Starting phenix.real_space_refine on Thu Mar 21 15:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k43_22659/03_2024/7k43_22659.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.138 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 147 5.16 5 C 19341 2.51 5 N 4956 2.21 5 O 5946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1": "OE1" <-> "OE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 868": "OE1" <-> "OE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1139": "OD1" <-> "OD2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1": "OE1" <-> "OE2" Residue "G TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30390 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.64, per 1000 atoms: 0.48 Number of scatterers: 30390 At special positions: 0 Unit cell: (144.9, 138.6, 185.85, 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 147 16.00 O 5946 8.00 N 4956 7.00 C 19341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.83 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.15 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.83 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.17 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.08 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=1.83 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.15 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.05 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.06 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.01 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.17 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG Z 1 " - " FUC Z 4 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 61 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 343 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN E 17 " " NAG Y 1 " - " ASN E 122 " " NAG Z 1 " - " ASN E 343 " " NAG a 1 " - " ASN E 717 " " NAG b 1 " - " ASN E 801 " " NAG c 1 " - " ASN E1098 " " NAG d 1 " - " ASN E1134 " Time building additional restraints: 12.58 Conformation dependent library (CDL) restraints added in 5.8 seconds 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 66 sheets defined 23.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.193A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.977A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.888A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.977A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.887A pdb=" N TYR C 111 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.772A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.978A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.888A pdb=" N TYR F 111 " --> pdb=" O GLY F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.728A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.510A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 4.142A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.823A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.984A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.039A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.731A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.510A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 132 through 141 removed outlier: 4.141A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.823A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.732A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 114 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.509A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 132 through 141 removed outlier: 4.141A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.824A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.984A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.731A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3528 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: 16.54 Time building geometry restraints manager: 13.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5502 1.32 - 1.45: 10265 1.45 - 1.59: 15106 1.59 - 1.73: 30 1.73 - 1.86: 186 Bond restraints: 31089 Sorted by residual: bond pdb=" C CYS A 662 " pdb=" O CYS A 662 " ideal model delta sigma weight residual 1.234 1.348 -0.113 1.20e-02 6.94e+03 8.90e+01 bond pdb=" C CYS E 662 " pdb=" O CYS E 662 " ideal model delta sigma weight residual 1.234 1.348 -0.113 1.20e-02 6.94e+03 8.87e+01 bond pdb=" C CYS B 662 " pdb=" O CYS B 662 " ideal model delta sigma weight residual 1.234 1.347 -0.113 1.20e-02 6.94e+03 8.85e+01 bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.233 1.336 -0.103 1.28e-02 6.10e+03 6.43e+01 bond pdb=" C ASN E 61 " pdb=" O ASN E 61 " ideal model delta sigma weight residual 1.233 1.336 -0.103 1.28e-02 6.10e+03 6.43e+01 ... (remaining 31084 not shown) Histogram of bond angle deviations from ideal: 92.26 - 100.64: 12 100.64 - 109.02: 3642 109.02 - 117.40: 19458 117.40 - 125.78: 18833 125.78 - 134.17: 370 Bond angle restraints: 42315 Sorted by residual: angle pdb=" CD1 LEU L 34 " pdb=" CG LEU L 34 " pdb=" CD2 LEU L 34 " ideal model delta sigma weight residual 110.80 133.02 -22.22 2.20e+00 2.07e-01 1.02e+02 angle pdb=" CD1 LEU D 34 " pdb=" CG LEU D 34 " pdb=" CD2 LEU D 34 " ideal model delta sigma weight residual 110.80 133.01 -22.21 2.20e+00 2.07e-01 1.02e+02 angle pdb=" CD1 LEU G 34 " pdb=" CG LEU G 34 " pdb=" CD2 LEU G 34 " ideal model delta sigma weight residual 110.80 133.01 -22.21 2.20e+00 2.07e-01 1.02e+02 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 112.46 128.16 -15.70 1.57e+00 4.06e-01 1.00e+02 angle pdb=" N ASN E 165 " pdb=" CA ASN E 165 " pdb=" CB ASN E 165 " ideal model delta sigma weight residual 112.46 128.15 -15.69 1.57e+00 4.06e-01 9.98e+01 ... (remaining 42310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 18765 21.94 - 43.88: 471 43.88 - 65.81: 96 65.81 - 87.75: 57 87.75 - 109.69: 18 Dihedral angle restraints: 19407 sinusoidal: 8427 harmonic: 10980 Sorted by residual: dihedral pdb=" N ASN E 165 " pdb=" C ASN E 165 " pdb=" CA ASN E 165 " pdb=" CB ASN E 165 " ideal model delta harmonic sigma weight residual 122.80 154.52 -31.72 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" N ASN A 165 " pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta harmonic sigma weight residual 122.80 154.51 -31.71 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" N ASN B 165 " pdb=" C ASN B 165 " pdb=" CA ASN B 165 " pdb=" CB ASN B 165 " ideal model delta harmonic sigma weight residual 122.80 154.48 -31.68 0 2.50e+00 1.60e-01 1.61e+02 ... (remaining 19404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 4775 0.248 - 0.496: 193 0.496 - 0.744: 9 0.744 - 0.992: 0 0.992 - 1.240: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.53e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.49e+01 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.45e+01 ... (remaining 4977 not shown) Planarity restraints: 5403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 106 " 0.038 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 106 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 106 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 106 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP C 106 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 106 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 106 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 106 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP C 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 106 " -0.039 2.00e-02 2.50e+03 2.20e-02 1.22e+01 pdb=" CG TRP F 106 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP F 106 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 106 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 106 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP F 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 106 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 106 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 106 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP F 106 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 106 " -0.038 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP H 106 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP H 106 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 106 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP H 106 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 106 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 106 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 106 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP H 106 " -0.022 2.00e-02 2.50e+03 ... (remaining 5400 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 14379 2.94 - 3.43: 27078 3.43 - 3.92: 52505 3.92 - 4.41: 60955 4.41 - 4.90: 98482 Nonbonded interactions: 253399 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.456 2.520 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.456 2.520 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.456 2.520 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.466 2.496 nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.466 2.496 ... (remaining 253394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'Z' } 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.320 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 85.550 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.460 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.018 0.174 31089 Z= 1.155 Angle : 1.498 22.220 42315 Z= 0.987 Chirality : 0.109 1.240 4980 Planarity : 0.006 0.053 5352 Dihedral : 11.436 109.691 12219 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % Rotamer: Outliers : 0.09 % Allowed : 1.69 % Favored : 98.22 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 1.61 % 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: 0.34 (0.12), residues: 3723 helix: -0.24 (0.17), residues: 717 sheet: 0.80 (0.14), residues: 1104 loop : 0.21 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP F 106 HIS 0.006 0.002 HIS B1088 PHE 0.023 0.004 PHE B 718 TYR 0.040 0.005 TYR B 495 ARG 0.005 0.001 ARG E1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 627 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 GLN cc_start: 0.8104 (mt0) cc_final: 0.7838 (mt0) REVERT: A 1041 ASP cc_start: 0.7616 (m-30) cc_final: 0.7357 (m-30) REVERT: H 81 MET cc_start: 0.7215 (tpp) cc_final: 0.6660 (tmm) REVERT: L 73 THR cc_start: 0.8297 (p) cc_final: 0.8092 (t) REVERT: B 535 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7644 (mtmm) REVERT: B 755 GLN cc_start: 0.8226 (mt0) cc_final: 0.7770 (mt0) REVERT: B 1041 ASP cc_start: 0.7665 (m-30) cc_final: 0.7414 (m-30) REVERT: E 535 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7562 (mtmm) REVERT: E 821 LEU cc_start: 0.8833 (mt) cc_final: 0.8519 (mt) REVERT: E 904 TYR cc_start: 0.7372 (m-10) cc_final: 0.7010 (m-10) REVERT: E 1041 ASP cc_start: 0.7703 (m-30) cc_final: 0.7412 (m-30) REVERT: E 1058 HIS cc_start: 0.8310 (m-70) cc_final: 0.8109 (m-70) outliers start: 3 outliers final: 4 residues processed: 627 average time/residue: 1.3888 time to fit residues: 1021.2179 Evaluate side-chains 395 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 391 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain E residue 1135 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.9980 chunk 284 optimal weight: 0.6980 chunk 157 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 340 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 52 GLN A 271 GLN A 498 GLN A 779 GLN A 907 ASN A1058 HIS A1071 GLN B 30 ASN B 271 GLN B 498 GLN B 580 GLN B 613 GLN B 779 GLN B 907 ASN B1071 GLN E 30 ASN E 52 GLN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN E 613 GLN E 764 ASN E 907 ASN E1071 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31089 Z= 0.236 Angle : 0.623 11.748 42315 Z= 0.331 Chirality : 0.046 0.372 4980 Planarity : 0.005 0.068 5352 Dihedral : 6.782 67.392 5702 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.59 % Allowed : 8.50 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.80 (0.13), residues: 3723 helix: 1.59 (0.20), residues: 681 sheet: 0.95 (0.16), residues: 1029 loop : 0.01 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 64 HIS 0.004 0.001 HIS B 207 PHE 0.019 0.002 PHE A 592 TYR 0.024 0.002 TYR B 28 ARG 0.009 0.001 ARG E 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 443 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.6967 (tpt90) cc_final: 0.6759 (tpt90) REVERT: A 755 GLN cc_start: 0.7851 (mt0) cc_final: 0.7649 (mt0) REVERT: A 1041 ASP cc_start: 0.7601 (m-30) cc_final: 0.7348 (m-30) REVERT: L 11 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5706 (mp) REVERT: B 177 MET cc_start: 0.6668 (ttm) cc_final: 0.6356 (ttp) REVERT: B 556 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7179 (m110) REVERT: B 755 GLN cc_start: 0.8031 (mt0) cc_final: 0.7773 (mt0) REVERT: B 1041 ASP cc_start: 0.7576 (m-30) cc_final: 0.7360 (m-30) REVERT: C 3 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6138 (mp10) REVERT: C 81 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6656 (tmm) REVERT: E 821 LEU cc_start: 0.8917 (mt) cc_final: 0.8630 (mt) REVERT: E 1041 ASP cc_start: 0.7629 (m-30) cc_final: 0.7364 (m-30) REVERT: E 1058 HIS cc_start: 0.8326 (m-70) cc_final: 0.8103 (m-70) REVERT: F 81 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6661 (tmm) outliers start: 83 outliers final: 29 residues processed: 487 average time/residue: 1.3131 time to fit residues: 758.1899 Evaluate side-chains 403 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 369 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 4 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 283 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 273 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 271 GLN A 779 GLN A1058 HIS B 52 GLN B 115 GLN B 271 GLN B 779 GLN E 81 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31089 Z= 0.210 Angle : 0.564 8.588 42315 Z= 0.295 Chirality : 0.044 0.228 4980 Planarity : 0.004 0.072 5352 Dihedral : 5.373 55.377 5696 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.87 % Allowed : 10.65 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.85 (0.13), residues: 3723 helix: 1.74 (0.19), residues: 705 sheet: 0.86 (0.15), residues: 1116 loop : 0.01 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 106 HIS 0.004 0.001 HIS E1083 PHE 0.016 0.002 PHE C 29 TYR 0.027 0.001 TYR E 28 ARG 0.014 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 384 time to evaluate : 3.284 Fit side-chains REVERT: A 466 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7030 (mtp180) REVERT: A 725 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 755 GLN cc_start: 0.7918 (mt0) cc_final: 0.7655 (mt0) REVERT: A 1041 ASP cc_start: 0.7613 (m-30) cc_final: 0.7351 (m-30) REVERT: A 1113 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: H 98 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7709 (ttt180) REVERT: B 556 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7194 (m110) REVERT: B 755 GLN cc_start: 0.8009 (mt0) cc_final: 0.7733 (mt0) REVERT: B 1041 ASP cc_start: 0.7544 (m-30) cc_final: 0.7340 (m-30) REVERT: C 3 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6111 (mp10) REVERT: C 81 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6892 (tmm) REVERT: E 821 LEU cc_start: 0.8869 (mt) cc_final: 0.8579 (mt) REVERT: E 1029 MET cc_start: 0.8864 (tpp) cc_final: 0.8586 (tpp) REVERT: E 1041 ASP cc_start: 0.7673 (m-30) cc_final: 0.7398 (m-30) REVERT: E 1058 HIS cc_start: 0.8390 (m-70) cc_final: 0.8167 (m-70) REVERT: F 70 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7351 (mtt) REVERT: F 81 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6875 (tmm) outliers start: 92 outliers final: 35 residues processed: 442 average time/residue: 1.2812 time to fit residues: 675.8728 Evaluate side-chains 396 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 352 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.6980 chunk 256 optimal weight: 0.0980 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 0.0070 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 314 GLN A 779 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 271 GLN B 779 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31089 Z= 0.348 Angle : 0.622 8.801 42315 Z= 0.325 Chirality : 0.046 0.234 4980 Planarity : 0.005 0.097 5352 Dihedral : 5.194 54.204 5694 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.94 % Allowed : 11.06 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.13), residues: 3723 helix: 1.67 (0.19), residues: 699 sheet: 0.70 (0.15), residues: 1059 loop : -0.36 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 106 HIS 0.008 0.002 HIS C 35 PHE 0.021 0.002 PHE B 592 TYR 0.027 0.002 TYR L 92 ARG 0.017 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 365 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7390 (mtp180) REVERT: A 725 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 755 GLN cc_start: 0.7970 (mt0) cc_final: 0.7646 (mt0) REVERT: A 918 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: A 1038 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7505 (mmtt) REVERT: A 1041 ASP cc_start: 0.7621 (m-30) cc_final: 0.7357 (m-30) REVERT: A 1113 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7814 (mm-40) REVERT: H 98 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7735 (ttt180) REVERT: L 27 GLN cc_start: 0.7056 (mt0) cc_final: 0.6844 (pt0) REVERT: L 64 SER cc_start: 0.7251 (p) cc_final: 0.6950 (t) REVERT: L 101 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: B 556 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7248 (m110) REVERT: B 755 GLN cc_start: 0.8049 (mt0) cc_final: 0.7723 (mt0) REVERT: B 1041 ASP cc_start: 0.7460 (m-30) cc_final: 0.7251 (m-30) REVERT: C 3 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: C 81 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6761 (tmm) REVERT: D 101 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: E 466 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7719 (mtp180) REVERT: E 586 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7123 (t0) REVERT: E 821 LEU cc_start: 0.8976 (mt) cc_final: 0.8699 (mt) REVERT: E 1041 ASP cc_start: 0.7670 (m-30) cc_final: 0.7400 (m-30) REVERT: F 46 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: F 70 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: F 81 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6997 (tmm) REVERT: G 34 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8357 (tm) outliers start: 126 outliers final: 62 residues processed: 448 average time/residue: 1.2683 time to fit residues: 679.5769 Evaluate side-chains 420 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 341 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 947 LYS Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 chunk 325 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN A 271 GLN A 314 GLN A 779 GLN A 901 GLN A1088 HIS B 188 ASN B 271 GLN B 314 GLN B 613 GLN B 779 GLN B 901 GLN E 81 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31089 Z= 0.297 Angle : 0.602 14.007 42315 Z= 0.312 Chirality : 0.045 0.234 4980 Planarity : 0.005 0.086 5352 Dihedral : 5.010 49.769 5694 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.84 % Allowed : 12.00 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.43 (0.13), residues: 3723 helix: 1.76 (0.19), residues: 696 sheet: 0.67 (0.15), residues: 1041 loop : -0.43 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 106 HIS 0.005 0.001 HIS B1048 PHE 0.024 0.002 PHE E 133 TYR 0.023 0.002 TYR E 28 ARG 0.011 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 359 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7050 (mtp180) REVERT: A 580 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: A 725 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 755 GLN cc_start: 0.7957 (mt0) cc_final: 0.7642 (mt0) REVERT: A 918 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: A 995 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7447 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7512 (mmtt) REVERT: A 1041 ASP cc_start: 0.7634 (m-30) cc_final: 0.7378 (m-30) REVERT: A 1113 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: H 81 MET cc_start: 0.7583 (tpt) cc_final: 0.7335 (tpt) REVERT: L 64 SER cc_start: 0.7259 (p) cc_final: 0.6963 (t) REVERT: L 101 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: B 556 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7229 (m110) REVERT: B 580 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: B 755 GLN cc_start: 0.8029 (mt0) cc_final: 0.7700 (mt0) REVERT: B 1041 ASP cc_start: 0.7421 (m-30) cc_final: 0.7198 (m-30) REVERT: C 3 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6226 (mp10) REVERT: C 81 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6750 (tmm) REVERT: D 101 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: E 821 LEU cc_start: 0.8974 (mt) cc_final: 0.8702 (mt) REVERT: E 1041 ASP cc_start: 0.7657 (m-30) cc_final: 0.7389 (m-30) REVERT: F 46 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: F 70 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7258 (mtt) REVERT: F 81 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6977 (tmm) REVERT: G 34 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8357 (tm) outliers start: 123 outliers final: 63 residues processed: 442 average time/residue: 1.2523 time to fit residues: 662.4358 Evaluate side-chains 426 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 346 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.3980 chunk 326 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 167 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 188 ASN A 271 GLN A 314 GLN B 115 GLN B 271 GLN B 501 ASN B 779 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31089 Z= 0.185 Angle : 0.535 10.032 42315 Z= 0.276 Chirality : 0.043 0.229 4980 Planarity : 0.004 0.078 5352 Dihedral : 4.622 42.068 5694 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.19 % Allowed : 12.87 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.56 (0.13), residues: 3723 helix: 2.07 (0.20), residues: 681 sheet: 0.67 (0.16), residues: 1011 loop : -0.35 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 106 HIS 0.004 0.001 HIS C 35 PHE 0.026 0.001 PHE E 592 TYR 0.025 0.001 TYR A 28 ARG 0.015 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 388 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6960 (mtp180) REVERT: A 725 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 755 GLN cc_start: 0.7916 (mt0) cc_final: 0.7597 (mt0) REVERT: A 1038 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7667 (mmtt) REVERT: A 1041 ASP cc_start: 0.7611 (m-30) cc_final: 0.7353 (m-30) REVERT: H 98 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7765 (ttt180) REVERT: L 64 SER cc_start: 0.7208 (p) cc_final: 0.6906 (t) REVERT: B 556 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7241 (m110) REVERT: B 755 GLN cc_start: 0.8033 (mt0) cc_final: 0.7701 (mt0) REVERT: B 1041 ASP cc_start: 0.7370 (m-30) cc_final: 0.7165 (m-30) REVERT: C 3 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: C 81 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6728 (tmm) REVERT: E 821 LEU cc_start: 0.8932 (mt) cc_final: 0.8677 (mt) REVERT: E 1041 ASP cc_start: 0.7646 (m-30) cc_final: 0.7379 (m-30) REVERT: E 1123 SER cc_start: 0.7153 (m) cc_final: 0.6929 (m) REVERT: F 70 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7316 (mtt) REVERT: F 81 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6760 (tmm) REVERT: G 27 GLN cc_start: 0.7264 (pt0) cc_final: 0.6975 (pm20) REVERT: G 34 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8357 (tm) outliers start: 102 outliers final: 57 residues processed: 454 average time/residue: 1.2768 time to fit residues: 693.9485 Evaluate side-chains 418 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 351 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 725 GLU Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 206 optimal weight: 0.3980 chunk 264 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 305 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 361 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 188 ASN A 314 GLN A 779 GLN A 907 ASN B 115 GLN B 271 GLN B 498 GLN B 501 ASN B 779 GLN E 81 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31089 Z= 0.205 Angle : 0.546 9.126 42315 Z= 0.281 Chirality : 0.043 0.203 4980 Planarity : 0.004 0.083 5352 Dihedral : 4.567 36.633 5694 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.50 % Allowed : 13.28 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.55 (0.13), residues: 3723 helix: 2.14 (0.20), residues: 681 sheet: 0.60 (0.15), residues: 1041 loop : -0.36 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.003 0.001 HIS C 35 PHE 0.025 0.001 PHE E 592 TYR 0.026 0.001 TYR A 28 ARG 0.012 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 364 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5512 (tmm) REVERT: A 466 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6982 (mtp180) REVERT: A 580 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: A 725 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: A 755 GLN cc_start: 0.7923 (mt0) cc_final: 0.7557 (mt0) REVERT: A 995 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7507 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7663 (mmtt) REVERT: A 1041 ASP cc_start: 0.7618 (m-30) cc_final: 0.7358 (m-30) REVERT: L 27 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: L 64 SER cc_start: 0.7230 (p) cc_final: 0.6918 (t) REVERT: B 556 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7240 (m110) REVERT: B 755 GLN cc_start: 0.8033 (mt0) cc_final: 0.7709 (mt0) REVERT: B 1041 ASP cc_start: 0.7370 (m-30) cc_final: 0.7153 (m-30) REVERT: C 3 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6231 (mp10) REVERT: C 81 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6738 (tmm) REVERT: E 821 LEU cc_start: 0.8856 (mt) cc_final: 0.8611 (mt) REVERT: E 1041 ASP cc_start: 0.7637 (m-30) cc_final: 0.7365 (m-30) REVERT: F 70 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7263 (mtt) REVERT: F 81 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: G 34 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8352 (tm) outliers start: 112 outliers final: 62 residues processed: 438 average time/residue: 1.2516 time to fit residues: 659.9091 Evaluate side-chains 430 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 355 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 725 GLU Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 229 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 188 ASN A 271 GLN A 314 GLN A 779 GLN A 804 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 501 ASN B 779 GLN B1135 ASN E 81 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31089 Z= 0.389 Angle : 0.645 9.174 42315 Z= 0.333 Chirality : 0.047 0.303 4980 Planarity : 0.005 0.106 5352 Dihedral : 5.027 29.400 5694 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.69 % Allowed : 13.09 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.33 (0.13), residues: 3723 helix: 1.78 (0.20), residues: 681 sheet: 0.60 (0.15), residues: 1035 loop : -0.51 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 36 HIS 0.006 0.002 HIS C 35 PHE 0.026 0.002 PHE B 592 TYR 0.027 0.002 TYR L 92 ARG 0.014 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 368 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7451 (mtp180) REVERT: A 580 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: A 725 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: A 755 GLN cc_start: 0.7963 (mt0) cc_final: 0.7707 (mt0) REVERT: A 918 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: A 995 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7559 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7521 (mmtt) REVERT: L 27 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: L 64 SER cc_start: 0.7289 (p) cc_final: 0.6977 (t) REVERT: B 556 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7189 (m110) REVERT: B 658 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7333 (m-40) REVERT: B 755 GLN cc_start: 0.8054 (mt0) cc_final: 0.7742 (mt0) REVERT: B 1041 ASP cc_start: 0.7386 (m-30) cc_final: 0.7158 (m-30) REVERT: C 3 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6438 (mp10) REVERT: C 81 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6768 (tmm) REVERT: D 101 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: E 466 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7797 (mtp-110) REVERT: E 821 LEU cc_start: 0.8907 (mt) cc_final: 0.8658 (mt) REVERT: E 1041 ASP cc_start: 0.7620 (m-30) cc_final: 0.7395 (m-30) REVERT: F 46 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: F 70 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7350 (mtt) REVERT: F 81 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6976 (tmm) REVERT: G 27 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: G 34 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8397 (tm) outliers start: 118 outliers final: 62 residues processed: 440 average time/residue: 1.1886 time to fit residues: 625.1498 Evaluate side-chains 434 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 354 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 725 GLU Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 336 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 304 optimal weight: 0.9980 chunk 318 optimal weight: 0.6980 chunk 335 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 188 ASN A 314 GLN A 501 ASN A 779 GLN B 271 GLN B 501 ASN E 81 ASN E 115 GLN E 188 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31089 Z= 0.224 Angle : 0.567 8.298 42315 Z= 0.291 Chirality : 0.043 0.231 4980 Planarity : 0.004 0.088 5352 Dihedral : 4.822 44.566 5694 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 14.21 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.43 (0.13), residues: 3723 helix: 2.01 (0.20), residues: 681 sheet: 0.51 (0.15), residues: 1032 loop : -0.41 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 64 HIS 0.003 0.001 HIS B1048 PHE 0.029 0.001 PHE E 592 TYR 0.016 0.001 TYR E 265 ARG 0.014 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 358 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5611 (tmm) REVERT: A 466 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6998 (mtp180) REVERT: A 580 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: A 725 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: A 755 GLN cc_start: 0.7970 (mt0) cc_final: 0.7707 (mt0) REVERT: A 918 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6958 (mt-10) REVERT: A 995 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7554 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7571 (mmtt) REVERT: L 27 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: L 64 SER cc_start: 0.7249 (p) cc_final: 0.6936 (t) REVERT: B 556 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7209 (m110) REVERT: B 658 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7350 (m-40) REVERT: B 755 GLN cc_start: 0.8027 (mt0) cc_final: 0.7713 (mt0) REVERT: B 1041 ASP cc_start: 0.7362 (m-30) cc_final: 0.7122 (m-30) REVERT: C 3 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: C 81 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6752 (tmm) REVERT: D 101 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: E 466 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: E 821 LEU cc_start: 0.8865 (mt) cc_final: 0.8637 (mt) REVERT: E 1041 ASP cc_start: 0.7620 (m-30) cc_final: 0.7381 (m-30) REVERT: F 46 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: F 81 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: G 27 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: G 34 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8370 (tm) outliers start: 93 outliers final: 55 residues processed: 418 average time/residue: 1.3170 time to fit residues: 658.4447 Evaluate side-chains 421 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 348 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 725 GLU Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.2980 chunk 356 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 chunk 343 optimal weight: 0.2980 chunk 297 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 188 ASN A 271 GLN A 314 GLN A 779 GLN B 271 GLN B 501 ASN B 779 GLN E 81 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31089 Z= 0.238 Angle : 0.572 8.965 42315 Z= 0.294 Chirality : 0.043 0.200 4980 Planarity : 0.005 0.086 5352 Dihedral : 4.735 38.340 5694 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.84 % Allowed : 14.37 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.46 (0.13), residues: 3723 helix: 2.02 (0.20), residues: 684 sheet: 0.50 (0.15), residues: 1032 loop : -0.38 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.004 0.001 HIS C 35 PHE 0.030 0.001 PHE B 592 TYR 0.017 0.001 TYR L 92 ARG 0.015 0.001 ARG E 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 356 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.5652 (tmm) REVERT: A 466 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6995 (mtp180) REVERT: A 580 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6654 (mp10) REVERT: A 725 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: A 755 GLN cc_start: 0.7968 (mt0) cc_final: 0.7706 (mt0) REVERT: A 918 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: A 995 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7551 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7558 (mmtt) REVERT: L 27 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: L 64 SER cc_start: 0.7242 (p) cc_final: 0.6940 (t) REVERT: B 556 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7211 (m110) REVERT: B 658 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: B 755 GLN cc_start: 0.8044 (mt0) cc_final: 0.7706 (mt0) REVERT: B 1041 ASP cc_start: 0.7385 (m-30) cc_final: 0.7144 (m-30) REVERT: C 3 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: C 81 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6767 (tmm) REVERT: D 101 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: E 466 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: E 821 LEU cc_start: 0.8868 (mt) cc_final: 0.8643 (mt) REVERT: E 1041 ASP cc_start: 0.7622 (m-30) cc_final: 0.7385 (m-30) REVERT: F 46 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: F 81 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: G 27 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: G 34 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8377 (tm) REVERT: G 62 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7274 (ttm170) outliers start: 91 outliers final: 58 residues processed: 412 average time/residue: 1.2480 time to fit residues: 614.5639 Evaluate side-chains 425 residues out of total 3270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 348 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 558 LYS Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 725 GLU Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 4.9990 chunk 316 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 54 optimal weight: 0.7980 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 271 GLN A 314 GLN A 779 GLN B 271 GLN B 501 ASN E 137 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.171808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145575 restraints weight = 30565.365| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.70 r_work: 0.3290 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31089 Z= 0.197 Angle : 0.543 8.108 42315 Z= 0.279 Chirality : 0.043 0.190 4980 Planarity : 0.004 0.077 5352 Dihedral : 4.526 36.092 5694 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 14.50 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.53 (0.13), residues: 3723 helix: 2.15 (0.20), residues: 684 sheet: 0.51 (0.15), residues: 1032 loop : -0.34 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 106 HIS 0.003 0.001 HIS C 35 PHE 0.033 0.001 PHE A 592 TYR 0.016 0.001 TYR E 265 ARG 0.015 0.001 ARG E 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11171.98 seconds wall clock time: 198 minutes 13.78 seconds (11893.78 seconds total)