH 207 " pdb=" N LYSWH 208 " pdb=" CA LYSWH 208 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASPGH 207 " pdb=" C ASPGH 207 " pdb=" N LYSGH 208 " pdb=" CA LYSGH 208 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 24783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4394 0.040 - 0.080: 1402 0.080 - 0.120: 636 0.120 - 0.161: 145 0.161 - 0.201: 29 Chirality restraints: 6606 Sorted by residual: chirality pdb=" CA ASPGH 183 " pdb=" N ASPGH 183 " pdb=" C ASPGH 183 " pdb=" CB ASPGH 183 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASPZH 183 " pdb=" N ASPZH 183 " pdb=" C ASPZH 183 " pdb=" CB ASPZH 183 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA ASPWH 183 " pdb=" N ASPWH 183 " pdb=" C ASPWH 183 " pdb=" CB ASPWH 183 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 6603 not shown) Planarity restraints: 7218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILEFF 216 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PROFF 217 " 0.110 5.00e-02 4.00e+02 pdb=" CA PROFF 217 " -0.033 5.00e-02 4.00e+02 pdb=" CD PROFF 217 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILELF 216 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PROLF 217 " -0.110 5.00e-02 4.00e+02 pdb=" CA PROLF 217 " 0.032 5.00e-02 4.00e+02 pdb=" CD PROLF 217 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEYF 216 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PROYF 217 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROYF 217 " 0.032 5.00e-02 4.00e+02 pdb=" CD PROYF 217 " 0.035 5.00e-02 4.00e+02 ... (remaining 7215 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 13234 2.86 - 3.37: 31493 3.37 - 3.88: 62662 3.88 - 4.39: 70093 4.39 - 4.90: 124796 Nonbonded interactions: 302278 Sorted by model distance: nonbonded pdb=" O SERJF 269 " pdb=" OG SERJF 269 " model vdw 2.345 2.440 nonbonded pdb=" O SERVF 269 " pdb=" OG SERVF 269 " model vdw 2.346 2.440 nonbonded pdb=" O SERBF 269 " pdb=" OG SERBF 269 " model vdw 2.346 2.440 nonbonded pdb=" O SERLF 269 " pdb=" OG SERLF 269 " model vdw 2.347 2.440 nonbonded pdb=" O SERWF 269 " pdb=" OG SERWF 269 " model vdw 2.347 2.440 ... (remaining 302273 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 'AF' selection = chain 'BF' selection = chain 'CF' selection = chain 'DF' selection = chain 'EF' selection = chain 'FF' selection = chain 'GF' selection = chain 'HF' selection = chain 'IF' selection = chain 'JF' selection = chain 'KF' selection = chain 'LF' selection = chain 'MF' selection = chain 'VF' selection = chain 'WF' selection = chain 'XF' selection = chain 'YF' selection = chain 'ZF' } ncs_group { reference = chain 'AG' selection = chain 'BG' selection = chain 'CG' selection = chain 'DG' selection = chain 'EG' selection = chain 'FG' selection = chain 'GG' selection = chain 'HG' selection = chain 'IG' selection = chain 'JG' selection = chain 'KG' selection = chain 'LG' selection = chain 'MG' selection = chain 'VG' selection = chain 'WG' selection = chain 'XG' selection = chain 'YG' selection = chain 'ZG' } ncs_group { reference = chain 'AH' selection = chain 'BH' selection = chain 'CH' selection = chain 'DH' selection = chain 'EH' selection = chain 'FH' selection = chain 'GH' selection = chain 'HH' selection = chain 'IH' selection = chain 'JH' selection = chain 'KH' selection = chain 'LH' selection = chain 'MH' selection = chain 'VH' selection = chain 'WH' selection = chain 'XH' selection = chain 'YH' selection = chain 'ZH' } ncs_group { reference = chain 'AX' selection = chain 'BX' selection = chain 'CX' selection = chain 'DX' selection = chain 'EX' selection = chain 'FX' selection = chain 'GX' selection = chain 'HX' selection = chain 'IX' selection = chain 'JX' selection = chain 'KX' selection = chain 'LX' selection = chain 'MX' selection = chain 'VX' selection = chain 'WX' selection = chain 'XX' selection = chain 'YX' selection = chain 'ZX' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 28.650 Check model and map are aligned: 0.690 Set scattering table: 0.380 Process input model: 99.340 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.650 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.004 0.052 40950 Z= 0.228 Angle : 0.777 11.833 55818 Z= 0.395 Chirality : 0.050 0.201 6606 Planarity : 0.007 0.072 7218 Dihedral : 13.972 88.974 14490 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.29 (0.12), residues: 4518 helix: -3.30 (0.07), residues: 1026 sheet: 0.95 (0.15), residues: 1224 loop : -0.59 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPMH 206 PHE 0.008 0.001 PHEVF 264 TYR 0.011 0.001 TYRBH 194 ARG 0.017 0.001 ARGKH 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1012 time to evaluate : 4.867 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: XH 110 LYS cc_start: 0.8496 (tptm) cc_final: 0.8255 (mmmm) REVERT: XH 114 ASP cc_start: 0.8273 (m-30) cc_final: 0.7867 (m-30) REVERT: XH 118 ASN cc_start: 0.8668 (m110) cc_final: 0.8457 (m-40) REVERT: XH 238 MET cc_start: 0.9207 (mmm) cc_final: 0.8604 (mmm) REVERT: YH 125 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7884 (tm-30) REVERT: ZH 110 LYS cc_start: 0.8485 (tptm) cc_final: 0.8095 (mmmm) REVERT: ZH 114 ASP cc_start: 0.8112 (m-30) cc_final: 0.7625 (m-30) REVERT: GF 225 SER cc_start: 0.8950 (m) cc_final: 0.8560 (p) REVERT: HF 255 LEU cc_start: 0.8986 (mm) cc_final: 0.8785 (mm) REVERT: JF 263 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8593 (mtpp) REVERT: ZF 225 SER cc_start: 0.8947 (m) cc_final: 0.8585 (p) REVERT: BG 792 GLN cc_start: 0.8057 (tp40) cc_final: 0.7749 (tm-30) REVERT: DG 813 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8588 (mmtp) REVERT: JG 792 GLN cc_start: 0.7999 (tp40) cc_final: 0.7792 (tm-30) REVERT: JG 807 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8360 (tp-100) REVERT: VG 807 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8365 (tp-100) REVERT: WG 792 GLN cc_start: 0.7895 (tp40) cc_final: 0.7591 (tm-30) REVERT: YG 802 LEU cc_start: 0.8844 (tp) cc_final: 0.8634 (tp) REVERT: AH 109 LYS cc_start: 0.8459 (mppt) cc_final: 0.8166 (mppt) REVERT: AH 110 LYS cc_start: 0.8389 (tptm) cc_final: 0.8131 (mmmm) REVERT: AH 114 ASP cc_start: 0.8253 (m-30) cc_final: 0.8012 (m-30) REVERT: BH 110 LYS cc_start: 0.8498 (tptm) cc_final: 0.8228 (mmmm) REVERT: BH 114 ASP cc_start: 0.8259 (m-30) cc_final: 0.7843 (m-30) REVERT: BH 118 ASN cc_start: 0.8663 (m110) cc_final: 0.8457 (m-40) REVERT: CH 109 LYS cc_start: 0.8427 (mppt) cc_final: 0.8132 (mppt) REVERT: DH 109 LYS cc_start: 0.8398 (mppt) cc_final: 0.8008 (mppt) REVERT: EH 109 LYS cc_start: 0.8463 (mppt) cc_final: 0.8157 (mppt) REVERT: FH 118 ASN cc_start: 0.8631 (m110) cc_final: 0.8403 (m-40) REVERT: FH 135 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8517 (mt-10) REVERT: HH 109 LYS cc_start: 0.8470 (mppt) cc_final: 0.8174 (mppt) REVERT: HH 110 LYS cc_start: 0.8389 (tptm) cc_final: 0.7910 (mmmm) REVERT: HH 114 ASP cc_start: 0.8251 (m-30) cc_final: 0.7936 (m-30) REVERT: IH 109 LYS cc_start: 0.8498 (mppt) cc_final: 0.8197 (mppt) REVERT: IH 113 LYS cc_start: 0.8429 (mptt) cc_final: 0.8219 (mmtm) REVERT: JH 109 LYS cc_start: 0.8550 (mppt) cc_final: 0.8219 (mppt) REVERT: KH 109 LYS cc_start: 0.8468 (mppt) cc_final: 0.8227 (mppt) REVERT: LH 109 LYS cc_start: 0.8438 (mppt) cc_final: 0.8134 (mppt) REVERT: LH 114 ASP cc_start: 0.8096 (m-30) cc_final: 0.7801 (m-30) REVERT: LH 118 ASN cc_start: 0.8626 (m110) cc_final: 0.8409 (m-40) REVERT: LH 135 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8513 (mt-10) outliers start: 0 outliers final: 12 residues processed: 1012 average time/residue: 1.8809 time to fit residues: 2227.1632 Evaluate side-chains 910 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 898 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AF residue 248 ASP Chi-restraints excluded: chain DF residue 248 ASP Chi-restraints excluded: chain FF residue 248 ASP Chi-restraints excluded: chain GF residue 248 ASP Chi-restraints excluded: chain JF residue 248 ASP Chi-restraints excluded: chain KF residue 248 ASP Chi-restraints excluded: chain LF residue 248 ASP Chi-restraints excluded: chain MF residue 248 ASP Chi-restraints excluded: chain VF residue 248 ASP Chi-restraints excluded: chain WF residue 248 ASP Chi-restraints excluded: chain YF residue 248 ASP Chi-restraints excluded: chain ZF residue 248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 440 optimal weight: 1.9990 chunk 395 optimal weight: 0.0980 chunk 219 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 266 optimal weight: 0.4980 chunk 211 optimal weight: 2.9990 chunk 409 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 474 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AF 226 ASN BF 226 ASN BF 260 GLN CF 226 ASN EF 266 GLN FF 226 ASN FF 260 GLN GF 226 ASN IF 226 ASN LF 226 ASN LF 266 GLN XF 226 ASN YF 266 GLN ZF 226 ASN BG 810 GLN DG 810 GLN DG 814 GLN KG 810 GLN KG 814 GLN XG 810 GLN AH 159 ASN DH 118 ASN HH 159 ASN IH 118 ASN KH 118 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40950 Z= 0.189 Angle : 0.578 6.926 55818 Z= 0.297 Chirality : 0.042 0.158 6606 Planarity : 0.005 0.043 7218 Dihedral : 6.595 113.851 5838 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 10.76 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.12), residues: 4518 helix: 1.19 (0.15), residues: 1026 sheet: 0.88 (0.14), residues: 1224 loop : -0.36 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPJF 221 PHE 0.007 0.001 PHEJF 264 TYR 0.010 0.001 TYRLH 194 ARG 0.008 0.001 ARGHH 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 879 time to evaluate : 4.768 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: AF 248 ASP cc_start: 0.8721 (t0) cc_final: 0.8403 (t0) REVERT: XH 114 ASP cc_start: 0.8201 (m-30) cc_final: 0.7975 (m-30) REVERT: BF 243 MET cc_start: 0.7880 (tpp) cc_final: 0.7622 (mmm) REVERT: YH 110 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8461 (mmmm) REVERT: ZH 114 ASP cc_start: 0.8033 (m-30) cc_final: 0.7830 (m-30) REVERT: CF 233 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8104 (ptt-90) REVERT: CF 237 LYS cc_start: 0.8360 (mmpt) cc_final: 0.7652 (mptt) REVERT: CF 248 ASP cc_start: 0.8724 (t0) cc_final: 0.8354 (t0) REVERT: DF 248 ASP cc_start: 0.8806 (t0) cc_final: 0.8548 (t0) REVERT: EF 248 ASP cc_start: 0.8715 (t0) cc_final: 0.8450 (t0) REVERT: FF 248 ASP cc_start: 0.8659 (t0) cc_final: 0.8306 (t0) REVERT: GF 225 SER cc_start: 0.8906 (m) cc_final: 0.8542 (p) REVERT: GF 248 ASP cc_start: 0.8745 (t0) cc_final: 0.8456 (t0) REVERT: HF 243 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7585 (mmm) REVERT: HF 248 ASP cc_start: 0.8761 (t0) cc_final: 0.8471 (t0) REVERT: IF 233 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8085 (ptt-90) REVERT: IF 237 LYS cc_start: 0.8360 (mmpt) cc_final: 0.7651 (mptt) REVERT: IF 245 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8564 (mmmm) REVERT: IF 248 ASP cc_start: 0.8692 (t0) cc_final: 0.8371 (t0) REVERT: JF 248 ASP cc_start: 0.8792 (t0) cc_final: 0.8468 (t0) REVERT: KF 248 ASP cc_start: 0.8802 (t0) cc_final: 0.8549 (t0) REVERT: LF 248 ASP cc_start: 0.8642 (t0) cc_final: 0.8252 (t0) REVERT: MF 248 ASP cc_start: 0.8572 (t0) cc_final: 0.8225 (t0) REVERT: VF 248 ASP cc_start: 0.8779 (t0) cc_final: 0.8459 (t0) REVERT: WF 248 ASP cc_start: 0.8565 (t0) cc_final: 0.8224 (t0) REVERT: XF 243 MET cc_start: 0.7838 (tpp) cc_final: 0.7621 (mmm) REVERT: YF 243 MET cc_start: 0.7829 (mmm) cc_final: 0.7590 (tpp) REVERT: ZF 209 ILE cc_start: 0.9174 (mm) cc_final: 0.8888 (mt) REVERT: ZF 248 ASP cc_start: 0.8762 (t0) cc_final: 0.8477 (t0) REVERT: EG 801 MET cc_start: 0.8589 (mtt) cc_final: 0.8325 (mtt) REVERT: KG 800 ASP cc_start: 0.8234 (m-30) cc_final: 0.8031 (m-30) REVERT: WG 796 GLN cc_start: 0.7982 (tp40) cc_final: 0.7605 (tp40) REVERT: WG 800 ASP cc_start: 0.7983 (m-30) cc_final: 0.7730 (m-30) REVERT: ZG 813 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8506 (mmtp) REVERT: AH 114 ASP cc_start: 0.8161 (m-30) cc_final: 0.7778 (m-30) REVERT: BH 114 ASP cc_start: 0.8235 (m-30) cc_final: 0.7960 (m-30) REVERT: DH 114 ASP cc_start: 0.7941 (m-30) cc_final: 0.7685 (m-30) REVERT: FH 118 ASN cc_start: 0.8395 (m110) cc_final: 0.8077 (m-40) REVERT: GH 115 MET cc_start: 0.9080 (tmm) cc_final: 0.8867 (tmm) REVERT: HH 114 ASP cc_start: 0.8221 (m-30) cc_final: 0.7866 (m-30) REVERT: IH 113 LYS cc_start: 0.8493 (mptt) cc_final: 0.8049 (mmtm) REVERT: MH 208 LYS cc_start: 0.8769 (mptm) cc_final: 0.8463 (mptt) REVERT: VH 114 ASP cc_start: 0.8231 (m-30) cc_final: 0.8014 (m-30) REVERT: VH 255 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7884 (mmt-90) REVERT: WH 208 LYS cc_start: 0.8780 (mptm) cc_final: 0.8481 (mptt) outliers start: 58 outliers final: 11 residues processed: 888 average time/residue: 1.7333 time to fit residues: 1812.9849 Evaluate side-chains 841 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 826 time to evaluate : 4.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain DF residue 243 MET Chi-restraints excluded: chain GF residue 243 MET Chi-restraints excluded: chain HF residue 243 MET Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 245 LYS Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain JH residue 169 ILE Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain VH residue 169 ILE Chi-restraints excluded: chain WH residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 394 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 474 optimal weight: 1.9990 chunk 513 optimal weight: 2.9990 chunk 422 optimal weight: 0.9990 chunk 470 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 380 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: YH 118 ASN ZH 118 ASN EF 266 GLN HF 226 ASN WF 226 ASN YF 266 GLN BG 791 GLN CG 796 GLN DG 814 GLN KG 814 GLN XG 814 GLN YG 807 GLN YG 810 GLN EH 118 ASN JH 118 ASN KH 118 ASN MH 118 ASN VH 118 ASN WH 118 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 40950 Z= 0.240 Angle : 0.574 6.940 55818 Z= 0.294 Chirality : 0.043 0.159 6606 Planarity : 0.005 0.037 7218 Dihedral : 4.298 18.727 5814 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.86 % Allowed : 14.35 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.13), residues: 4518 helix: 2.79 (0.16), residues: 1026 sheet: 0.65 (0.14), residues: 1260 loop : -0.34 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPZH 206 PHE 0.010 0.001 PHELF 264 TYR 0.010 0.001 TYRAF 241 ARG 0.008 0.001 ARGJH 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 839 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8756 (t0) cc_final: 0.8468 (t0) REVERT: XH 114 ASP cc_start: 0.8206 (m-30) cc_final: 0.7952 (m-30) REVERT: XH 214 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: BF 233 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8065 (ptp90) REVERT: ZH 114 ASP cc_start: 0.8150 (m-30) cc_final: 0.7948 (m-30) REVERT: CF 233 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8170 (ptt-90) REVERT: CF 245 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8708 (mmmm) REVERT: CF 248 ASP cc_start: 0.8771 (t0) cc_final: 0.8499 (t0) REVERT: DF 237 LYS cc_start: 0.8524 (mptt) cc_final: 0.7825 (mptt) REVERT: DF 248 ASP cc_start: 0.8795 (t0) cc_final: 0.8417 (t0) REVERT: EF 248 ASP cc_start: 0.8736 (t0) cc_final: 0.8483 (t0) REVERT: FF 248 ASP cc_start: 0.8663 (t0) cc_final: 0.8343 (t0) REVERT: GF 225 SER cc_start: 0.8923 (m) cc_final: 0.8607 (p) REVERT: GF 237 LYS cc_start: 0.8462 (mmpt) cc_final: 0.8179 (mptt) REVERT: GF 248 ASP cc_start: 0.8694 (t0) cc_final: 0.8209 (t0) REVERT: HF 225 SER cc_start: 0.8900 (m) cc_final: 0.8628 (p) REVERT: HF 243 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7656 (mmm) REVERT: HF 248 ASP cc_start: 0.8761 (t0) cc_final: 0.8475 (t0) REVERT: IF 233 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8164 (ptt-90) REVERT: IF 245 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8705 (mmmm) REVERT: IF 248 ASP cc_start: 0.8764 (t0) cc_final: 0.8491 (t0) REVERT: JF 225 SER cc_start: 0.8787 (m) cc_final: 0.8370 (p) REVERT: JF 248 ASP cc_start: 0.8795 (t0) cc_final: 0.8389 (t0) REVERT: KF 248 ASP cc_start: 0.8787 (t0) cc_final: 0.8439 (t0) REVERT: LF 248 ASP cc_start: 0.8671 (t0) cc_final: 0.8339 (t0) REVERT: MF 248 ASP cc_start: 0.8678 (t0) cc_final: 0.8210 (t0) REVERT: VF 248 ASP cc_start: 0.8810 (t0) cc_final: 0.8479 (t0) REVERT: WF 248 ASP cc_start: 0.8674 (t0) cc_final: 0.8254 (t0) REVERT: XF 233 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8046 (ptp90) REVERT: YF 248 ASP cc_start: 0.8683 (t0) cc_final: 0.8402 (t0) REVERT: ZF 237 LYS cc_start: 0.8476 (mmpt) cc_final: 0.8142 (mptt) REVERT: ZF 248 ASP cc_start: 0.8648 (t0) cc_final: 0.8168 (t0) REVERT: EG 801 MET cc_start: 0.8553 (mtt) cc_final: 0.8286 (mtt) REVERT: EG 822 GLU cc_start: 0.7828 (tp30) cc_final: 0.7611 (tt0) REVERT: GG 813 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8677 (mmtp) REVERT: WG 800 ASP cc_start: 0.7958 (m-30) cc_final: 0.7723 (m-30) REVERT: AH 114 ASP cc_start: 0.8130 (m-30) cc_final: 0.7806 (m-30) REVERT: AH 125 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7974 (tm-30) REVERT: BH 114 ASP cc_start: 0.8222 (m-30) cc_final: 0.7982 (m-30) REVERT: BH 214 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: EH 219 LYS cc_start: 0.9005 (mttp) cc_final: 0.8774 (mmtp) REVERT: GH 109 LYS cc_start: 0.7992 (mppt) cc_final: 0.7614 (mppt) REVERT: HH 114 ASP cc_start: 0.8180 (m-30) cc_final: 0.7803 (m-30) REVERT: IH 109 LYS cc_start: 0.8000 (mppt) cc_final: 0.7679 (mttp) REVERT: IH 113 LYS cc_start: 0.8510 (mptt) cc_final: 0.8052 (mmtm) REVERT: IH 129 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8555 (mtmt) REVERT: IH 239 LEU cc_start: 0.8848 (mm) cc_final: 0.8646 (mm) REVERT: KH 110 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8071 (mmmm) REVERT: KH 114 ASP cc_start: 0.7988 (m-30) cc_final: 0.7684 (m-30) REVERT: LH 113 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8170 (mmtm) REVERT: MH 109 LYS cc_start: 0.7906 (mppt) cc_final: 0.7663 (mppt) REVERT: VH 114 ASP cc_start: 0.8251 (m-30) cc_final: 0.8034 (m-30) outliers start: 74 outliers final: 30 residues processed: 865 average time/residue: 1.7947 time to fit residues: 1824.3275 Evaluate side-chains 856 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 817 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 214 MET Chi-restraints excluded: chain BF residue 233 ARG Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 245 LYS Chi-restraints excluded: chain EF residue 246 LEU Chi-restraints excluded: chain HF residue 223 ILE Chi-restraints excluded: chain HF residue 243 MET Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 245 LYS Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain XF residue 233 ARG Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain BG residue 813 LYS Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain LG residue 799 SER Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 169 ILE Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain BH residue 214 MET Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain WH residue 144 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 469 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 226 optimal weight: 0.9980 chunk 318 optimal weight: 0.0570 chunk 476 optimal weight: 0.5980 chunk 504 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 451 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AF 226 ASN YH 118 ASN EF 266 GLN HF 266 GLN YF 266 GLN ZF 226 ASN DG 807 GLN DG 810 GLN DG 814 GLN KG 807 GLN KG 810 GLN KG 814 GLN EH 118 ASN FH 118 ASN JH 118 ASN KH 118 ASN MH 118 ASN VH 118 ASN WH 118 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 40950 Z= 0.157 Angle : 0.504 7.628 55818 Z= 0.255 Chirality : 0.042 0.159 6606 Planarity : 0.004 0.037 7218 Dihedral : 3.983 18.179 5814 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.71 % Allowed : 17.67 % Favored : 80.62 % 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: 1.35 (0.13), residues: 4518 helix: 3.40 (0.15), residues: 1026 sheet: 0.98 (0.14), residues: 1224 loop : -0.34 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPJF 221 PHE 0.007 0.001 PHEJF 264 TYR 0.010 0.001 TYRAH 194 ARG 0.009 0.000 ARGJH 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 844 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8727 (t0) cc_final: 0.8453 (t0) REVERT: XH 114 ASP cc_start: 0.8176 (m-30) cc_final: 0.7919 (m-30) REVERT: XH 214 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: CF 233 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8754 (t0) cc_final: 0.8494 (t0) REVERT: DF 248 ASP cc_start: 0.8775 (t0) cc_final: 0.8394 (t0) REVERT: FF 248 ASP cc_start: 0.8633 (t0) cc_final: 0.8314 (t0) REVERT: GF 225 SER cc_start: 0.8817 (m) cc_final: 0.8450 (p) REVERT: GF 248 ASP cc_start: 0.8597 (t0) cc_final: 0.8120 (t0) REVERT: HF 225 SER cc_start: 0.8885 (m) cc_final: 0.8625 (p) REVERT: HF 243 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7615 (mmm) REVERT: HF 248 ASP cc_start: 0.8739 (t0) cc_final: 0.8355 (t0) REVERT: IF 233 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8728 (t0) cc_final: 0.8478 (t0) REVERT: JF 225 SER cc_start: 0.8777 (m) cc_final: 0.8385 (p) REVERT: JF 248 ASP cc_start: 0.8760 (t0) cc_final: 0.8367 (t0) REVERT: KF 248 ASP cc_start: 0.8773 (t0) cc_final: 0.8352 (t0) REVERT: LF 248 ASP cc_start: 0.8632 (t0) cc_final: 0.8308 (t0) REVERT: MF 248 ASP cc_start: 0.8574 (t0) cc_final: 0.8164 (t0) REVERT: VF 248 ASP cc_start: 0.8756 (t0) cc_final: 0.8343 (t0) REVERT: WF 248 ASP cc_start: 0.8585 (t0) cc_final: 0.8144 (t0) REVERT: YF 248 ASP cc_start: 0.8727 (t0) cc_final: 0.8481 (t0) REVERT: ZF 248 ASP cc_start: 0.8601 (t0) cc_final: 0.8101 (t0) REVERT: EG 801 MET cc_start: 0.8508 (mtt) cc_final: 0.8262 (mtt) REVERT: LG 800 ASP cc_start: 0.8136 (m-30) cc_final: 0.7922 (m-30) REVERT: WG 800 ASP cc_start: 0.8044 (m-30) cc_final: 0.7764 (m-30) REVERT: BH 114 ASP cc_start: 0.8180 (m-30) cc_final: 0.7940 (m-30) REVERT: BH 214 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8057 (mtt) REVERT: EH 219 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8749 (mmtp) REVERT: GH 115 MET cc_start: 0.9070 (tmm) cc_final: 0.8716 (tmm) REVERT: HH 114 ASP cc_start: 0.8150 (m-30) cc_final: 0.7766 (m-30) REVERT: IH 109 LYS cc_start: 0.7939 (mppt) cc_final: 0.7665 (mttp) REVERT: IH 113 LYS cc_start: 0.8495 (mptt) cc_final: 0.8054 (mmtm) REVERT: IH 239 LEU cc_start: 0.8800 (mm) cc_final: 0.8599 (mm) REVERT: IH 255 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8228 (mtt90) REVERT: KH 110 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8441 (mmmm) REVERT: LH 113 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8136 (mmtm) REVERT: VH 114 ASP cc_start: 0.8240 (m-30) cc_final: 0.8004 (m-30) outliers start: 68 outliers final: 36 residues processed: 855 average time/residue: 1.9022 time to fit residues: 1947.8783 Evaluate side-chains 846 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 804 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 214 MET Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain DF residue 243 MET Chi-restraints excluded: chain EF residue 246 LEU Chi-restraints excluded: chain GF residue 243 MET Chi-restraints excluded: chain HF residue 243 MET Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain YF residue 243 MET Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain ZF residue 243 MET Chi-restraints excluded: chain BG residue 813 LYS Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain LG residue 799 SER Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain BH residue 214 MET Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 144 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain EH residue 219 LYS Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 154 THR Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain WH residue 144 THR Chi-restraints excluded: chain WH residue 154 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 420 optimal weight: 0.0770 chunk 286 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 375 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 430 optimal weight: 0.0980 chunk 348 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 452 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AF 226 ASN YH 118 ASN EF 266 GLN HF 266 GLN YF 266 GLN DG 814 GLN KG 807 GLN KG 814 GLN DH 118 ASN EH 118 ASN WH 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 40950 Z= 0.142 Angle : 0.488 6.921 55818 Z= 0.246 Chirality : 0.041 0.158 6606 Planarity : 0.004 0.041 7218 Dihedral : 3.815 17.540 5814 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.84 % Allowed : 18.88 % Favored : 79.29 % 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: 1.56 (0.13), residues: 4518 helix: 3.79 (0.15), residues: 1026 sheet: 1.09 (0.14), residues: 1224 loop : -0.31 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPJF 221 PHE 0.006 0.001 PHEJF 264 TYR 0.010 0.001 TYRBH 194 ARG 0.007 0.000 ARGFH 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 825 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8743 (t0) cc_final: 0.8444 (t0) REVERT: XH 114 ASP cc_start: 0.8139 (m-30) cc_final: 0.7909 (m-30) REVERT: CF 233 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7977 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8732 (t0) cc_final: 0.8468 (t0) REVERT: DF 248 ASP cc_start: 0.8757 (t0) cc_final: 0.8360 (t0) REVERT: EF 248 ASP cc_start: 0.8663 (t0) cc_final: 0.8413 (t0) REVERT: FF 248 ASP cc_start: 0.8619 (t0) cc_final: 0.8300 (t0) REVERT: IG 822 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: GF 248 ASP cc_start: 0.8495 (t0) cc_final: 0.8079 (t0) REVERT: HF 248 ASP cc_start: 0.8724 (t0) cc_final: 0.8344 (t0) REVERT: IF 233 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8721 (t0) cc_final: 0.8455 (t0) REVERT: JF 225 SER cc_start: 0.8849 (m) cc_final: 0.8474 (p) REVERT: JF 248 ASP cc_start: 0.8687 (t0) cc_final: 0.8313 (t0) REVERT: KF 248 ASP cc_start: 0.8756 (t0) cc_final: 0.8326 (t0) REVERT: LF 248 ASP cc_start: 0.8616 (t0) cc_final: 0.8294 (t0) REVERT: MF 248 ASP cc_start: 0.8558 (t0) cc_final: 0.8129 (t0) REVERT: VF 248 ASP cc_start: 0.8717 (t0) cc_final: 0.8336 (t0) REVERT: WF 248 ASP cc_start: 0.8558 (t0) cc_final: 0.8126 (t0) REVERT: YF 248 ASP cc_start: 0.8744 (t0) cc_final: 0.8459 (t0) REVERT: ZF 248 ASP cc_start: 0.8512 (t0) cc_final: 0.8075 (t0) REVERT: EG 801 MET cc_start: 0.8460 (mtt) cc_final: 0.8200 (mtt) REVERT: LG 800 ASP cc_start: 0.8132 (m-30) cc_final: 0.7932 (m-30) REVERT: WG 800 ASP cc_start: 0.8108 (m-30) cc_final: 0.7768 (m-30) REVERT: BH 114 ASP cc_start: 0.8138 (m-30) cc_final: 0.7902 (m-30) REVERT: EH 219 LYS cc_start: 0.8965 (mttp) cc_final: 0.8749 (mmtp) REVERT: GH 115 MET cc_start: 0.9078 (tmm) cc_final: 0.8752 (tmm) REVERT: IH 113 LYS cc_start: 0.8456 (mptt) cc_final: 0.8049 (mmtm) REVERT: LH 113 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8113 (mmtm) REVERT: VH 114 ASP cc_start: 0.8200 (m-30) cc_final: 0.7953 (m-30) REVERT: WH 114 ASP cc_start: 0.8115 (m-30) cc_final: 0.7866 (m-30) outliers start: 73 outliers final: 39 residues processed: 843 average time/residue: 1.7423 time to fit residues: 1734.1456 Evaluate side-chains 841 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 799 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain DF residue 243 MET Chi-restraints excluded: chain FF residue 246 LEU Chi-restraints excluded: chain IG residue 822 GLU Chi-restraints excluded: chain HF residue 246 LEU Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain YF residue 246 LEU Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain LG residue 799 SER Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 144 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain WH residue 144 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 169 optimal weight: 0.7980 chunk 454 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 505 optimal weight: 3.9990 chunk 419 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AF 226 ASN EF 266 GLN HF 266 GLN YF 266 GLN DG 814 GLN KG 814 GLN ** MG 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XG 814 GLN DH 118 ASN EH 118 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 40950 Z= 0.483 Angle : 0.716 8.274 55818 Z= 0.365 Chirality : 0.048 0.175 6606 Planarity : 0.006 0.040 7218 Dihedral : 4.863 20.623 5814 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.34 % Allowed : 19.13 % Favored : 78.53 % 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: 1.06 (0.12), residues: 4518 helix: 3.27 (0.15), residues: 1026 sheet: 0.99 (0.14), residues: 1206 loop : -0.71 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRPCH 206 PHE 0.014 0.002 PHELF 264 TYR 0.012 0.002 TYRHF 241 ARG 0.008 0.001 ARGGH 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 826 time to evaluate : 4.773 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: AF 248 ASP cc_start: 0.8778 (t0) cc_final: 0.8467 (t0) REVERT: XH 114 ASP cc_start: 0.8157 (m-30) cc_final: 0.7951 (m-30) REVERT: CF 233 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8480 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8824 (t0) cc_final: 0.8473 (t0) REVERT: DF 225 SER cc_start: 0.8792 (m) cc_final: 0.8480 (p) REVERT: DF 243 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7542 (mmm) REVERT: DF 248 ASP cc_start: 0.8817 (t0) cc_final: 0.8537 (t0) REVERT: FF 211 TYR cc_start: 0.9064 (m-80) cc_final: 0.8818 (m-80) REVERT: FF 248 ASP cc_start: 0.8723 (t0) cc_final: 0.8385 (t0) REVERT: GF 233 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8436 (ptt90) REVERT: GF 248 ASP cc_start: 0.8622 (t0) cc_final: 0.8089 (t0) REVERT: HF 248 ASP cc_start: 0.8794 (t0) cc_final: 0.8505 (t0) REVERT: IF 233 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8477 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8829 (t0) cc_final: 0.8507 (t0) REVERT: JF 225 SER cc_start: 0.8776 (m) cc_final: 0.8512 (p) REVERT: JF 248 ASP cc_start: 0.8829 (t0) cc_final: 0.8344 (t0) REVERT: JF 263 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8706 (mtpp) REVERT: KF 225 SER cc_start: 0.8813 (m) cc_final: 0.8462 (p) REVERT: LF 211 TYR cc_start: 0.9060 (m-80) cc_final: 0.8714 (m-80) REVERT: LF 248 ASP cc_start: 0.8732 (t0) cc_final: 0.8399 (t0) REVERT: MF 225 SER cc_start: 0.8954 (m) cc_final: 0.8629 (p) REVERT: MF 248 ASP cc_start: 0.8716 (t0) cc_final: 0.8229 (t0) REVERT: VF 248 ASP cc_start: 0.8788 (t0) cc_final: 0.8332 (t0) REVERT: WF 225 SER cc_start: 0.8909 (m) cc_final: 0.8674 (p) REVERT: WF 248 ASP cc_start: 0.8726 (t0) cc_final: 0.8268 (t0) REVERT: ZF 225 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (p) REVERT: ZF 248 ASP cc_start: 0.8630 (t0) cc_final: 0.8111 (t0) REVERT: WG 800 ASP cc_start: 0.8026 (m-30) cc_final: 0.7728 (m-30) REVERT: AH 255 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8314 (mpt-90) REVERT: BH 114 ASP cc_start: 0.8185 (m-30) cc_final: 0.7971 (m-30) REVERT: GH 109 LYS cc_start: 0.7804 (mttp) cc_final: 0.7476 (mptt) REVERT: GH 154 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8766 (p) REVERT: HH 255 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8318 (mpt-90) REVERT: IH 113 LYS cc_start: 0.8523 (mptt) cc_final: 0.8126 (mmtm) REVERT: KH 113 LYS cc_start: 0.8391 (mptt) cc_final: 0.8154 (mptt) REVERT: VH 214 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8257 (mtt) outliers start: 93 outliers final: 44 residues processed: 860 average time/residue: 1.8429 time to fit residues: 1860.1741 Evaluate side-chains 869 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 818 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain DF residue 243 MET Chi-restraints excluded: chain GF residue 233 ARG Chi-restraints excluded: chain HF residue 223 ILE Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain VF residue 230 LEU Chi-restraints excluded: chain YF residue 243 MET Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain LG residue 799 SER Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 179 LEU Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain EH residue 239 LEU Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 154 THR Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 179 LEU Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 154 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain VH residue 214 MET Chi-restraints excluded: chain WH residue 144 THR Chi-restraints excluded: chain WH residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 486 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 425 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 503 optimal weight: 0.2980 chunk 314 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AF 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 226 ASN HF 266 GLN IF 226 ASN BG 814 GLN DG 814 GLN KG 814 GLN XG 814 GLN YG 807 GLN EH 118 ASN JH 118 ASN VH 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 40950 Z= 0.191 Angle : 0.536 7.083 55818 Z= 0.271 Chirality : 0.042 0.163 6606 Planarity : 0.004 0.039 7218 Dihedral : 4.250 20.007 5814 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.81 % Allowed : 19.93 % Favored : 78.26 % 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: 1.40 (0.13), residues: 4518 helix: 3.74 (0.15), residues: 1026 sheet: 0.95 (0.14), residues: 1260 loop : -0.46 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPJF 221 PHE 0.007 0.001 PHELF 264 TYR 0.011 0.001 TYRXH 194 ARG 0.009 0.001 ARGJH 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 814 time to evaluate : 4.019 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: AF 248 ASP cc_start: 0.8776 (t0) cc_final: 0.8469 (t0) REVERT: XH 114 ASP cc_start: 0.8139 (m-30) cc_final: 0.7905 (m-30) REVERT: CF 233 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8130 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8792 (t0) cc_final: 0.8464 (t0) REVERT: DF 225 SER cc_start: 0.8815 (m) cc_final: 0.8479 (p) REVERT: DF 248 ASP cc_start: 0.8790 (t0) cc_final: 0.8432 (t0) REVERT: FF 211 TYR cc_start: 0.9050 (m-80) cc_final: 0.8727 (m-80) REVERT: FF 248 ASP cc_start: 0.8702 (t0) cc_final: 0.8360 (t0) REVERT: IG 822 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: GF 248 ASP cc_start: 0.8555 (t0) cc_final: 0.8123 (t0) REVERT: HF 248 ASP cc_start: 0.8799 (t0) cc_final: 0.8496 (t0) REVERT: IF 233 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8810 (t0) cc_final: 0.8466 (t0) REVERT: JF 225 SER cc_start: 0.8714 (m) cc_final: 0.8466 (p) REVERT: JF 248 ASP cc_start: 0.8739 (t0) cc_final: 0.8314 (t0) REVERT: KF 225 SER cc_start: 0.8813 (m) cc_final: 0.8477 (p) REVERT: KF 248 ASP cc_start: 0.8819 (t0) cc_final: 0.8433 (t0) REVERT: LF 211 TYR cc_start: 0.9071 (m-80) cc_final: 0.8806 (m-80) REVERT: LF 248 ASP cc_start: 0.8688 (t0) cc_final: 0.8331 (t0) REVERT: MF 225 SER cc_start: 0.8958 (m) cc_final: 0.8650 (p) REVERT: MF 248 ASP cc_start: 0.8643 (t0) cc_final: 0.8272 (t0) REVERT: VF 248 ASP cc_start: 0.8742 (t0) cc_final: 0.8290 (t0) REVERT: WF 225 SER cc_start: 0.8926 (m) cc_final: 0.8666 (p) REVERT: WF 248 ASP cc_start: 0.8656 (t0) cc_final: 0.8282 (t0) REVERT: YF 233 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8112 (ptt-90) REVERT: ZF 225 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8560 (p) REVERT: ZF 248 ASP cc_start: 0.8617 (t0) cc_final: 0.8139 (t0) REVERT: DG 822 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: EG 801 MET cc_start: 0.8503 (mtt) cc_final: 0.8285 (mtt) REVERT: WG 800 ASP cc_start: 0.8050 (m-30) cc_final: 0.7742 (m-30) REVERT: BH 114 ASP cc_start: 0.8155 (m-30) cc_final: 0.7935 (m-30) REVERT: GH 115 MET cc_start: 0.9091 (tmm) cc_final: 0.8793 (tmm) REVERT: GH 154 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8548 (p) REVERT: IH 109 LYS cc_start: 0.8051 (mppt) cc_final: 0.7311 (mppt) REVERT: IH 113 LYS cc_start: 0.8460 (mptt) cc_final: 0.7991 (mmtm) REVERT: MH 113 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8164 (mptt) REVERT: VH 214 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8163 (mtt) outliers start: 72 outliers final: 42 residues processed: 841 average time/residue: 1.7728 time to fit residues: 1758.4756 Evaluate side-chains 847 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 797 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 105 GLU Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain IG residue 822 GLU Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain JF residue 230 LEU Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain VF residue 230 LEU Chi-restraints excluded: chain YF residue 233 ARG Chi-restraints excluded: chain YF residue 243 MET Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain DG residue 822 GLU Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 105 GLU Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 154 THR Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 154 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain VH residue 214 MET Chi-restraints excluded: chain WH residue 144 THR Chi-restraints excluded: chain WH residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 311 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 342 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DG 814 GLN KG 814 GLN ** MG 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MG 807 GLN WG 807 GLN EH 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 40950 Z= 0.346 Angle : 0.635 8.765 55818 Z= 0.322 Chirality : 0.045 0.160 6606 Planarity : 0.005 0.040 7218 Dihedral : 4.619 20.192 5814 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.68 % Allowed : 20.54 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4518 helix: 3.50 (0.15), residues: 1026 sheet: 1.08 (0.14), residues: 1206 loop : -0.71 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPIH 206 PHE 0.011 0.002 PHELF 264 TYR 0.011 0.002 TYRHF 241 ARG 0.009 0.001 ARGAH 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 812 time to evaluate : 4.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8787 (t0) cc_final: 0.8488 (t0) REVERT: XH 114 ASP cc_start: 0.8173 (m-30) cc_final: 0.7940 (m-30) REVERT: CF 233 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8328 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8814 (t0) cc_final: 0.8469 (t0) REVERT: DF 225 SER cc_start: 0.8792 (m) cc_final: 0.8508 (p) REVERT: DF 248 ASP cc_start: 0.8806 (t0) cc_final: 0.8506 (t0) REVERT: FF 248 ASP cc_start: 0.8726 (t0) cc_final: 0.8371 (t0) REVERT: IG 822 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7817 (tp30) REVERT: GF 248 ASP cc_start: 0.8607 (t0) cc_final: 0.8087 (t0) REVERT: HF 248 ASP cc_start: 0.8814 (t0) cc_final: 0.8521 (t0) REVERT: IF 233 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8331 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8839 (t0) cc_final: 0.8477 (t0) REVERT: JF 225 SER cc_start: 0.8748 (m) cc_final: 0.8515 (p) REVERT: JF 248 ASP cc_start: 0.8758 (t0) cc_final: 0.8334 (t0) REVERT: KF 248 ASP cc_start: 0.8843 (t0) cc_final: 0.8479 (t0) REVERT: LF 211 TYR cc_start: 0.9100 (m-80) cc_final: 0.8649 (m-80) REVERT: LF 248 ASP cc_start: 0.8725 (t0) cc_final: 0.8397 (t0) REVERT: MF 225 SER cc_start: 0.8958 (m) cc_final: 0.8645 (p) REVERT: MF 248 ASP cc_start: 0.8670 (t0) cc_final: 0.8268 (t0) REVERT: VF 248 ASP cc_start: 0.8759 (t0) cc_final: 0.8301 (t0) REVERT: WF 225 SER cc_start: 0.8907 (m) cc_final: 0.8672 (p) REVERT: WF 248 ASP cc_start: 0.8679 (t0) cc_final: 0.8276 (t0) REVERT: YF 233 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8180 (ptt-90) REVERT: ZF 225 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8608 (p) REVERT: ZF 248 ASP cc_start: 0.8606 (t0) cc_final: 0.8088 (t0) REVERT: DG 822 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: WG 800 ASP cc_start: 0.8008 (m-30) cc_final: 0.7784 (m-30) REVERT: BH 114 ASP cc_start: 0.8158 (m-30) cc_final: 0.7921 (m-30) REVERT: FH 109 LYS cc_start: 0.8212 (mttp) cc_final: 0.7911 (mttt) REVERT: GH 154 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (p) REVERT: IH 109 LYS cc_start: 0.8119 (mppt) cc_final: 0.7473 (mppt) REVERT: IH 113 LYS cc_start: 0.8482 (mptt) cc_final: 0.8101 (mmtm) REVERT: IH 129 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8580 (mtmt) REVERT: KH 113 LYS cc_start: 0.8272 (mptt) cc_final: 0.8062 (mmtm) REVERT: VH 214 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8215 (mtt) outliers start: 67 outliers final: 42 residues processed: 842 average time/residue: 1.9192 time to fit residues: 1913.0910 Evaluate side-chains 861 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 811 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain IG residue 822 GLU Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain JF residue 230 LEU Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain VF residue 230 LEU Chi-restraints excluded: chain YF residue 233 ARG Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain DG residue 822 GLU Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 105 GLU Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain DH residue 239 LEU Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 154 THR Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 105 GLU Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 154 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain VH residue 214 MET Chi-restraints excluded: chain WH residue 144 THR Chi-restraints excluded: chain WH residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 457 optimal weight: 0.0980 chunk 482 optimal weight: 1.9990 chunk 439 optimal weight: 0.5980 chunk 468 optimal weight: 0.6980 chunk 481 optimal weight: 0.6980 chunk 282 optimal weight: 0.5980 chunk 204 optimal weight: 0.6980 chunk 368 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 423 optimal weight: 0.7980 chunk 443 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BG 814 GLN DG 814 GLN EG 807 GLN KG 814 GLN MG 807 GLN WG 807 GLN XG 814 GLN YG 807 GLN EH 118 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40950 Z= 0.170 Angle : 0.535 7.238 55818 Z= 0.270 Chirality : 0.042 0.160 6606 Planarity : 0.004 0.040 7218 Dihedral : 4.159 19.292 5814 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.61 % Allowed : 20.69 % Favored : 77.70 % 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: 1.49 (0.13), residues: 4518 helix: 3.84 (0.15), residues: 1026 sheet: 1.15 (0.14), residues: 1242 loop : -0.50 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPVF 221 PHE 0.007 0.001 PHEHF 264 TYR 0.011 0.001 TYRAH 194 ARG 0.009 0.001 ARGJH 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 796 time to evaluate : 4.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8770 (t0) cc_final: 0.8473 (t0) REVERT: CF 233 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8060 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8776 (t0) cc_final: 0.8448 (t0) REVERT: DF 225 SER cc_start: 0.8819 (m) cc_final: 0.8505 (p) REVERT: DF 248 ASP cc_start: 0.8780 (t0) cc_final: 0.8408 (t0) REVERT: FF 248 ASP cc_start: 0.8692 (t0) cc_final: 0.8328 (t0) REVERT: IG 822 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: GF 248 ASP cc_start: 0.8520 (t0) cc_final: 0.8066 (t0) REVERT: HF 248 ASP cc_start: 0.8795 (t0) cc_final: 0.8499 (t0) REVERT: IF 233 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8070 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8794 (t0) cc_final: 0.8432 (t0) REVERT: JF 225 SER cc_start: 0.8759 (m) cc_final: 0.8508 (p) REVERT: JF 248 ASP cc_start: 0.8741 (t0) cc_final: 0.8295 (t0) REVERT: KF 248 ASP cc_start: 0.8829 (t0) cc_final: 0.8392 (t0) REVERT: LF 211 TYR cc_start: 0.9080 (m-80) cc_final: 0.8658 (m-80) REVERT: LF 248 ASP cc_start: 0.8678 (t0) cc_final: 0.8311 (t0) REVERT: MF 225 SER cc_start: 0.8932 (m) cc_final: 0.8625 (p) REVERT: MF 248 ASP cc_start: 0.8627 (t0) cc_final: 0.8282 (t0) REVERT: VF 248 ASP cc_start: 0.8740 (t0) cc_final: 0.8297 (t0) REVERT: WF 225 SER cc_start: 0.8895 (m) cc_final: 0.8633 (p) REVERT: WF 248 ASP cc_start: 0.8639 (t0) cc_final: 0.8289 (t0) REVERT: YF 233 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8171 (ptt-90) REVERT: ZF 225 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (p) REVERT: ZF 248 ASP cc_start: 0.8554 (t0) cc_final: 0.8114 (t0) REVERT: BG 822 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: DG 822 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: WG 800 ASP cc_start: 0.8150 (m-30) cc_final: 0.7825 (m-30) REVERT: XG 822 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: BH 114 ASP cc_start: 0.8127 (m-30) cc_final: 0.7884 (m-30) REVERT: CH 180 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8867 (t) REVERT: GH 115 MET cc_start: 0.9053 (tmm) cc_final: 0.8765 (tmm) REVERT: GH 154 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (p) REVERT: IH 113 LYS cc_start: 0.8450 (mptt) cc_final: 0.8007 (mmtm) REVERT: KH 255 ARG cc_start: 0.8238 (mtt90) cc_final: 0.8036 (mtt90) REVERT: MH 113 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8205 (mptt) REVERT: VH 214 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8119 (mtt) outliers start: 64 outliers final: 44 residues processed: 821 average time/residue: 1.7949 time to fit residues: 1734.0750 Evaluate side-chains 844 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 789 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain IG residue 822 GLU Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain VF residue 230 LEU Chi-restraints excluded: chain XF residue 248 ASP Chi-restraints excluded: chain YF residue 233 ARG Chi-restraints excluded: chain YF residue 243 MET Chi-restraints excluded: chain ZF residue 225 SER Chi-restraints excluded: chain BG residue 822 GLU Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain DG residue 822 GLU Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain XG residue 822 GLU Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 105 GLU Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain CH residue 180 VAL Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain DH residue 239 LEU Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 154 THR Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 105 GLU Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 154 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain MH residue 241 LEU Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain VH residue 214 MET Chi-restraints excluded: chain WH residue 144 THR Chi-restraints excluded: chain WH residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 467 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 495 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 235 optimal weight: 0.6980 chunk 344 optimal weight: 1.9990 chunk 520 optimal weight: 2.9990 chunk 478 optimal weight: 0.9990 chunk 414 optimal weight: 0.0270 chunk 42 optimal weight: 0.3980 chunk 319 optimal weight: 0.3980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DF 226 ASN HF 266 GLN AG 807 GLN AG 814 GLN DG 814 GLN KG 814 GLN MG 807 GLN WG 807 GLN XG 814 GLN YG 807 GLN DH 118 ASN EH 118 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.002 0.028 40950 Z= 0.152 Angle : 0.516 8.234 55818 Z= 0.259 Chirality : 0.042 0.158 6606 Planarity : 0.004 0.040 7218 Dihedral : 3.940 18.630 5814 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.41 % Allowed : 21.02 % Favored : 77.58 % 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: 1.65 (0.13), residues: 4518 helix: 3.97 (0.15), residues: 1026 sheet: 1.31 (0.14), residues: 1224 loop : -0.43 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPHF 221 PHE 0.007 0.001 PHEIF 264 TYR 0.012 0.001 TYRXH 194 ARG 0.010 0.001 ARGBH 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 804 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AF 248 ASP cc_start: 0.8756 (t0) cc_final: 0.8427 (t0) REVERT: XH 114 ASP cc_start: 0.8096 (m-30) cc_final: 0.7851 (m-30) REVERT: ZH 115 MET cc_start: 0.8966 (tmm) cc_final: 0.8729 (tmm) REVERT: CF 233 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (ptt-90) REVERT: CF 248 ASP cc_start: 0.8745 (t0) cc_final: 0.8412 (t0) REVERT: DF 248 ASP cc_start: 0.8782 (t0) cc_final: 0.8333 (t0) REVERT: FF 248 ASP cc_start: 0.8653 (t0) cc_final: 0.8296 (t0) REVERT: GF 248 ASP cc_start: 0.8335 (t0) cc_final: 0.7932 (t0) REVERT: HF 248 ASP cc_start: 0.8779 (t0) cc_final: 0.8456 (t0) REVERT: IF 233 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8023 (ptt-90) REVERT: IF 248 ASP cc_start: 0.8769 (t0) cc_final: 0.8381 (t0) REVERT: JF 225 SER cc_start: 0.8757 (m) cc_final: 0.8511 (p) REVERT: JF 248 ASP cc_start: 0.8704 (t0) cc_final: 0.8253 (t0) REVERT: KF 248 ASP cc_start: 0.8788 (t0) cc_final: 0.8349 (t0) REVERT: LF 211 TYR cc_start: 0.9075 (m-80) cc_final: 0.8661 (m-80) REVERT: LF 248 ASP cc_start: 0.8657 (t0) cc_final: 0.8315 (t0) REVERT: MF 248 ASP cc_start: 0.8599 (t0) cc_final: 0.8243 (t0) REVERT: VF 248 ASP cc_start: 0.8700 (t0) cc_final: 0.8221 (t0) REVERT: WF 225 SER cc_start: 0.8899 (m) cc_final: 0.8615 (p) REVERT: WF 248 ASP cc_start: 0.8610 (t0) cc_final: 0.8261 (t0) REVERT: YF 233 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8473 (ptm-80) REVERT: ZF 248 ASP cc_start: 0.8428 (t0) cc_final: 0.8016 (t0) REVERT: BG 822 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: DG 822 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: KG 822 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: WG 800 ASP cc_start: 0.8159 (m-30) cc_final: 0.7862 (m-30) REVERT: XG 822 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: BH 114 ASP cc_start: 0.8088 (m-30) cc_final: 0.7865 (m-30) REVERT: FH 109 LYS cc_start: 0.8227 (mttp) cc_final: 0.8005 (mttt) REVERT: GH 115 MET cc_start: 0.9050 (tmm) cc_final: 0.8745 (tmm) REVERT: GH 154 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8367 (p) REVERT: IH 113 LYS cc_start: 0.8466 (mptt) cc_final: 0.8042 (mmtm) REVERT: LH 113 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8123 (mmtm) REVERT: MH 113 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8194 (mptt) outliers start: 56 outliers final: 40 residues processed: 825 average time/residue: 1.7800 time to fit residues: 1731.0502 Evaluate side-chains 838 residues out of total 3978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 790 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain XH residue 144 THR Chi-restraints excluded: chain XH residue 180 VAL Chi-restraints excluded: chain YH residue 144 THR Chi-restraints excluded: chain YH residue 180 VAL Chi-restraints excluded: chain ZH residue 180 VAL Chi-restraints excluded: chain CF residue 233 ARG Chi-restraints excluded: chain CF residue 243 MET Chi-restraints excluded: chain GF residue 243 MET Chi-restraints excluded: chain IF residue 233 ARG Chi-restraints excluded: chain IF residue 243 MET Chi-restraints excluded: chain KF residue 243 MET Chi-restraints excluded: chain VF residue 230 LEU Chi-restraints excluded: chain YF residue 233 ARG Chi-restraints excluded: chain BG residue 822 GLU Chi-restraints excluded: chain CG residue 800 ASP Chi-restraints excluded: chain CG residue 802 LEU Chi-restraints excluded: chain DG residue 822 GLU Chi-restraints excluded: chain HG residue 800 ASP Chi-restraints excluded: chain KG residue 822 GLU Chi-restraints excluded: chain XG residue 822 GLU Chi-restraints excluded: chain AH residue 144 THR Chi-restraints excluded: chain AH residue 180 VAL Chi-restraints excluded: chain BH residue 144 THR Chi-restraints excluded: chain BH residue 180 VAL Chi-restraints excluded: chain CH residue 105 GLU Chi-restraints excluded: chain CH residue 154 THR Chi-restraints excluded: chain DH residue 154 THR Chi-restraints excluded: chain DH residue 180 VAL Chi-restraints excluded: chain EH residue 144 THR Chi-restraints excluded: chain EH residue 180 VAL Chi-restraints excluded: chain FH residue 144 THR Chi-restraints excluded: chain FH residue 180 VAL Chi-restraints excluded: chain GH residue 154 THR Chi-restraints excluded: chain GH residue 180 VAL Chi-restraints excluded: chain HH residue 144 THR Chi-restraints excluded: chain HH residue 180 VAL Chi-restraints excluded: chain IH residue 105 GLU Chi-restraints excluded: chain IH residue 154 THR Chi-restraints excluded: chain JH residue 144 THR Chi-restraints excluded: chain KH residue 154 THR Chi-restraints excluded: chain KH residue 180 VAL Chi-restraints excluded: chain LH residue 144 THR Chi-restraints excluded: chain LH residue 180 VAL Chi-restraints excluded: chain MH residue 144 THR Chi-restraints excluded: chain MH residue 219 LYS Chi-restraints excluded: chain MH residue 241 LEU Chi-restraints excluded: chain VH residue 144 THR Chi-restraints excluded: chain WH residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 253 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 441 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 381 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 414 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: XF 226 ASN AG 814 GLN DG 814 GLN HG 814 GLN KG 814 GLN ** MG 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MG 807 GLN WG 807 GLN EH 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.077125 restraints weight = 59038.425| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.16 r_work: 0.2710 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 40950 Z= 0.256 Angle : 0.584 7.798 55818 Z= 0.296 Chirality : 0.043 0.160 6606 Planarity : 0.005 0.045 7218 Dihedral : 4.302 19.622 5814 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.46 % Allowed : 20.92 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.13), residues: 4518 helix: 3.81 (0.15), residues: 1026 sheet: 1.26 (0.14), residues: 1224 loop : -0.58 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPGH 206 PHE 0.010 0.001 PHEFF 264 TYR 0.011 0.001 TYRBH 194 ARG 0.009 0.001 ARGJH 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23164.00 seconds wall clock time: 405 minutes 30.27 seconds (24330.27 seconds total)