Starting phenix.real_space_refine on Wed Feb 14 06:58:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/02_2024/7z4w_14509.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 264 5.16 5 C 37056 2.51 5 N 9648 2.21 5 O 11974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "a ARG 73": "NH1" <-> "NH2" Residue "b ARG 73": "NH1" <-> "NH2" Residue "1 GLU 3": "OE1" <-> "OE2" Residue "1 GLU 16": "OE1" <-> "OE2" Residue "1 ARG 73": "NH1" <-> "NH2" Residue "1 ARG 77": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 73": "NH1" <-> "NH2" Residue "d ARG 73": "NH1" <-> "NH2" Residue "2 GLU 3": "OE1" <-> "OE2" Residue "2 GLU 4": "OE1" <-> "OE2" Residue "2 GLU 16": "OE1" <-> "OE2" Residue "2 GLU 45": "OE1" <-> "OE2" Residue "2 ARG 73": "NH1" <-> "NH2" Residue "2 ARG 77": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "E GLU 462": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 455": "OE1" <-> "OE2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 462": "OE1" <-> "OE2" Residue "e GLU 35": "OE1" <-> "OE2" Residue "e ARG 73": "NH1" <-> "NH2" Residue "f GLU 35": "OE1" <-> "OE2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "3 GLU 3": "OE1" <-> "OE2" Residue "3 GLU 16": "OE1" <-> "OE2" Residue "3 GLU 45": "OE1" <-> "OE2" Residue "3 ARG 73": "NH1" <-> "NH2" Residue "3 ARG 77": "NH1" <-> "NH2" Residue "3 GLU 103": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 227": "NH1" <-> "NH2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G GLU 424": "OE1" <-> "OE2" Residue "G ARG 459": "NH1" <-> "NH2" Residue "G GLU 462": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 227": "NH1" <-> "NH2" Residue "H ARG 459": "NH1" <-> "NH2" Residue "H GLU 462": "OE1" <-> "OE2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "4 GLU 3": "OE1" <-> "OE2" Residue "4 GLU 16": "OE1" <-> "OE2" Residue "4 ARG 73": "NH1" <-> "NH2" Residue "4 ARG 77": "NH1" <-> "NH2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 227": "NH1" <-> "NH2" Residue "I GLU 251": "OE1" <-> "OE2" Residue "I GLU 323": "OE1" <-> "OE2" Residue "I GLU 332": "OE1" <-> "OE2" Residue "I GLU 424": "OE1" <-> "OE2" Residue "I ARG 459": "NH1" <-> "NH2" Residue "I GLU 462": "OE1" <-> "OE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 227": "NH1" <-> "NH2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J GLU 334": "OE1" <-> "OE2" Residue "J GLU 352": "OE1" <-> "OE2" Residue "J ARG 459": "NH1" <-> "NH2" Residue "J GLU 462": "OE1" <-> "OE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "j ARG 73": "NH1" <-> "NH2" Residue "5 GLU 3": "OE1" <-> "OE2" Residue "5 GLU 4": "OE1" <-> "OE2" Residue "5 GLU 16": "OE1" <-> "OE2" Residue "5 GLU 45": "OE1" <-> "OE2" Residue "5 ARG 73": "NH1" <-> "NH2" Residue "5 ARG 77": "NH1" <-> "NH2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 154": "OE1" <-> "OE2" Residue "K ARG 227": "NH1" <-> "NH2" Residue "K GLU 424": "OE1" <-> "OE2" Residue "K ARG 459": "NH1" <-> "NH2" Residue "K GLU 462": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L GLU 151": "OE1" <-> "OE2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 227": "NH1" <-> "NH2" Residue "L GLU 352": "OE1" <-> "OE2" Residue "L GLU 454": "OE1" <-> "OE2" Residue "L GLU 455": "OE1" <-> "OE2" Residue "L ARG 459": "NH1" <-> "NH2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "k GLU 35": "OE1" <-> "OE2" Residue "k ARG 73": "NH1" <-> "NH2" Residue "l ARG 73": "NH1" <-> "NH2" Residue "6 GLU 3": "OE1" <-> "OE2" Residue "6 GLU 16": "OE1" <-> "OE2" Residue "6 GLU 45": "OE1" <-> "OE2" Residue "6 ARG 73": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 GLU 103": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58942 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "b" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "1" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "d" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "2" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "f" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "3" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "h" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "4" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "j" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "5" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3622 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "l" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "6" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "a" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "b" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "d" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "e" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "f" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "g" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "h" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "i" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "j" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "k" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "l" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 22.34, per 1000 atoms: 0.38 Number of scatterers: 58942 At special positions: 0 Unit cell: (189.75, 191.13, 200.79, 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 264 16.00 O 11974 8.00 N 9648 7.00 C 37056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.15 Conformation dependent library (CDL) restraints added in 7.8 seconds 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13620 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 79 sheets defined 49.1% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 123 through 141 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.566A pdb=" N LYS A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.553A pdb=" N ILE A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.736A pdb=" N ARG A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 345 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.901A pdb=" N ILE A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 367 through 399 removed outlier: 3.622A pdb=" N MET A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 452 through 469 removed outlier: 3.537A pdb=" N ASN A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.687A pdb=" N GLN B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 54 removed outlier: 3.640A pdb=" N LYS B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.517A pdb=" N LEU B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.668A pdb=" N GLU B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 141 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.574A pdb=" N LYS B 258 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 281 removed outlier: 3.562A pdb=" N ILE B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 326 through 345 removed outlier: 3.716A pdb=" N ARG B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.663A pdb=" N ILE B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 367 through 398 removed outlier: 3.629A pdb=" N MET B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.542A pdb=" N ALA B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 removed outlier: 3.624A pdb=" N LEU B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 17 through 37 removed outlier: 3.682A pdb=" N GLU a 23 " --> pdb=" O GLU a 19 " (cutoff:3.500A) Proline residue: a 26 - end of helix Processing helix chain 'a' and resid 50 through 64 Processing helix chain 'a' and resid 87 through 92 Processing helix chain 'a' and resid 93 through 98 Proline residue: a 96 - end of helix No H-bonds generated for 'chain 'a' and resid 93 through 98' Processing helix chain 'b' and resid 2 through 10 Processing helix chain 'b' and resid 17 through 37 removed outlier: 3.567A pdb=" N GLU b 23 " --> pdb=" O GLU b 19 " (cutoff:3.500A) Proline residue: b 26 - end of helix Processing helix chain 'b' and resid 50 through 64 Processing helix chain 'b' and resid 87 through 92 Processing helix chain 'b' and resid 93 through 98 Proline residue: b 96 - end of helix No H-bonds generated for 'chain 'b' and resid 93 through 98' Processing helix chain '1' and resid 42 through 50 removed outlier: 4.299A pdb=" N TYR 1 47 " --> pdb=" O GLN 1 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS 1 48 " --> pdb=" O GLU 1 44 " (cutoff:3.500A) Processing helix chain '1' and resid 91 through 93 No H-bonds generated for 'chain '1' and resid 91 through 93' Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 123 through 141 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.572A pdb=" N LYS C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.559A pdb=" N ILE C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Processing helix chain 'C' and resid 326 through 345 removed outlier: 3.734A pdb=" N ARG C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN C 345 " --> pdb=" O TYR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.911A pdb=" N ILE C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 367 through 399 removed outlier: 3.631A pdb=" N MET C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.562A pdb=" N LEU C 410 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.557A pdb=" N ASN C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 468 " --> pdb=" O MET C 464 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.738A pdb=" N GLN D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.673A pdb=" N LYS D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLY D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 87 through 102 removed outlier: 3.501A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.676A pdb=" N GLU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 141 Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.589A pdb=" N LYS D 258 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 281 removed outlier: 3.557A pdb=" N ILE D 264 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 307 Processing helix chain 'D' and resid 326 through 345 removed outlier: 3.699A pdb=" N ARG D 335 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.664A pdb=" N ILE D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 Processing helix chain 'D' and resid 367 through 398 removed outlier: 3.627A pdb=" N MET D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.532A pdb=" N ALA D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 470 removed outlier: 3.627A pdb=" N LEU D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 11 Processing helix chain 'c' and resid 17 through 37 removed outlier: 3.669A pdb=" N GLU c 23 " --> pdb=" O GLU c 19 " (cutoff:3.500A) Proline residue: c 26 - end of helix Processing helix chain 'c' and resid 50 through 64 Processing helix chain 'c' and resid 87 through 92 Processing helix chain 'c' and resid 93 through 98 Proline residue: c 96 - end of helix No H-bonds generated for 'chain 'c' and resid 93 through 98' Processing helix chain 'd' and resid 2 through 10 Processing helix chain 'd' and resid 17 through 37 removed outlier: 3.590A pdb=" N GLU d 23 " --> pdb=" O GLU d 19 " (cutoff:3.500A) Proline residue: d 26 - end of helix Processing helix chain 'd' and resid 50 through 64 Processing helix chain 'd' and resid 87 through 92 Processing helix chain 'd' and resid 93 through 98 Proline residue: d 96 - end of helix No H-bonds generated for 'chain 'd' and resid 93 through 98' Processing helix chain '2' and resid 42 through 50 removed outlier: 4.321A pdb=" N TYR 2 47 " --> pdb=" O GLN 2 43 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 2 48 " --> pdb=" O GLU 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 93 No H-bonds generated for 'chain '2' and resid 91 through 93' Processing helix chain 'E' and resid 31 through 40 Processing helix chain 'E' and resid 47 through 54 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 87 through 102 removed outlier: 3.503A pdb=" N LEU E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 123 through 141 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.583A pdb=" N LYS E 258 " --> pdb=" O SER E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 281 removed outlier: 3.549A pdb=" N ILE E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 Processing helix chain 'E' and resid 326 through 344 removed outlier: 3.752A pdb=" N ARG E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 342 " --> pdb=" O ASP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 357 removed outlier: 3.917A pdb=" N ILE E 354 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 367 through 399 removed outlier: 3.634A pdb=" N MET E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG E 379 " --> pdb=" O ASN E 375 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 439 through 446 Processing helix chain 'E' and resid 452 through 469 removed outlier: 3.529A pdb=" N ASN E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR E 467 " --> pdb=" O GLU E 463 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 468 " --> pdb=" O MET E 464 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.690A pdb=" N GLN F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 54 removed outlier: 3.643A pdb=" N LYS F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.511A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 removed outlier: 3.686A pdb=" N GLU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 141 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.547A pdb=" N LYS F 258 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 281 removed outlier: 3.558A pdb=" N ILE F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 307 Processing helix chain 'F' and resid 326 through 345 removed outlier: 3.741A pdb=" N ARG F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR F 341 " --> pdb=" O GLN F 337 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS F 342 " --> pdb=" O ASP F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 357 removed outlier: 3.691A pdb=" N ILE F 354 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY F 357 " --> pdb=" O THR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 367 Processing helix chain 'F' and resid 367 through 398 removed outlier: 3.629A pdb=" N MET F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG F 379 " --> pdb=" O ASN F 375 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 409 Processing helix chain 'F' and resid 421 through 436 Processing helix chain 'F' and resid 439 through 446 removed outlier: 3.536A pdb=" N ALA F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 470 removed outlier: 3.525A pdb=" N LEU F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU F 469 " --> pdb=" O ASN F 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET F 470 " --> pdb=" O GLN F 466 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 10 Processing helix chain 'e' and resid 17 through 37 removed outlier: 3.677A pdb=" N GLU e 23 " --> pdb=" O GLU e 19 " (cutoff:3.500A) Proline residue: e 26 - end of helix Processing helix chain 'e' and resid 50 through 64 Processing helix chain 'e' and resid 87 through 92 Processing helix chain 'e' and resid 93 through 98 Proline residue: e 96 - end of helix No H-bonds generated for 'chain 'e' and resid 93 through 98' Processing helix chain 'f' and resid 2 through 10 Processing helix chain 'f' and resid 17 through 37 removed outlier: 3.576A pdb=" N GLU f 23 " --> pdb=" O GLU f 19 " (cutoff:3.500A) Proline residue: f 26 - end of helix Processing helix chain 'f' and resid 50 through 64 Processing helix chain 'f' and resid 87 through 92 Processing helix chain 'f' and resid 93 through 98 Proline residue: f 96 - end of helix No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain '3' and resid 42 through 50 removed outlier: 4.314A pdb=" N TYR 3 47 " --> pdb=" O GLN 3 43 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS 3 48 " --> pdb=" O GLU 3 44 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 93 No H-bonds generated for 'chain '3' and resid 91 through 93' Processing helix chain 'G' and resid 31 through 40 Processing helix chain 'G' and resid 47 through 54 Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 87 through 102 Processing helix chain 'G' and resid 111 through 122 Processing helix chain 'G' and resid 123 through 141 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.566A pdb=" N LYS G 258 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 281 removed outlier: 3.553A pdb=" N ILE G 264 " --> pdb=" O TYR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 307 Processing helix chain 'G' and resid 326 through 345 removed outlier: 3.736A pdb=" N ARG G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS G 342 " --> pdb=" O ASP G 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN G 345 " --> pdb=" O TYR G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 357 removed outlier: 3.903A pdb=" N ILE G 354 " --> pdb=" O SER G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 367 Processing helix chain 'G' and resid 367 through 399 removed outlier: 3.622A pdb=" N MET G 376 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG G 379 " --> pdb=" O ASN G 375 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 380 " --> pdb=" O MET G 376 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 409 Processing helix chain 'G' and resid 421 through 435 Processing helix chain 'G' and resid 439 through 446 Processing helix chain 'G' and resid 452 through 469 removed outlier: 3.536A pdb=" N ASN G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR G 467 " --> pdb=" O GLU G 463 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA G 468 " --> pdb=" O MET G 464 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU G 469 " --> pdb=" O ASN G 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 removed outlier: 3.687A pdb=" N GLN H 35 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 54 removed outlier: 3.640A pdb=" N LYS H 48 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.517A pdb=" N LEU H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 122 removed outlier: 3.668A pdb=" N GLU H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR H 117 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 141 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.574A pdb=" N LYS H 258 " --> pdb=" O SER H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 281 removed outlier: 3.561A pdb=" N ILE H 264 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER H 277 " --> pdb=" O SER H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 307 Processing helix chain 'H' and resid 326 through 345 removed outlier: 3.716A pdb=" N ARG H 335 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR H 341 " --> pdb=" O GLN H 337 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 342 " --> pdb=" O ASP H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 357 removed outlier: 3.662A pdb=" N ILE H 354 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY H 357 " --> pdb=" O THR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 367 Processing helix chain 'H' and resid 367 through 398 removed outlier: 3.629A pdb=" N MET H 376 " --> pdb=" O LEU H 372 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG H 379 " --> pdb=" O ASN H 375 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS H 380 " --> pdb=" O MET H 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU H 387 " --> pdb=" O ALA H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 409 Processing helix chain 'H' and resid 421 through 436 Processing helix chain 'H' and resid 439 through 446 removed outlier: 3.542A pdb=" N ALA H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 470 removed outlier: 3.625A pdb=" N LEU H 457 " --> pdb=" O PRO H 453 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU H 469 " --> pdb=" O ASN H 465 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET H 470 " --> pdb=" O GLN H 466 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 10 Processing helix chain 'g' and resid 17 through 37 removed outlier: 3.683A pdb=" N GLU g 23 " --> pdb=" O GLU g 19 " (cutoff:3.500A) Proline residue: g 26 - end of helix Processing helix chain 'g' and resid 50 through 64 Processing helix chain 'g' and resid 87 through 92 Processing helix chain 'g' and resid 93 through 98 Proline residue: g 96 - end of helix No H-bonds generated for 'chain 'g' and resid 93 through 98' Processing helix chain 'h' and resid 2 through 10 Processing helix chain 'h' and resid 17 through 37 removed outlier: 3.567A pdb=" N GLU h 23 " --> pdb=" O GLU h 19 " (cutoff:3.500A) Proline residue: h 26 - end of helix Processing helix chain 'h' and resid 50 through 64 Processing helix chain 'h' and resid 87 through 92 Processing helix chain 'h' and resid 93 through 98 Proline residue: h 96 - end of helix No H-bonds generated for 'chain 'h' and resid 93 through 98' Processing helix chain '4' and resid 42 through 50 removed outlier: 4.299A pdb=" N TYR 4 47 " --> pdb=" O GLN 4 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS 4 48 " --> pdb=" O GLU 4 44 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 93 No H-bonds generated for 'chain '4' and resid 91 through 93' Processing helix chain 'I' and resid 31 through 40 Processing helix chain 'I' and resid 47 through 54 Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 87 through 102 Processing helix chain 'I' and resid 111 through 122 Processing helix chain 'I' and resid 123 through 141 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 255 through 259 removed outlier: 3.568A pdb=" N LYS I 258 " --> pdb=" O SER I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 281 removed outlier: 3.552A pdb=" N ILE I 264 " --> pdb=" O TYR I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 307 Processing helix chain 'I' and resid 326 through 345 removed outlier: 3.737A pdb=" N ARG I 335 " --> pdb=" O LYS I 331 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 342 " --> pdb=" O ASP I 338 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN I 345 " --> pdb=" O TYR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 357 removed outlier: 3.931A pdb=" N ILE I 354 " --> pdb=" O SER I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 367 Processing helix chain 'I' and resid 367 through 399 removed outlier: 3.630A pdb=" N MET I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG I 379 " --> pdb=" O ASN I 375 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS I 380 " --> pdb=" O MET I 376 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 410 Processing helix chain 'I' and resid 421 through 435 Processing helix chain 'I' and resid 439 through 446 Processing helix chain 'I' and resid 452 through 469 removed outlier: 3.538A pdb=" N ASN I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR I 467 " --> pdb=" O GLU I 463 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA I 468 " --> pdb=" O MET I 464 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU I 469 " --> pdb=" O ASN I 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 40 removed outlier: 3.735A pdb=" N GLN J 35 " --> pdb=" O THR J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 54 removed outlier: 3.672A pdb=" N LYS J 48 " --> pdb=" O GLU J 44 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY J 49 " --> pdb=" O PRO J 45 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL J 50 " --> pdb=" O LEU J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 Processing helix chain 'J' and resid 87 through 102 removed outlier: 3.500A pdb=" N LEU J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 122 removed outlier: 3.675A pdb=" N GLU J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 141 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.587A pdb=" N LYS J 258 " --> pdb=" O SER J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 281 removed outlier: 3.558A pdb=" N ILE J 264 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 277 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 307 Processing helix chain 'J' and resid 326 through 345 removed outlier: 3.698A pdb=" N ARG J 335 " --> pdb=" O LYS J 331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR J 341 " --> pdb=" O GLN J 337 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS J 342 " --> pdb=" O ASP J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 357 removed outlier: 3.665A pdb=" N ILE J 354 " --> pdb=" O SER J 350 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY J 357 " --> pdb=" O THR J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 367 Processing helix chain 'J' and resid 367 through 398 removed outlier: 3.630A pdb=" N MET J 376 " --> pdb=" O LEU J 372 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG J 379 " --> pdb=" O ASN J 375 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS J 380 " --> pdb=" O MET J 376 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 409 Processing helix chain 'J' and resid 421 through 436 Processing helix chain 'J' and resid 439 through 446 removed outlier: 3.533A pdb=" N ALA J 445 " --> pdb=" O GLU J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 470 removed outlier: 3.621A pdb=" N LEU J 457 " --> pdb=" O PRO J 453 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU J 469 " --> pdb=" O ASN J 465 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET J 470 " --> pdb=" O GLN J 466 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 10 Processing helix chain 'i' and resid 17 through 37 removed outlier: 3.668A pdb=" N GLU i 23 " --> pdb=" O GLU i 19 " (cutoff:3.500A) Proline residue: i 26 - end of helix Processing helix chain 'i' and resid 50 through 64 Processing helix chain 'i' and resid 87 through 92 Processing helix chain 'i' and resid 93 through 98 Proline residue: i 96 - end of helix No H-bonds generated for 'chain 'i' and resid 93 through 98' Processing helix chain 'j' and resid 2 through 10 Processing helix chain 'j' and resid 17 through 37 removed outlier: 3.590A pdb=" N GLU j 23 " --> pdb=" O GLU j 19 " (cutoff:3.500A) Proline residue: j 26 - end of helix Processing helix chain 'j' and resid 50 through 64 Processing helix chain 'j' and resid 87 through 92 Processing helix chain 'j' and resid 93 through 98 Proline residue: j 96 - end of helix No H-bonds generated for 'chain 'j' and resid 93 through 98' Processing helix chain '5' and resid 42 through 50 removed outlier: 4.324A pdb=" N TYR 5 47 " --> pdb=" O GLN 5 43 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS 5 48 " --> pdb=" O GLU 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain 'K' and resid 31 through 40 Processing helix chain 'K' and resid 47 through 54 Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 87 through 102 removed outlier: 3.503A pdb=" N LEU K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 122 Processing helix chain 'K' and resid 123 through 141 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.582A pdb=" N LYS K 258 " --> pdb=" O SER K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 281 removed outlier: 3.551A pdb=" N ILE K 264 " --> pdb=" O TYR K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 307 Processing helix chain 'K' and resid 326 through 344 removed outlier: 3.746A pdb=" N ARG K 335 " --> pdb=" O LYS K 331 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS K 342 " --> pdb=" O ASP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 357 removed outlier: 3.938A pdb=" N ILE K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 367 Processing helix chain 'K' and resid 367 through 399 removed outlier: 3.633A pdb=" N MET K 376 " --> pdb=" O LEU K 372 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG K 379 " --> pdb=" O ASN K 375 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS K 380 " --> pdb=" O MET K 376 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 421 through 435 Processing helix chain 'K' and resid 439 through 446 Processing helix chain 'K' and resid 452 through 469 removed outlier: 3.527A pdb=" N ASN K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR K 467 " --> pdb=" O GLU K 463 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA K 468 " --> pdb=" O MET K 464 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU K 469 " --> pdb=" O ASN K 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 40 removed outlier: 3.689A pdb=" N GLN L 35 " --> pdb=" O THR L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 54 removed outlier: 3.642A pdb=" N LYS L 48 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLY L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 62 Processing helix chain 'L' and resid 87 through 102 removed outlier: 3.510A pdb=" N LEU L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 122 removed outlier: 3.685A pdb=" N GLU L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 141 Processing helix chain 'L' and resid 161 through 163 No H-bonds generated for 'chain 'L' and resid 161 through 163' Processing helix chain 'L' and resid 255 through 259 removed outlier: 3.545A pdb=" N LYS L 258 " --> pdb=" O SER L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 281 removed outlier: 3.559A pdb=" N ILE L 264 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER L 277 " --> pdb=" O SER L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 307 Processing helix chain 'L' and resid 326 through 345 removed outlier: 3.740A pdb=" N ARG L 335 " --> pdb=" O LYS L 331 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR L 341 " --> pdb=" O GLN L 337 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS L 342 " --> pdb=" O ASP L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 3.691A pdb=" N ILE L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY L 357 " --> pdb=" O THR L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 367 Processing helix chain 'L' and resid 367 through 398 removed outlier: 3.629A pdb=" N MET L 376 " --> pdb=" O LEU L 372 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG L 379 " --> pdb=" O ASN L 375 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS L 380 " --> pdb=" O MET L 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 409 Processing helix chain 'L' and resid 421 through 436 Processing helix chain 'L' and resid 439 through 446 removed outlier: 3.537A pdb=" N ALA L 445 " --> pdb=" O GLU L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 470 removed outlier: 3.518A pdb=" N LEU L 457 " --> pdb=" O PRO L 453 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA L 458 " --> pdb=" O GLU L 454 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU L 469 " --> pdb=" O ASN L 465 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET L 470 " --> pdb=" O GLN L 466 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 10 Processing helix chain 'k' and resid 17 through 37 removed outlier: 3.676A pdb=" N GLU k 23 " --> pdb=" O GLU k 19 " (cutoff:3.500A) Proline residue: k 26 - end of helix Processing helix chain 'k' and resid 50 through 64 Processing helix chain 'k' and resid 87 through 92 Processing helix chain 'k' and resid 93 through 98 Proline residue: k 96 - end of helix No H-bonds generated for 'chain 'k' and resid 93 through 98' Processing helix chain 'l' and resid 2 through 10 Processing helix chain 'l' and resid 17 through 37 removed outlier: 3.577A pdb=" N GLU l 23 " --> pdb=" O GLU l 19 " (cutoff:3.500A) Proline residue: l 26 - end of helix Processing helix chain 'l' and resid 50 through 64 Processing helix chain 'l' and resid 87 through 92 Processing helix chain 'l' and resid 93 through 98 Proline residue: l 96 - end of helix No H-bonds generated for 'chain 'l' and resid 93 through 98' Processing helix chain '6' and resid 42 through 50 removed outlier: 4.316A pdb=" N TYR 6 47 " --> pdb=" O GLN 6 43 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS 6 48 " --> pdb=" O GLU 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 91 through 93 No H-bonds generated for 'chain '6' and resid 91 through 93' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 109 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 160 removed outlier: 3.779A pdb=" N TYR A 144 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE A 166 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA A 180 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 168 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN A 195 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE A 166 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA A 180 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 168 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN A 195 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 321 Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.441A pdb=" N ILE A 309 " --> pdb=" O LEU L 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 160 removed outlier: 3.754A pdb=" N TYR B 144 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.532A pdb=" N ILE B 166 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA B 180 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 168 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN B 195 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.532A pdb=" N ILE B 166 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA B 180 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 168 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN B 195 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 316 through 321 Processing sheet with id=AB5, first strand: chain 'a' and resid 70 through 75 removed outlier: 5.942A pdb=" N THR a 71 " --> pdb=" O PHE a 82 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER a 79 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG b 73 " --> pdb=" O SER a 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN a 81 " --> pdb=" O THR b 71 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR b 71 " --> pdb=" O PHE b 82 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER b 79 " --> pdb=" O ARG c 73 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG c 73 " --> pdb=" O SER b 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN b 81 " --> pdb=" O THR c 71 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR c 71 " --> pdb=" O PHE c 82 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER c 79 " --> pdb=" O ARG d 73 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG d 73 " --> pdb=" O SER c 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN c 81 " --> pdb=" O THR d 71 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR d 71 " --> pdb=" O PHE d 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER d 79 " --> pdb=" O ARG e 73 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG e 73 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN d 81 " --> pdb=" O THR e 71 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR e 71 " --> pdb=" O PHE e 82 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER e 79 " --> pdb=" O ARG f 73 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG f 73 " --> pdb=" O SER e 79 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN e 81 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR f 71 " --> pdb=" O PHE f 82 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER f 79 " --> pdb=" O ARG g 73 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG g 73 " --> pdb=" O SER f 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN f 81 " --> pdb=" O THR g 71 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR g 71 " --> pdb=" O PHE g 82 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER g 79 " --> pdb=" O ARG h 73 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG h 73 " --> pdb=" O SER g 79 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN g 81 " --> pdb=" O THR h 71 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR h 71 " --> pdb=" O PHE h 82 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER h 79 " --> pdb=" O ARG i 73 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG i 73 " --> pdb=" O SER h 79 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN h 81 " --> pdb=" O THR i 71 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR i 71 " --> pdb=" O PHE i 82 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER i 79 " --> pdb=" O ARG j 73 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG j 73 " --> pdb=" O SER i 79 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN i 81 " --> pdb=" O THR j 71 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N THR j 71 " --> pdb=" O PHE j 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER j 79 " --> pdb=" O ARG k 73 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG k 73 " --> pdb=" O SER j 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN j 81 " --> pdb=" O THR k 71 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR k 71 " --> pdb=" O PHE k 82 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER k 79 " --> pdb=" O ARG l 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG l 73 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN k 81 " --> pdb=" O THR l 71 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR l 71 " --> pdb=" O PHE l 82 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER l 79 " --> pdb=" O ARG a 73 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG a 73 " --> pdb=" O SER l 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN l 81 " --> pdb=" O THR a 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 88 through 89 removed outlier: 4.989A pdb=" N ILE 1 80 " --> pdb=" O ASP 1 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE 1 32 " --> pdb=" O PHE 1 11 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER 1 13 " --> pdb=" O ASP 1 30 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASP 1 30 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL 1 15 " --> pdb=" O TRP 1 28 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP 1 28 " --> pdb=" O VAL 1 15 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA 1 35 " --> pdb=" O PRO 1 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AB8, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB9, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.779A pdb=" N TYR C 144 " --> pdb=" O PHE C 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 165 through 169 removed outlier: 6.575A pdb=" N ILE C 166 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 180 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 168 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN C 195 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 165 through 169 removed outlier: 6.575A pdb=" N ILE C 166 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 180 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 168 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN C 195 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 321 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 Processing sheet with id=AC5, first strand: chain 'D' and resid 106 through 109 Processing sheet with id=AC6, first strand: chain 'D' and resid 155 through 160 removed outlier: 3.744A pdb=" N TYR D 144 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 165 through 169 removed outlier: 6.513A pdb=" N ILE D 166 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 180 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL D 168 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLN D 195 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 165 through 169 removed outlier: 6.513A pdb=" N ILE D 166 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 180 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL D 168 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLN D 195 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 316 through 321 Processing sheet with id=AD1, first strand: chain '2' and resid 88 through 89 removed outlier: 4.987A pdb=" N ILE 2 80 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE 2 32 " --> pdb=" O PHE 2 11 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER 2 13 " --> pdb=" O ASP 2 30 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP 2 30 " --> pdb=" O SER 2 13 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL 2 15 " --> pdb=" O TRP 2 28 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP 2 28 " --> pdb=" O VAL 2 15 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA 2 35 " --> pdb=" O PRO 2 63 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AD3, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.770A pdb=" N TYR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 165 through 169 removed outlier: 6.578A pdb=" N ILE E 166 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA E 180 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 168 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN E 195 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 165 through 169 removed outlier: 6.578A pdb=" N ILE E 166 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA E 180 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 168 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN E 195 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 316 through 321 Processing sheet with id=AD8, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AD9, first strand: chain 'F' and resid 106 through 109 Processing sheet with id=AE1, first strand: chain 'F' and resid 155 through 160 removed outlier: 3.748A pdb=" N TYR F 144 " --> pdb=" O PHE F 160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 165 through 169 removed outlier: 6.525A pdb=" N ILE F 166 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA F 180 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL F 168 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN F 195 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 165 through 169 removed outlier: 6.525A pdb=" N ILE F 166 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA F 180 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL F 168 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN F 195 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 316 through 321 Processing sheet with id=AE5, first strand: chain '3' and resid 88 through 89 removed outlier: 4.998A pdb=" N ILE 3 80 " --> pdb=" O ASP 3 104 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE 3 32 " --> pdb=" O PHE 3 11 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER 3 13 " --> pdb=" O ASP 3 30 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP 3 30 " --> pdb=" O SER 3 13 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL 3 15 " --> pdb=" O TRP 3 28 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP 3 28 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA 3 35 " --> pdb=" O PRO 3 63 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 65 through 67 Processing sheet with id=AE7, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AE8, first strand: chain 'G' and resid 155 through 160 removed outlier: 3.779A pdb=" N TYR G 144 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE G 166 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA G 180 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL G 168 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN G 195 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE G 166 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA G 180 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL G 168 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN G 195 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 316 through 321 Processing sheet with id=AF3, first strand: chain 'H' and resid 65 through 67 Processing sheet with id=AF4, first strand: chain 'H' and resid 106 through 109 Processing sheet with id=AF5, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.755A pdb=" N TYR H 144 " --> pdb=" O PHE H 160 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 165 through 169 removed outlier: 6.532A pdb=" N ILE H 166 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA H 180 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 168 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN H 195 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 165 through 169 removed outlier: 6.532A pdb=" N ILE H 166 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA H 180 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 168 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN H 195 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 316 through 321 Processing sheet with id=AF9, first strand: chain '4' and resid 88 through 89 removed outlier: 4.989A pdb=" N ILE 4 80 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE 4 32 " --> pdb=" O PHE 4 11 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER 4 13 " --> pdb=" O ASP 4 30 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASP 4 30 " --> pdb=" O SER 4 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL 4 15 " --> pdb=" O TRP 4 28 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP 4 28 " --> pdb=" O VAL 4 15 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA 4 35 " --> pdb=" O PRO 4 63 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 65 through 67 Processing sheet with id=AG2, first strand: chain 'I' and resid 106 through 108 Processing sheet with id=AG3, first strand: chain 'I' and resid 155 through 160 removed outlier: 3.777A pdb=" N TYR I 144 " --> pdb=" O PHE I 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE I 166 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA I 180 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 168 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN I 195 " --> pdb=" O LYS I 210 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.566A pdb=" N ILE I 166 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA I 180 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 168 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN I 195 " --> pdb=" O LYS I 210 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 316 through 321 Processing sheet with id=AG7, first strand: chain 'J' and resid 65 through 67 Processing sheet with id=AG8, first strand: chain 'J' and resid 106 through 109 Processing sheet with id=AG9, first strand: chain 'J' and resid 155 through 160 removed outlier: 3.744A pdb=" N TYR J 144 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 165 through 169 removed outlier: 6.513A pdb=" N ILE J 166 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA J 180 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL J 168 " --> pdb=" O LEU J 178 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN J 195 " --> pdb=" O LYS J 210 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 165 through 169 removed outlier: 6.513A pdb=" N ILE J 166 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA J 180 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL J 168 " --> pdb=" O LEU J 178 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN J 195 " --> pdb=" O LYS J 210 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 316 through 321 Processing sheet with id=AH4, first strand: chain '5' and resid 88 through 89 removed outlier: 4.989A pdb=" N ILE 5 80 " --> pdb=" O ASP 5 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE 5 32 " --> pdb=" O PHE 5 11 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER 5 13 " --> pdb=" O ASP 5 30 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP 5 30 " --> pdb=" O SER 5 13 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL 5 15 " --> pdb=" O TRP 5 28 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP 5 28 " --> pdb=" O VAL 5 15 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA 5 35 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 65 through 67 Processing sheet with id=AH6, first strand: chain 'K' and resid 106 through 108 Processing sheet with id=AH7, first strand: chain 'K' and resid 155 through 160 removed outlier: 3.769A pdb=" N TYR K 144 " --> pdb=" O PHE K 160 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 165 through 169 removed outlier: 6.577A pdb=" N ILE K 166 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA K 180 " --> pdb=" O ILE K 166 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL K 168 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN K 195 " --> pdb=" O LYS K 210 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 165 through 169 removed outlier: 6.577A pdb=" N ILE K 166 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA K 180 " --> pdb=" O ILE K 166 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL K 168 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN K 195 " --> pdb=" O LYS K 210 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 316 through 321 Processing sheet with id=AI2, first strand: chain 'L' and resid 65 through 67 Processing sheet with id=AI3, first strand: chain 'L' and resid 106 through 109 Processing sheet with id=AI4, first strand: chain 'L' and resid 155 through 160 removed outlier: 3.748A pdb=" N TYR L 144 " --> pdb=" O PHE L 160 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 165 through 169 removed outlier: 6.526A pdb=" N ILE L 166 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA L 180 " --> pdb=" O ILE L 166 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL L 168 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN L 195 " --> pdb=" O LYS L 210 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 165 through 169 removed outlier: 6.526A pdb=" N ILE L 166 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA L 180 " --> pdb=" O ILE L 166 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL L 168 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN L 195 " --> pdb=" O LYS L 210 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '6' and resid 88 through 89 removed outlier: 4.998A pdb=" N ILE 6 80 " --> pdb=" O ASP 6 104 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE 6 32 " --> pdb=" O PHE 6 11 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER 6 13 " --> pdb=" O ASP 6 30 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP 6 30 " --> pdb=" O SER 6 13 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL 6 15 " --> pdb=" O TRP 6 28 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP 6 28 " --> pdb=" O VAL 6 15 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA 6 35 " --> pdb=" O PRO 6 63 " (cutoff:3.500A) 3035 hydrogen bonds defined for protein. 8649 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: 21.28 Time building geometry restraints manager: 17.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 10326 1.28 - 1.42: 15186 1.42 - 1.55: 33603 1.55 - 1.68: 147 1.68 - 1.82: 504 Bond restraints: 59766 Sorted by residual: bond pdb=" C PHE 2 11 " pdb=" O PHE 2 11 " ideal model delta sigma weight residual 1.235 1.149 0.087 1.22e-02 6.72e+03 5.06e+01 bond pdb=" C PHE 5 11 " pdb=" O PHE 5 11 " ideal model delta sigma weight residual 1.235 1.149 0.086 1.22e-02 6.72e+03 5.01e+01 bond pdb=" C PHE 1 11 " pdb=" O PHE 1 11 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.22e-02 6.72e+03 4.11e+01 bond pdb=" C PHE 4 11 " pdb=" O PHE 4 11 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.22e-02 6.72e+03 4.11e+01 bond pdb=" C PHE 6 11 " pdb=" O PHE 6 11 " ideal model delta sigma weight residual 1.235 1.157 0.078 1.22e-02 6.72e+03 4.10e+01 ... (remaining 59761 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.58: 1161 105.58 - 112.70: 28769 112.70 - 119.82: 22408 119.82 - 126.94: 27930 126.94 - 134.07: 570 Bond angle restraints: 80838 Sorted by residual: angle pdb=" O MET i 75 " pdb=" C MET i 75 " pdb=" N ASP i 76 " ideal model delta sigma weight residual 123.40 128.98 -5.58 1.13e+00 7.83e-01 2.44e+01 angle pdb=" O MET c 75 " pdb=" C MET c 75 " pdb=" N ASP c 76 " ideal model delta sigma weight residual 123.40 128.97 -5.57 1.13e+00 7.83e-01 2.43e+01 angle pdb=" N GLY 3 22 " pdb=" CA GLY 3 22 " pdb=" C GLY 3 22 " ideal model delta sigma weight residual 113.18 101.98 11.20 2.37e+00 1.78e-01 2.23e+01 angle pdb=" N GLY 6 22 " pdb=" CA GLY 6 22 " pdb=" C GLY 6 22 " ideal model delta sigma weight residual 113.18 102.00 11.18 2.37e+00 1.78e-01 2.23e+01 angle pdb=" O MET g 75 " pdb=" C MET g 75 " pdb=" N ASP g 76 " ideal model delta sigma weight residual 123.40 128.72 -5.32 1.13e+00 7.83e-01 2.22e+01 ... (remaining 80833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 32554 17.86 - 35.73: 2885 35.73 - 53.59: 402 53.59 - 71.46: 176 71.46 - 89.32: 49 Dihedral angle restraints: 36066 sinusoidal: 14802 harmonic: 21264 Sorted by residual: dihedral pdb=" CA ASP B 171 " pdb=" C ASP B 171 " pdb=" N ASN B 172 " pdb=" CA ASN B 172 " ideal model delta harmonic sigma weight residual 180.00 116.11 63.89 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ASP H 171 " pdb=" C ASP H 171 " pdb=" N ASN H 172 " pdb=" CA ASN H 172 " ideal model delta harmonic sigma weight residual 180.00 116.13 63.87 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ASP L 171 " pdb=" C ASP L 171 " pdb=" N ASN L 172 " pdb=" CA ASN L 172 " ideal model delta harmonic sigma weight residual 180.00 117.54 62.46 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 36063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 7155 0.073 - 0.145: 1335 0.145 - 0.218: 150 0.218 - 0.290: 21 0.290 - 0.363: 9 Chirality restraints: 8670 Sorted by residual: chirality pdb=" CA ASP i 76 " pdb=" N ASP i 76 " pdb=" C ASP i 76 " pdb=" CB ASP i 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ASP c 76 " pdb=" N ASP c 76 " pdb=" C ASP c 76 " pdb=" CB ASP c 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA PHE i 31 " pdb=" N PHE i 31 " pdb=" C PHE i 31 " pdb=" CB PHE i 31 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 8667 not shown) Planarity restraints: 10620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET c 75 " -0.019 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C MET c 75 " 0.071 2.00e-02 2.50e+03 pdb=" O MET c 75 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP c 76 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET i 75 " 0.019 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C MET i 75 " -0.071 2.00e-02 2.50e+03 pdb=" O MET i 75 " 0.028 2.00e-02 2.50e+03 pdb=" N ASP i 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET g 75 " 0.018 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C MET g 75 " -0.067 2.00e-02 2.50e+03 pdb=" O MET g 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP g 76 " 0.023 2.00e-02 2.50e+03 ... (remaining 10617 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 7007 2.76 - 3.29: 51635 3.29 - 3.83: 94536 3.83 - 4.36: 119119 4.36 - 4.90: 197142 Nonbonded interactions: 469439 Sorted by model distance: nonbonded pdb=" OE1 GLU J 103 " pdb=" OG1 THR J 417 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLU D 103 " pdb=" OG1 THR D 417 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR J 99 " pdb=" OD1 ASP J 371 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR D 99 " pdb=" OD1 ASP D 371 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR G 99 " pdb=" OD1 ASP G 371 " model vdw 2.282 2.440 ... (remaining 469434 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 4.820 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: 0.050 Extract box with map and model: 20.060 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 114.530 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.006 0.087 59766 Z= 0.382 Angle : 0.887 12.991 80838 Z= 0.514 Chirality : 0.058 0.363 8670 Planarity : 0.007 0.060 10620 Dihedral : 14.326 89.323 22446 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 0.16 % Allowed : 3.37 % Favored : 96.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.08), residues: 7158 helix: -1.27 (0.07), residues: 3216 sheet: -0.35 (0.14), residues: 1044 loop : -1.57 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 239 HIS 0.010 0.001 HIS L 229 PHE 0.035 0.003 PHE a 31 TYR 0.018 0.002 TYR 4 14 ARG 0.010 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1347 time to evaluate : 5.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6985 (mtt180) REVERT: A 289 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7732 (tptt) REVERT: A 440 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8136 (tppp) REVERT: B 289 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7706 (tptt) REVERT: B 334 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6792 (mt-10) REVERT: a 92 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8377 (mmtt) REVERT: b 92 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8133 (mmtp) REVERT: C 190 MET cc_start: 0.6340 (mmm) cc_final: 0.6056 (mmm) REVERT: C 241 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7255 (ttm-80) REVERT: C 289 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7900 (tptt) REVERT: D 289 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7926 (tptt) REVERT: D 334 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6931 (mt-10) REVERT: E 289 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8114 (tptt) REVERT: E 408 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7749 (mptp) REVERT: F 289 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8182 (tptt) REVERT: F 394 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7642 (mm-30) REVERT: F 465 ASN cc_start: 0.7071 (m-40) cc_final: 0.6715 (m-40) REVERT: 3 3 GLU cc_start: 0.7073 (mp0) cc_final: 0.6864 (mp0) REVERT: G 289 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8138 (tptt) REVERT: G 470 MET cc_start: 0.5122 (mtm) cc_final: 0.4262 (ttm) REVERT: H 127 ASP cc_start: 0.7852 (m-30) cc_final: 0.7486 (m-30) REVERT: H 289 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8183 (tptt) REVERT: H 334 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6583 (mt-10) REVERT: h 79 SER cc_start: 0.8692 (p) cc_final: 0.8477 (p) REVERT: 4 3 GLU cc_start: 0.7061 (mp0) cc_final: 0.6713 (mp0) REVERT: I 289 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7979 (tptt) REVERT: I 407 ASP cc_start: 0.7105 (m-30) cc_final: 0.6706 (m-30) REVERT: I 462 GLU cc_start: 0.7172 (tt0) cc_final: 0.6969 (tt0) REVERT: J 127 ASP cc_start: 0.8124 (m-30) cc_final: 0.7761 (m-30) REVERT: J 289 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8003 (tptt) REVERT: J 334 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6688 (mt-10) REVERT: 5 44 GLU cc_start: 0.7007 (mp0) cc_final: 0.6783 (mp0) REVERT: K 289 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7945 (mmtt) REVERT: K 462 GLU cc_start: 0.7077 (tt0) cc_final: 0.6858 (tt0) REVERT: L 127 ASP cc_start: 0.8007 (m-30) cc_final: 0.7726 (m-30) REVERT: L 190 MET cc_start: 0.6583 (mmt) cc_final: 0.6109 (mpp) REVERT: L 227 ARG cc_start: 0.6231 (ttt180) cc_final: 0.5802 (ttt180) REVERT: L 289 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7873 (tptt) REVERT: L 334 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6914 (mt-10) outliers start: 10 outliers final: 6 residues processed: 1353 average time/residue: 1.4917 time to fit residues: 2520.3985 Evaluate side-chains 1074 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1068 time to evaluate : 5.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain K residue 354 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 6.9990 chunk 536 optimal weight: 0.0020 chunk 297 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 554 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 413 optimal weight: 9.9990 chunk 642 optimal weight: 3.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 98 GLN A 119 ASN A 283 GLN A 302 ASN ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN B 35 GLN B 131 ASN B 136 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 302 ASN B 431 GLN b 17 HIS b 46 ASN 1 53 GLN C 35 GLN C 98 GLN C 119 ASN C 283 GLN C 302 ASN C 349 ASN C 431 GLN C 466 GLN D 35 GLN D 136 ASN D 204 HIS D 224 ASN D 283 GLN D 302 ASN d 17 HIS d 46 ASN 2 17 GLN 2 53 GLN E 35 GLN E 98 GLN E 119 ASN ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 302 ASN E 427 GLN E 431 GLN E 451 GLN F 35 GLN F 136 ASN F 224 ASN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN F 302 ASN F 431 GLN F 451 GLN f 17 HIS f 46 ASN 3 17 GLN 3 51 GLN G 35 GLN G 98 GLN G 119 ASN G 283 GLN G 302 ASN G 349 ASN G 431 GLN G 451 GLN H 35 GLN H 131 ASN H 136 ASN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN H 302 ASN H 431 GLN H 451 GLN h 17 HIS h 46 ASN 4 17 GLN 4 51 GLN 4 53 GLN I 35 GLN I 98 GLN I 195 GLN I 283 GLN I 302 ASN I 345 GLN ** I 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 451 GLN J 35 GLN J 131 ASN J 136 ASN J 224 ASN J 283 GLN J 302 ASN J 398 ASN J 451 GLN j 17 HIS j 46 ASN 5 51 GLN K 98 GLN K 119 ASN K 195 GLN ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 GLN K 302 ASN K 349 ASN K 431 GLN K 451 GLN L 35 GLN L 131 ASN L 136 ASN L 224 ASN L 283 GLN L 302 ASN ** L 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 431 GLN l 17 HIS l 46 ASN 6 17 GLN 6 53 GLN 6 59 ASN Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 59766 Z= 0.300 Angle : 0.660 9.839 80838 Z= 0.364 Chirality : 0.048 0.174 8670 Planarity : 0.006 0.050 10620 Dihedral : 5.615 53.634 7982 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 1.95 % Allowed : 10.40 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.35 (0.09), residues: 7158 helix: 0.63 (0.09), residues: 3204 sheet: 0.06 (0.15), residues: 1032 loop : -1.26 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 239 HIS 0.007 0.001 HIS L 229 PHE 0.019 0.002 PHE d 31 TYR 0.017 0.002 TYR H 186 ARG 0.004 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1105 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6906 (mtt) REVERT: A 289 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8122 (tptt) REVERT: A 427 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: B 36 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7149 (tttm) REVERT: B 289 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8153 (tptt) REVERT: B 334 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6884 (mt-10) REVERT: B 401 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7577 (mttm) REVERT: B 461 GLU cc_start: 0.7280 (pt0) cc_final: 0.6898 (pt0) REVERT: B 465 ASN cc_start: 0.7134 (m-40) cc_final: 0.6841 (m110) REVERT: a 35 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: b 44 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: b 65 MET cc_start: 0.8883 (mtt) cc_final: 0.8567 (mtp) REVERT: C 289 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8068 (tptt) REVERT: C 427 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: D 289 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8101 (tptt) REVERT: D 334 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6922 (mt-10) REVERT: c 16 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8089 (mptt) REVERT: d 19 GLU cc_start: 0.7832 (tt0) cc_final: 0.7575 (tt0) REVERT: d 65 MET cc_start: 0.8746 (mtt) cc_final: 0.8463 (mtp) REVERT: E 39 ASP cc_start: 0.7019 (m-30) cc_final: 0.6758 (m-30) REVERT: E 289 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8128 (tptt) REVERT: F 289 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8158 (tptt) REVERT: F 323 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: F 334 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6798 (mt-10) REVERT: G 289 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8186 (tptt) REVERT: G 297 LYS cc_start: 0.8358 (tttt) cc_final: 0.8068 (ttpt) REVERT: G 427 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: H 127 ASP cc_start: 0.7906 (m-30) cc_final: 0.7567 (m-30) REVERT: H 135 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8446 (ttmt) REVERT: H 289 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8162 (tptt) REVERT: H 334 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6840 (mt-10) REVERT: H 465 ASN cc_start: 0.6965 (m-40) cc_final: 0.6553 (m110) REVERT: h 65 MET cc_start: 0.8856 (mtt) cc_final: 0.8604 (mtp) REVERT: h 74 SER cc_start: 0.8996 (p) cc_final: 0.8683 (p) REVERT: 4 3 GLU cc_start: 0.7206 (mp0) cc_final: 0.6922 (mp0) REVERT: I 33 MET cc_start: 0.6239 (tpp) cc_final: 0.5916 (tpp) REVERT: I 289 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8127 (tptt) REVERT: J 127 ASP cc_start: 0.7943 (m-30) cc_final: 0.7611 (m-30) REVERT: J 289 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8189 (tptt) REVERT: J 334 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6817 (mt-10) REVERT: J 467 TYR cc_start: 0.7453 (t80) cc_final: 0.7223 (t80) REVERT: j 65 MET cc_start: 0.8874 (mtt) cc_final: 0.8629 (mtp) REVERT: j 75 MET cc_start: 0.7909 (ttp) cc_final: 0.7647 (ttm) REVERT: K 217 MET cc_start: 0.7047 (mmt) cc_final: 0.6782 (mpp) REVERT: K 289 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8126 (tptt) REVERT: L 127 ASP cc_start: 0.7924 (m-30) cc_final: 0.7646 (m-30) REVERT: L 190 MET cc_start: 0.6519 (mmt) cc_final: 0.6071 (mpp) REVERT: L 289 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8160 (tptt) REVERT: L 323 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: L 334 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6808 (mt-10) REVERT: L 455 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: L 470 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.5434 (ttp) REVERT: l 44 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: l 85 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8427 (mm-30) REVERT: 6 77 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7064 (mtt-85) outliers start: 124 outliers final: 44 residues processed: 1158 average time/residue: 1.4845 time to fit residues: 2158.9946 Evaluate side-chains 1113 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1053 time to evaluate : 5.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain a residue 35 GLU Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain b residue 44 ASP Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain 2 residue 27 LYS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 187 LYS Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 454 GLU Chi-restraints excluded: chain L residue 455 GLU Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 74 SER Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 535 optimal weight: 7.9990 chunk 437 optimal weight: 0.2980 chunk 177 optimal weight: 9.9990 chunk 644 optimal weight: 4.9990 chunk 695 optimal weight: 6.9990 chunk 573 optimal weight: 2.9990 chunk 638 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 516 optimal weight: 10.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN 1 51 GLN 1 53 GLN D 365 ASN D 431 GLN D 451 GLN 2 51 GLN F 451 GLN 3 51 GLN H 431 GLN H 451 GLN g 46 ASN 4 51 GLN 4 53 GLN I 119 ASN I 345 GLN I 431 GLN I 451 GLN J 398 ASN J 451 GLN 5 53 GLN K 35 GLN ** L 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 451 GLN 6 53 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 59766 Z= 0.254 Angle : 0.613 9.695 80838 Z= 0.336 Chirality : 0.046 0.166 8670 Planarity : 0.005 0.042 10620 Dihedral : 5.300 47.658 7968 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.16 % Allowed : 11.86 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.26 (0.10), residues: 7158 helix: 1.32 (0.09), residues: 3192 sheet: 0.34 (0.15), residues: 1008 loop : -1.17 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 5 28 HIS 0.004 0.001 HIS F 229 PHE 0.016 0.002 PHE d 31 TYR 0.015 0.001 TYR H 186 ARG 0.004 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1077 time to evaluate : 5.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8146 (tptt) REVERT: A 427 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 36 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7080 (tttm) REVERT: B 227 ARG cc_start: 0.6233 (ttt180) cc_final: 0.5881 (ttt180) REVERT: B 280 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6447 (m-30) REVERT: B 289 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8144 (tptt) REVERT: B 334 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6848 (mt-10) REVERT: B 401 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7525 (mttm) REVERT: B 461 GLU cc_start: 0.7273 (pt0) cc_final: 0.6926 (pt0) REVERT: B 465 ASN cc_start: 0.7072 (m-40) cc_final: 0.6797 (m110) REVERT: b 44 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6352 (m-30) REVERT: 1 77 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6886 (mtt-85) REVERT: C 190 MET cc_start: 0.6464 (mmm) cc_final: 0.5965 (mmm) REVERT: C 289 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8081 (tptt) REVERT: C 427 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: D 289 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8158 (tptt) REVERT: D 334 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6919 (mt-10) REVERT: c 16 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: d 65 MET cc_start: 0.8798 (mtt) cc_final: 0.8572 (mtp) REVERT: 2 27 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7259 (ttmt) REVERT: E 289 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8114 (tptt) REVERT: F 289 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8173 (tptt) REVERT: F 334 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6812 (mt-10) REVERT: G 39 ASP cc_start: 0.7058 (m-30) cc_final: 0.6849 (m-30) REVERT: G 190 MET cc_start: 0.6068 (mmm) cc_final: 0.5497 (mmm) REVERT: G 289 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8162 (tptt) REVERT: G 297 LYS cc_start: 0.8225 (tttt) cc_final: 0.7963 (ttpt) REVERT: G 427 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: H 127 ASP cc_start: 0.7794 (m-30) cc_final: 0.7514 (m-30) REVERT: H 289 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8161 (tptt) REVERT: H 334 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6825 (mt-10) REVERT: H 465 ASN cc_start: 0.7049 (m-40) cc_final: 0.6785 (m110) REVERT: h 65 MET cc_start: 0.8834 (mtt) cc_final: 0.8593 (mtp) REVERT: 4 3 GLU cc_start: 0.7182 (mp0) cc_final: 0.6910 (mp0) REVERT: I 289 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8122 (tptt) REVERT: J 127 ASP cc_start: 0.7892 (m-30) cc_final: 0.7600 (m-30) REVERT: J 289 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8176 (tptt) REVERT: J 334 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6844 (mt-10) REVERT: J 455 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: J 465 ASN cc_start: 0.6922 (m-40) cc_final: 0.6676 (m110) REVERT: J 467 TYR cc_start: 0.7445 (t80) cc_final: 0.7229 (t80) REVERT: j 44 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: j 65 MET cc_start: 0.8869 (mtt) cc_final: 0.8626 (mtp) REVERT: j 75 MET cc_start: 0.7882 (ttp) cc_final: 0.7610 (ttm) REVERT: K 190 MET cc_start: 0.6350 (mmm) cc_final: 0.5900 (mmm) REVERT: K 289 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8130 (tptt) REVERT: L 127 ASP cc_start: 0.7846 (m-30) cc_final: 0.7568 (m-30) REVERT: L 190 MET cc_start: 0.6466 (mmt) cc_final: 0.6042 (mpp) REVERT: L 227 ARG cc_start: 0.6133 (ttm170) cc_final: 0.5793 (ttm170) REVERT: L 289 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8145 (tptt) REVERT: L 334 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6783 (mt-10) REVERT: L 455 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: L 470 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5438 (ttp) REVERT: l 44 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: l 85 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8421 (mm-30) REVERT: 6 77 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7120 (mtt-85) outliers start: 137 outliers final: 61 residues processed: 1119 average time/residue: 1.4627 time to fit residues: 2062.7507 Evaluate side-chains 1126 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1049 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain b residue 44 ASP Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain 2 residue 27 LYS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 187 LYS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 217 MET Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain i residue 74 SER Chi-restraints excluded: chain j residue 44 ASP Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 454 GLU Chi-restraints excluded: chain L residue 455 GLU Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain k residue 74 SER Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 0.9980 chunk 484 optimal weight: 7.9990 chunk 334 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 646 optimal weight: 0.7980 chunk 684 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 612 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 451 GLN 1 51 GLN C 345 GLN C 349 ASN D 398 ASN D 451 GLN 2 51 GLN 2 53 GLN E 345 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN 3 51 GLN 3 53 GLN H 451 GLN 4 51 GLN 4 53 GLN I 451 GLN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN J 398 ASN J 451 GLN K 349 ASN ** L 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 451 GLN 6 53 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 59766 Z= 0.145 Angle : 0.520 9.262 80838 Z= 0.282 Chirality : 0.043 0.149 8670 Planarity : 0.004 0.041 10620 Dihedral : 4.886 44.022 7968 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer: Outliers : 2.00 % Allowed : 13.03 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.68 (0.10), residues: 7158 helix: 1.80 (0.09), residues: 3180 sheet: 0.12 (0.15), residues: 1122 loop : -0.97 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 239 HIS 0.002 0.001 HIS B 229 PHE 0.011 0.001 PHE c 31 TYR 0.012 0.001 TYR J 186 ARG 0.002 0.000 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1106 time to evaluate : 5.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: A 132 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 179 PHE cc_start: 0.9016 (p90) cc_final: 0.8801 (p90) REVERT: A 289 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8131 (tptt) REVERT: A 427 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: B 36 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7047 (tttm) REVERT: B 280 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6178 (m-30) REVERT: B 289 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8144 (tptt) REVERT: B 334 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6793 (mt-10) REVERT: B 401 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7526 (mttm) REVERT: B 465 ASN cc_start: 0.6915 (m-40) cc_final: 0.6650 (m110) REVERT: 1 77 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6855 (mtt-85) REVERT: C 190 MET cc_start: 0.6408 (mmm) cc_final: 0.6041 (mmm) REVERT: C 289 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8040 (tptt) REVERT: C 427 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: D 289 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8138 (tptt) REVERT: D 334 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 470 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5267 (ttp) REVERT: 2 66 ASP cc_start: 0.7339 (p0) cc_final: 0.7112 (p0) REVERT: E 289 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8109 (tptt) REVERT: E 427 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7836 (tp40) REVERT: F 179 PHE cc_start: 0.8271 (p90) cc_final: 0.8065 (p90) REVERT: F 217 MET cc_start: 0.7082 (mmt) cc_final: 0.6572 (mmt) REVERT: F 227 ARG cc_start: 0.6106 (ttm-80) cc_final: 0.5904 (ttm170) REVERT: F 289 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8165 (tptt) REVERT: F 334 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6734 (mt-10) REVERT: G 39 ASP cc_start: 0.6989 (m-30) cc_final: 0.6759 (m-30) REVERT: G 116 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: G 289 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8136 (tptt) REVERT: G 427 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: H 127 ASP cc_start: 0.7718 (m-30) cc_final: 0.7455 (m-30) REVERT: H 289 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8148 (tptt) REVERT: H 334 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6787 (mt-10) REVERT: H 465 ASN cc_start: 0.6909 (m-40) cc_final: 0.6670 (m110) REVERT: h 65 MET cc_start: 0.8790 (mtt) cc_final: 0.8587 (mtp) REVERT: 4 3 GLU cc_start: 0.7131 (mp0) cc_final: 0.6851 (mp0) REVERT: I 33 MET cc_start: 0.6462 (tpp) cc_final: 0.6146 (tpp) REVERT: I 289 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8088 (tptt) REVERT: J 127 ASP cc_start: 0.7706 (m-30) cc_final: 0.7467 (m-30) REVERT: J 289 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8153 (tptt) REVERT: J 334 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6774 (mt-10) REVERT: J 455 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6670 (tp30) REVERT: J 465 ASN cc_start: 0.6928 (m-40) cc_final: 0.6608 (m110) REVERT: J 467 TYR cc_start: 0.7417 (t80) cc_final: 0.7216 (t80) REVERT: j 75 MET cc_start: 0.7795 (ttp) cc_final: 0.7563 (ttm) REVERT: K 289 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8106 (tptt) REVERT: K 470 MET cc_start: 0.5376 (mtt) cc_final: 0.4773 (mtp) REVERT: L 127 ASP cc_start: 0.7756 (m-30) cc_final: 0.7484 (m-30) REVERT: L 190 MET cc_start: 0.6273 (mmt) cc_final: 0.5998 (mpp) REVERT: L 227 ARG cc_start: 0.6088 (ttm170) cc_final: 0.5820 (ttm-80) REVERT: L 289 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8156 (tptt) REVERT: L 323 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: L 334 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6734 (mt-10) REVERT: L 470 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5532 (ttp) REVERT: l 44 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: 6 77 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7083 (mtt-85) outliers start: 127 outliers final: 45 residues processed: 1159 average time/residue: 1.4091 time to fit residues: 2064.9099 Evaluate side-chains 1134 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1073 time to evaluate : 5.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 217 MET Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain i residue 74 SER Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain L residue 464 MET Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain k residue 74 SER Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 509 optimal weight: 0.8980 chunk 282 optimal weight: 0.4980 chunk 583 optimal weight: 10.0000 chunk 473 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 614 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN D 465 ASN 2 51 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 451 GLN 3 51 GLN H 431 GLN H 451 GLN 4 51 GLN 4 53 GLN 4 59 ASN J 451 GLN ** L 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 451 GLN 6 51 GLN 6 53 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 59766 Z= 0.160 Angle : 0.520 9.001 80838 Z= 0.281 Chirality : 0.043 0.151 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.749 40.906 7968 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.02 % Allowed : 13.91 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.10), residues: 7158 helix: 1.99 (0.09), residues: 3192 sheet: 0.18 (0.15), residues: 1110 loop : -0.94 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.004 0.001 HIS d 17 PHE 0.013 0.001 PHE c 31 TYR 0.012 0.001 TYR H 186 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1093 time to evaluate : 5.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: A 132 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 190 MET cc_start: 0.5806 (mmm) cc_final: 0.5398 (mmm) REVERT: A 289 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8128 (tptt) REVERT: A 427 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: B 36 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7068 (tttm) REVERT: B 280 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6136 (m-30) REVERT: B 289 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8138 (tptt) REVERT: B 334 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6771 (mt-10) REVERT: B 401 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7505 (mttm) REVERT: B 465 ASN cc_start: 0.6925 (m-40) cc_final: 0.6629 (m110) REVERT: b 65 MET cc_start: 0.8776 (mtt) cc_final: 0.8542 (mtp) REVERT: 1 77 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6842 (mtt-85) REVERT: C 190 MET cc_start: 0.6296 (mmm) cc_final: 0.6036 (mmm) REVERT: C 289 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8051 (tptt) REVERT: C 427 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: D 289 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8135 (tptt) REVERT: D 334 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6842 (mt-10) REVERT: D 467 TYR cc_start: 0.7309 (t80) cc_final: 0.7071 (t80) REVERT: D 470 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5217 (ttp) REVERT: 2 66 ASP cc_start: 0.7290 (p0) cc_final: 0.7073 (p0) REVERT: E 289 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8117 (tptt) REVERT: E 297 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7397 (tttm) REVERT: E 378 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: E 427 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: F 289 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8160 (tptt) REVERT: F 334 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6736 (mt-10) REVERT: F 465 ASN cc_start: 0.6915 (m-40) cc_final: 0.6621 (m110) REVERT: G 39 ASP cc_start: 0.6999 (m-30) cc_final: 0.6749 (m-30) REVERT: G 116 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: G 190 MET cc_start: 0.5859 (mmm) cc_final: 0.5435 (mmm) REVERT: G 289 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8126 (tptt) REVERT: G 427 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: H 127 ASP cc_start: 0.7723 (m-30) cc_final: 0.7462 (m-30) REVERT: H 135 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8410 (ttmt) REVERT: H 289 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8147 (tptt) REVERT: H 334 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6776 (mt-10) REVERT: H 465 ASN cc_start: 0.6926 (m-40) cc_final: 0.6672 (m110) REVERT: h 65 MET cc_start: 0.8794 (mtt) cc_final: 0.8580 (mtp) REVERT: h 74 SER cc_start: 0.8948 (p) cc_final: 0.8605 (p) REVERT: 4 3 GLU cc_start: 0.7124 (mp0) cc_final: 0.6848 (mp0) REVERT: I 289 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8084 (tptt) REVERT: I 427 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: J 127 ASP cc_start: 0.7712 (m-30) cc_final: 0.7481 (m-30) REVERT: J 289 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8149 (tptt) REVERT: J 334 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6812 (mt-10) REVERT: J 455 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: J 465 ASN cc_start: 0.6941 (m-40) cc_final: 0.6657 (m110) REVERT: j 75 MET cc_start: 0.7901 (ttp) cc_final: 0.7624 (ttm) REVERT: K 190 MET cc_start: 0.6057 (mmm) cc_final: 0.5573 (mmm) REVERT: K 289 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8115 (tptt) REVERT: K 470 MET cc_start: 0.5298 (mtt) cc_final: 0.4766 (mtp) REVERT: L 127 ASP cc_start: 0.7735 (m-30) cc_final: 0.7456 (m-30) REVERT: L 190 MET cc_start: 0.6292 (mmt) cc_final: 0.6031 (mpp) REVERT: L 227 ARG cc_start: 0.6115 (ttm170) cc_final: 0.5879 (ttm-80) REVERT: L 289 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8157 (tptt) REVERT: L 323 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: L 334 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6715 (mt-10) REVERT: L 455 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: k 16 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8004 (mppt) REVERT: 6 77 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7106 (mtt-85) outliers start: 128 outliers final: 58 residues processed: 1139 average time/residue: 1.4359 time to fit residues: 2066.5553 Evaluate side-chains 1143 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1065 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain I residue 427 GLN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 217 MET Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain i residue 74 SER Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain L residue 455 GLU Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 0.9980 chunk 616 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 685 optimal weight: 7.9990 chunk 568 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN D 465 ASN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 451 GLN 4 51 GLN 4 53 GLN 4 59 ASN J 204 HIS J 451 GLN 5 51 GLN 5 59 ASN L 398 ASN L 451 GLN 6 51 GLN 6 53 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 59766 Z= 0.218 Angle : 0.565 9.804 80838 Z= 0.307 Chirality : 0.045 0.157 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.882 40.248 7968 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.98 % Allowed : 14.34 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7158 helix: 1.95 (0.09), residues: 3192 sheet: 0.58 (0.15), residues: 1050 loop : -1.02 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 5 28 HIS 0.004 0.001 HIS j 17 PHE 0.016 0.001 PHE c 31 TYR 0.012 0.001 TYR B 186 ARG 0.002 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1080 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: A 190 MET cc_start: 0.5804 (mmm) cc_final: 0.5408 (mmm) REVERT: A 289 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8151 (tptt) REVERT: A 427 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 36 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7081 (tttm) REVERT: B 280 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6324 (m-30) REVERT: B 289 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8151 (tptt) REVERT: B 334 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6810 (mt-10) REVERT: B 401 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7523 (mttm) REVERT: B 465 ASN cc_start: 0.6993 (m-40) cc_final: 0.6710 (m110) REVERT: 1 77 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6871 (mtt-85) REVERT: C 289 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8072 (tptt) REVERT: C 427 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: D 289 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8160 (tptt) REVERT: D 334 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6847 (mt-10) REVERT: D 467 TYR cc_start: 0.7373 (t80) cc_final: 0.7138 (t80) REVERT: D 470 MET cc_start: 0.5556 (OUTLIER) cc_final: 0.5140 (ttp) REVERT: c 16 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7982 (mptt) REVERT: E 289 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8116 (tptt) REVERT: E 297 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7381 (tttm) REVERT: E 378 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: E 427 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: F 227 ARG cc_start: 0.6336 (ttm-80) cc_final: 0.5937 (ttm170) REVERT: F 289 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8161 (tptt) REVERT: F 334 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6769 (mt-10) REVERT: F 465 ASN cc_start: 0.6911 (m-40) cc_final: 0.6624 (m110) REVERT: G 39 ASP cc_start: 0.7032 (m-30) cc_final: 0.6766 (m-30) REVERT: G 190 MET cc_start: 0.5906 (mmm) cc_final: 0.5358 (mmm) REVERT: G 289 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8152 (tptt) REVERT: G 297 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7890 (ttpt) REVERT: G 427 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: H 127 ASP cc_start: 0.7789 (m-30) cc_final: 0.7508 (m-30) REVERT: H 135 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8462 (ttmt) REVERT: H 289 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8156 (tptt) REVERT: H 334 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6822 (mt-10) REVERT: H 465 ASN cc_start: 0.7028 (m-40) cc_final: 0.6677 (m110) REVERT: h 65 MET cc_start: 0.8826 (mtt) cc_final: 0.8580 (mtp) REVERT: 4 3 GLU cc_start: 0.7148 (mp0) cc_final: 0.6862 (mp0) REVERT: I 33 MET cc_start: 0.6648 (tpp) cc_final: 0.6355 (tpp) REVERT: I 289 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8107 (tptt) REVERT: J 127 ASP cc_start: 0.7757 (m-30) cc_final: 0.7520 (m-30) REVERT: J 289 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8173 (tptt) REVERT: J 334 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6834 (mt-10) REVERT: J 455 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: J 465 ASN cc_start: 0.7055 (m-40) cc_final: 0.6822 (m110) REVERT: j 75 MET cc_start: 0.7979 (ttp) cc_final: 0.7755 (ttm) REVERT: K 116 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: K 190 MET cc_start: 0.6091 (mmm) cc_final: 0.5678 (mmm) REVERT: K 289 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8127 (tptt) REVERT: K 427 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: K 470 MET cc_start: 0.5382 (mtt) cc_final: 0.4858 (mtp) REVERT: L 127 ASP cc_start: 0.7776 (m-30) cc_final: 0.7491 (m-30) REVERT: L 190 MET cc_start: 0.6380 (mmt) cc_final: 0.6098 (mpp) REVERT: L 227 ARG cc_start: 0.6169 (ttm170) cc_final: 0.5924 (ttm-80) REVERT: L 289 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8150 (tptt) REVERT: L 323 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: L 334 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6774 (mt-10) REVERT: L 455 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: k 16 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8034 (mppt) REVERT: l 44 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6355 (m-30) REVERT: 6 77 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7126 (mtt-85) outliers start: 126 outliers final: 76 residues processed: 1139 average time/residue: 1.4592 time to fit residues: 2097.3469 Evaluate side-chains 1165 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1066 time to evaluate : 5.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 217 MET Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain i residue 74 SER Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 427 GLN Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain L residue 454 GLU Chi-restraints excluded: chain L residue 455 GLU Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain l residue 44 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 390 optimal weight: 6.9990 chunk 500 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 576 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 682 optimal weight: 0.1980 chunk 427 optimal weight: 5.9990 chunk 416 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN D 465 ASN 2 51 GLN F 365 ASN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN G 349 ASN H 431 GLN H 451 GLN 4 51 GLN 4 59 ASN J 451 GLN L 398 ASN L 451 GLN 6 51 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 59766 Z= 0.157 Angle : 0.520 9.688 80838 Z= 0.280 Chirality : 0.043 0.151 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.683 37.887 7968 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.81 % Allowed : 14.89 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.10), residues: 7158 helix: 2.14 (0.09), residues: 3180 sheet: 0.51 (0.15), residues: 1074 loop : -0.89 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.004 0.001 HIS d 17 PHE 0.012 0.001 PHE c 31 TYR 0.012 0.001 TYR B 186 ARG 0.001 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1099 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5834 (mmm) cc_final: 0.5571 (mmm) REVERT: A 289 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8134 (tptt) REVERT: A 427 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 36 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7089 (tttt) REVERT: B 190 MET cc_start: 0.6219 (mmt) cc_final: 0.5957 (mpp) REVERT: B 280 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 289 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8141 (tptt) REVERT: B 334 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 401 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7519 (mttm) REVERT: B 465 ASN cc_start: 0.6957 (m-40) cc_final: 0.6672 (m110) REVERT: b 65 MET cc_start: 0.8752 (mtt) cc_final: 0.8530 (mtp) REVERT: 1 77 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6833 (mtt-85) REVERT: C 289 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8054 (tptt) REVERT: C 427 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: D 289 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8135 (tptt) REVERT: D 334 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6843 (mt-10) REVERT: D 467 TYR cc_start: 0.7332 (t80) cc_final: 0.7113 (t80) REVERT: 2 1 MET cc_start: 0.6711 (mpt) cc_final: 0.6472 (mpp) REVERT: E 289 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8121 (tptt) REVERT: E 297 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7367 (tttm) REVERT: E 427 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: F 289 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8162 (tptt) REVERT: F 334 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6735 (mt-10) REVERT: F 465 ASN cc_start: 0.6867 (m-40) cc_final: 0.6591 (m110) REVERT: f 44 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: G 39 ASP cc_start: 0.7017 (m-30) cc_final: 0.6796 (m-30) REVERT: G 137 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: G 190 MET cc_start: 0.5746 (mmm) cc_final: 0.5252 (mmm) REVERT: G 289 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8132 (tptt) REVERT: G 297 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (ttpt) REVERT: G 427 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: H 127 ASP cc_start: 0.7730 (m-30) cc_final: 0.7461 (m-30) REVERT: H 135 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8383 (ttmt) REVERT: H 289 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8141 (tptt) REVERT: H 334 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6772 (mt-10) REVERT: H 465 ASN cc_start: 0.6865 (m-40) cc_final: 0.6647 (m110) REVERT: h 65 MET cc_start: 0.8792 (mtt) cc_final: 0.8576 (mtp) REVERT: 4 3 GLU cc_start: 0.7122 (mp0) cc_final: 0.6840 (mp0) REVERT: I 33 MET cc_start: 0.6661 (tpp) cc_final: 0.6258 (tpp) REVERT: I 289 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8088 (tptt) REVERT: J 127 ASP cc_start: 0.7694 (m-30) cc_final: 0.7477 (m-30) REVERT: J 289 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8148 (tptt) REVERT: J 334 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6822 (mt-10) REVERT: J 455 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: J 465 ASN cc_start: 0.6988 (m-40) cc_final: 0.6756 (m110) REVERT: J 470 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5130 (ttp) REVERT: j 75 MET cc_start: 0.7962 (ttp) cc_final: 0.7740 (ttm) REVERT: K 289 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8119 (tptt) REVERT: K 427 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: K 470 MET cc_start: 0.5330 (mtt) cc_final: 0.4899 (mtp) REVERT: L 127 ASP cc_start: 0.7689 (m-30) cc_final: 0.7416 (m-30) REVERT: L 190 MET cc_start: 0.6296 (mmt) cc_final: 0.6010 (mpp) REVERT: L 217 MET cc_start: 0.7045 (mmt) cc_final: 0.6640 (mmt) REVERT: L 289 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8153 (tptt) REVERT: L 323 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: L 334 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6758 (mt-10) REVERT: k 16 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8005 (mppt) REVERT: 6 77 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7104 (mtt-85) outliers start: 115 outliers final: 64 residues processed: 1152 average time/residue: 1.4130 time to fit residues: 2059.3457 Evaluate side-chains 1163 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1080 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 244 ILE Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 230 MET Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 427 GLN Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 323 GLU Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 407 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 433 optimal weight: 1.9990 chunk 464 optimal weight: 10.0000 chunk 337 optimal weight: 0.0670 chunk 63 optimal weight: 5.9990 chunk 536 optimal weight: 0.9980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN 2 51 GLN 2 59 ASN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 451 GLN 4 17 GLN 4 51 GLN 4 59 ASN J 451 GLN 5 51 GLN L 398 ASN L 451 GLN 6 51 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 59766 Z= 0.145 Angle : 0.506 9.557 80838 Z= 0.272 Chirality : 0.043 0.145 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.545 36.284 7968 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.81 % Allowed : 15.14 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.10), residues: 7158 helix: 2.25 (0.09), residues: 3180 sheet: 0.31 (0.15), residues: 1122 loop : -0.78 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.002 0.001 HIS j 17 PHE 0.011 0.001 PHE c 31 TYR 0.012 0.001 TYR B 186 ARG 0.002 0.000 ARG H 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1100 time to evaluate : 5.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8122 (tptt) REVERT: A 427 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: B 36 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7081 (tttt) REVERT: B 187 LYS cc_start: 0.7927 (tppt) cc_final: 0.7696 (tttm) REVERT: B 280 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6043 (m-30) REVERT: B 289 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8137 (tptt) REVERT: B 334 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6754 (mt-10) REVERT: B 465 ASN cc_start: 0.6883 (m-40) cc_final: 0.6611 (m110) REVERT: b 65 MET cc_start: 0.8772 (mtt) cc_final: 0.8516 (mtp) REVERT: 1 77 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6838 (mtt-85) REVERT: C 289 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8062 (tptt) REVERT: C 427 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: D 289 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8131 (tptt) REVERT: D 334 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6809 (mt-10) REVERT: D 467 TYR cc_start: 0.7387 (t80) cc_final: 0.7171 (t80) REVERT: E 289 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8116 (tptt) REVERT: E 297 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7351 (tttm) REVERT: E 378 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: E 427 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: E 470 MET cc_start: 0.5254 (mtt) cc_final: 0.4870 (mtp) REVERT: F 227 ARG cc_start: 0.6319 (ttm-80) cc_final: 0.5940 (ttm170) REVERT: F 289 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8167 (tptt) REVERT: F 334 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6712 (mt-10) REVERT: F 465 ASN cc_start: 0.6806 (m-40) cc_final: 0.6523 (m110) REVERT: f 44 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: G 39 ASP cc_start: 0.7001 (m-30) cc_final: 0.6775 (m-30) REVERT: G 116 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: G 289 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8115 (tptt) REVERT: G 427 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: H 127 ASP cc_start: 0.7710 (m-30) cc_final: 0.7458 (m-30) REVERT: H 135 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8351 (ttmt) REVERT: H 289 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8143 (tptt) REVERT: H 334 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6753 (mt-10) REVERT: H 465 ASN cc_start: 0.6866 (m-40) cc_final: 0.6637 (m110) REVERT: h 65 MET cc_start: 0.8781 (mtt) cc_final: 0.8571 (mtp) REVERT: 4 3 GLU cc_start: 0.7084 (mp0) cc_final: 0.6807 (mp0) REVERT: I 289 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8092 (tptt) REVERT: I 427 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: J 127 ASP cc_start: 0.7653 (m-30) cc_final: 0.7439 (m-30) REVERT: J 289 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8146 (tptt) REVERT: J 334 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6797 (mt-10) REVERT: J 455 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6759 (tp30) REVERT: J 465 ASN cc_start: 0.6970 (m-40) cc_final: 0.6737 (m110) REVERT: j 75 MET cc_start: 0.7955 (ttp) cc_final: 0.7732 (ttm) REVERT: K 190 MET cc_start: 0.5696 (mmm) cc_final: 0.5191 (mmm) REVERT: K 289 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8115 (tptt) REVERT: K 427 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: K 470 MET cc_start: 0.5275 (mtt) cc_final: 0.4869 (mtp) REVERT: L 127 ASP cc_start: 0.7669 (m-30) cc_final: 0.7404 (m-30) REVERT: L 190 MET cc_start: 0.6277 (mmt) cc_final: 0.6025 (mpp) REVERT: L 217 MET cc_start: 0.7003 (mmt) cc_final: 0.6660 (mmt) REVERT: L 289 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8159 (tptt) REVERT: L 334 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6699 (mt-10) REVERT: k 16 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7984 (mppt) REVERT: 6 77 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7057 (mtt-85) outliers start: 115 outliers final: 60 residues processed: 1152 average time/residue: 1.3903 time to fit residues: 2032.6599 Evaluate side-chains 1159 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1082 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain H residue 470 MET Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain h residue 44 ASP Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain I residue 427 GLN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 427 GLN Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 6.9990 chunk 653 optimal weight: 3.9990 chunk 596 optimal weight: 8.9990 chunk 635 optimal weight: 0.9980 chunk 382 optimal weight: 7.9990 chunk 277 optimal weight: 0.7980 chunk 499 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 574 optimal weight: 0.0570 chunk 601 optimal weight: 3.9990 chunk 633 optimal weight: 4.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 431 GLN H 451 GLN 4 51 GLN 4 59 ASN J 431 GLN J 451 GLN 5 51 GLN L 398 ASN L 451 GLN 6 51 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 59766 Z= 0.205 Angle : 0.556 9.961 80838 Z= 0.302 Chirality : 0.045 0.149 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.726 36.106 7968 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.61 % Allowed : 15.55 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 7158 helix: 2.11 (0.09), residues: 3192 sheet: 0.55 (0.15), residues: 1074 loop : -0.94 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.007 0.001 HIS d 17 PHE 0.016 0.001 PHE a 31 TYR 0.013 0.001 TYR D 186 ARG 0.003 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1082 time to evaluate : 5.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8146 (tptt) REVERT: A 427 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 36 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7117 (tttt) REVERT: B 187 LYS cc_start: 0.8008 (tppt) cc_final: 0.7745 (tttm) REVERT: B 280 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: B 289 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8146 (tptt) REVERT: B 334 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6803 (mt-10) REVERT: B 401 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (mttm) REVERT: B 465 ASN cc_start: 0.6970 (m-40) cc_final: 0.6688 (m110) REVERT: b 65 MET cc_start: 0.8802 (mtt) cc_final: 0.8544 (mtp) REVERT: 1 77 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6861 (mtt-85) REVERT: C 289 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8068 (tptt) REVERT: C 427 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: D 289 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8153 (tptt) REVERT: D 334 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6871 (mt-10) REVERT: 2 1 MET cc_start: 0.6656 (mpt) cc_final: 0.6420 (mpp) REVERT: E 289 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8119 (tptt) REVERT: E 297 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7457 (tttm) REVERT: E 378 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: E 427 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: E 470 MET cc_start: 0.5213 (mtt) cc_final: 0.4843 (mtp) REVERT: F 227 ARG cc_start: 0.6267 (ttm-80) cc_final: 0.5870 (ttm170) REVERT: F 289 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8165 (tptt) REVERT: F 334 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6712 (mt-10) REVERT: F 465 ASN cc_start: 0.6945 (m-40) cc_final: 0.6651 (m110) REVERT: G 39 ASP cc_start: 0.7008 (m-30) cc_final: 0.6770 (m-30) REVERT: G 289 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8146 (tptt) REVERT: G 427 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: H 127 ASP cc_start: 0.7801 (m-30) cc_final: 0.7516 (m-30) REVERT: H 135 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8455 (ttmt) REVERT: H 187 LYS cc_start: 0.7955 (tppt) cc_final: 0.7748 (tttm) REVERT: H 289 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8153 (tptt) REVERT: H 334 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6796 (mt-10) REVERT: H 465 ASN cc_start: 0.7010 (m-40) cc_final: 0.6768 (m110) REVERT: h 65 MET cc_start: 0.8821 (mtt) cc_final: 0.8580 (mtp) REVERT: 4 3 GLU cc_start: 0.7137 (mp0) cc_final: 0.6852 (mp0) REVERT: I 289 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8097 (tptt) REVERT: I 427 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: J 127 ASP cc_start: 0.7746 (m-30) cc_final: 0.7519 (m-30) REVERT: J 289 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8169 (tptt) REVERT: J 334 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6861 (mt-10) REVERT: J 455 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: J 465 ASN cc_start: 0.7080 (m-40) cc_final: 0.6825 (m110) REVERT: j 75 MET cc_start: 0.7972 (ttp) cc_final: 0.7743 (ttm) REVERT: K 190 MET cc_start: 0.5740 (mmm) cc_final: 0.5279 (mmm) REVERT: K 289 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8123 (tptt) REVERT: K 427 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: K 470 MET cc_start: 0.5345 (mtt) cc_final: 0.4909 (mtp) REVERT: L 127 ASP cc_start: 0.7725 (m-30) cc_final: 0.7437 (m-30) REVERT: L 190 MET cc_start: 0.6302 (mmt) cc_final: 0.6026 (mpp) REVERT: L 289 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8154 (tptt) REVERT: L 334 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6760 (mt-10) REVERT: k 16 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8034 (mppt) REVERT: 6 77 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7087 (mtt-85) outliers start: 102 outliers final: 72 residues processed: 1133 average time/residue: 1.4018 time to fit residues: 2012.4719 Evaluate side-chains 1160 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1072 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 25 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain h residue 44 ASP Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain I residue 427 GLN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 427 GLN Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain k residue 16 LYS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 66 ASP Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 3.9990 chunk 672 optimal weight: 2.9990 chunk 410 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 467 optimal weight: 3.9990 chunk 705 optimal weight: 3.9990 chunk 649 optimal weight: 4.9990 chunk 561 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 433 optimal weight: 7.9990 chunk 344 optimal weight: 0.0030 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 43 GLN 1 51 GLN 1 59 ASN D 451 GLN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 451 GLN 4 51 GLN 4 53 GLN 4 59 ASN J 451 GLN 5 51 GLN L 398 ASN L 451 GLN 6 51 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 59766 Z= 0.236 Angle : 0.585 10.764 80838 Z= 0.318 Chirality : 0.046 0.153 8670 Planarity : 0.004 0.040 10620 Dihedral : 4.863 35.649 7968 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.58 % Allowed : 15.56 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.94 (0.10), residues: 7158 helix: 2.01 (0.09), residues: 3192 sheet: 0.66 (0.15), residues: 1050 loop : -0.98 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 2 28 HIS 0.006 0.001 HIS j 17 PHE 0.016 0.002 PHE a 31 TYR 0.014 0.001 TYR 1 14 ARG 0.003 0.000 ARG F 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1063 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.5596 (mmm) cc_final: 0.5075 (mmm) REVERT: A 289 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8156 (tptt) REVERT: A 427 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 36 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7132 (tttt) REVERT: B 187 LYS cc_start: 0.7988 (tppt) cc_final: 0.7757 (tttm) REVERT: B 280 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6376 (m-30) REVERT: B 289 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8149 (tptt) REVERT: B 334 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6842 (mt-10) REVERT: B 401 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7521 (mttm) REVERT: B 465 ASN cc_start: 0.7022 (m-40) cc_final: 0.6751 (m110) REVERT: 1 77 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7541 (mtm-85) REVERT: C 289 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8074 (tptt) REVERT: C 427 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: D 289 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8163 (tptt) REVERT: D 334 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6852 (mt-10) REVERT: c 16 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7976 (mptt) REVERT: E 289 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8128 (tptt) REVERT: E 297 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7475 (tttm) REVERT: E 378 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: E 427 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: E 470 MET cc_start: 0.5161 (mtt) cc_final: 0.4859 (mtp) REVERT: F 227 ARG cc_start: 0.6251 (ttm-80) cc_final: 0.5831 (ttm170) REVERT: F 289 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8161 (tptt) REVERT: F 334 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6741 (mt-10) REVERT: F 465 ASN cc_start: 0.6949 (m-40) cc_final: 0.6682 (m110) REVERT: G 39 ASP cc_start: 0.7019 (m-30) cc_final: 0.6798 (m-30) REVERT: G 289 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8160 (tptt) REVERT: G 427 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: H 127 ASP cc_start: 0.7826 (m-30) cc_final: 0.7539 (m-30) REVERT: H 135 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8454 (ttmt) REVERT: H 187 LYS cc_start: 0.7961 (tppt) cc_final: 0.7756 (tttm) REVERT: H 289 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8160 (tptt) REVERT: H 334 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6838 (mt-10) REVERT: H 465 ASN cc_start: 0.7017 (m-40) cc_final: 0.6767 (m110) REVERT: h 65 MET cc_start: 0.8834 (mtt) cc_final: 0.8578 (mtp) REVERT: 4 3 GLU cc_start: 0.7173 (mp0) cc_final: 0.6890 (mp0) REVERT: I 289 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8092 (tptt) REVERT: I 427 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: J 127 ASP cc_start: 0.7782 (m-30) cc_final: 0.7559 (m-30) REVERT: J 289 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8177 (tptt) REVERT: J 334 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6852 (mt-10) REVERT: J 455 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: J 465 ASN cc_start: 0.7114 (m-40) cc_final: 0.6857 (m110) REVERT: j 75 MET cc_start: 0.7971 (ttp) cc_final: 0.7755 (ttm) REVERT: K 289 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8125 (tptt) REVERT: K 427 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: K 470 MET cc_start: 0.5369 (mtt) cc_final: 0.4937 (mtp) REVERT: L 127 ASP cc_start: 0.7756 (m-30) cc_final: 0.7481 (m-30) REVERT: L 190 MET cc_start: 0.6315 (mmt) cc_final: 0.6057 (mpp) REVERT: L 289 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8154 (tptt) REVERT: L 334 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6774 (mt-10) REVERT: L 465 ASN cc_start: 0.6881 (m-40) cc_final: 0.6582 (m110) REVERT: 6 77 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7102 (mtt-85) outliers start: 100 outliers final: 69 residues processed: 1110 average time/residue: 1.4211 time to fit residues: 1996.3624 Evaluate side-chains 1136 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1051 time to evaluate : 5.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain a residue 16 LYS Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 135 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 464 MET Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain 4 residue 54 THR Chi-restraints excluded: chain 4 residue 74 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain I residue 413 THR Chi-restraints excluded: chain I residue 427 GLN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 217 MET Chi-restraints excluded: chain J residue 455 GLU Chi-restraints excluded: chain J residue 464 MET Chi-restraints excluded: chain i residue 13 THR Chi-restraints excluded: chain 5 residue 54 THR Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 74 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 427 GLN Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 152 GLU Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 66 ASP Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 0.0270 chunk 598 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 517 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 156 optimal weight: 1.9990 chunk 562 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 577 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 GLN 1 51 GLN 1 59 ASN D 451 GLN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 451 GLN 4 51 GLN 4 59 ASN J 451 GLN L 398 ASN L 451 GLN 6 51 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116642 restraints weight = 64052.963| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.47 r_work: 0.3052 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 59766 Z= 0.160 Angle : 0.526 10.324 80838 Z= 0.283 Chirality : 0.043 0.145 8670 Planarity : 0.004 0.040 10620 Dihedral : 4.639 34.616 7968 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.48 % Allowed : 15.58 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.10), residues: 7158 helix: 2.20 (0.09), residues: 3180 sheet: 0.57 (0.15), residues: 1074 loop : -0.86 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 4 28 HIS 0.004 0.001 HIS d 17 PHE 0.012 0.001 PHE c 31 TYR 0.012 0.001 TYR B 186 ARG 0.002 0.000 ARG f 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27918.69 seconds wall clock time: 481 minutes 46.88 seconds (28906.88 seconds total)