Starting phenix.real_space_refine on Fri Dec 8 17:45:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/12_2023/7z4w_14509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/12_2023/7z4w_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_14509/12_2023/7z4w_14509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/12_2023/7z4w_14509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/12_2023/7z4w_14509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4w_14509/12_2023/7z4w_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 22.90, per 1000 atoms: 0.39 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: 17.06 Conformation dependent library (CDL) restraints added in 8.3 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: 4.76 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: 21.50 Time building geometry restraints manager: 19.02 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 20.290 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 119.320 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.610 ------------------------------------------------------------------------------- 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 : 5.199 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 outliers start: 10 outliers final: 6 residues processed: 1353 average time/residue: 1.5397 time to fit residues: 2596.4533 Evaluate side-chains 1068 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1062 time to evaluate : 5.278 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 1.4263 time to fit residues: 10.6244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- 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 136 ASN H 224 ASN 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: 0.8320 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 59766 Z= 0.314 Angle : 0.673 9.917 80838 Z= 0.372 Chirality : 0.049 0.179 8670 Planarity : 0.006 0.053 10620 Dihedral : 5.576 53.285 7968 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 2.16 % Allowed : 10.51 % Favored : 87.33 % 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: -0.42 (0.09), residues: 7158 helix: 0.58 (0.09), residues: 3204 sheet: -0.24 (0.15), residues: 1080 loop : -1.21 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 239 HIS 0.007 0.001 HIS L 229 PHE 0.019 0.002 PHE C 414 TYR 0.017 0.002 TYR J 186 ARG 0.004 0.001 ARG B 397 *********************** 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 1231 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1094 time to evaluate : 5.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 49 residues processed: 1155 average time/residue: 1.4982 time to fit residues: 2178.4515 Evaluate side-chains 1098 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1049 time to evaluate : 5.277 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 21 residues processed: 30 average time/residue: 0.7115 time to fit residues: 39.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 535 optimal weight: 7.9990 chunk 437 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 644 optimal weight: 10.0000 chunk 695 optimal weight: 9.9990 chunk 573 optimal weight: 0.4980 chunk 638 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 516 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** A 427 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN B 451 GLN 1 51 GLN 1 53 GLN D 365 ASN D 431 GLN D 451 GLN 2 51 GLN 2 53 GLN F 431 GLN F 451 GLN 3 51 GLN G 427 GLN H 431 GLN H 451 GLN H 465 ASN g 46 ASN 4 51 GLN 4 53 GLN I 119 ASN 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 431 GLN L 451 GLN 6 53 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59766 Z= 0.213 Angle : 0.584 9.347 80838 Z= 0.320 Chirality : 0.045 0.173 8670 Planarity : 0.005 0.042 10620 Dihedral : 5.221 48.013 7968 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.91 % Allowed : 12.15 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.27 (0.10), residues: 7158 helix: 1.36 (0.09), residues: 3192 sheet: 0.20 (0.15), residues: 1032 loop : -1.15 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 239 HIS 0.004 0.001 HIS B 229 PHE 0.015 0.001 PHE i 31 TYR 0.015 0.001 TYR H 186 ARG 0.003 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 1211 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1090 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 62 residues processed: 1135 average time/residue: 1.5069 time to fit residues: 2164.1662 Evaluate side-chains 1110 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1048 time to evaluate : 5.262 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 29 residues processed: 36 average time/residue: 0.7968 time to fit residues: 49.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 0.9990 chunk 484 optimal weight: 7.9990 chunk 334 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 432 optimal weight: 0.9980 chunk 646 optimal weight: 0.7980 chunk 684 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 612 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN B 451 GLN 1 51 GLN C 345 GLN D 131 ASN D 398 ASN D 451 GLN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN H 131 ASN H 431 GLN H 451 GLN 4 51 GLN 4 53 GLN I 349 ASN I 451 GLN ** J 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 ASN J 451 GLN ** L 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 431 GLN L 451 GLN 6 53 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 59766 Z= 0.146 Angle : 0.511 8.323 80838 Z= 0.277 Chirality : 0.043 0.148 8670 Planarity : 0.004 0.040 10620 Dihedral : 4.784 42.973 7968 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.98 % Allowed : 12.87 % Favored : 85.14 % 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: 0.72 (0.10), residues: 7158 helix: 1.85 (0.09), residues: 3180 sheet: 0.10 (0.15), residues: 1110 loop : -0.94 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 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 0.003 0.000 ARG F 227 *********************** 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 1234 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1108 time to evaluate : 5.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 44 residues processed: 1165 average time/residue: 1.4656 time to fit residues: 2160.0529 Evaluate side-chains 1123 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1079 time to evaluate : 5.238 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 27 residues processed: 20 average time/residue: 1.0419 time to fit residues: 35.4762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 509 optimal weight: 0.6980 chunk 282 optimal weight: 0.5980 chunk 583 optimal weight: 9.9990 chunk 473 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 614 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 427 GLN B 204 HIS B 431 GLN B 451 GLN 1 51 GLN 1 59 ASN C 427 GLN D 451 GLN D 465 ASN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN G 427 GLN H 431 GLN H 451 GLN 4 51 GLN 4 53 GLN 4 59 ASN I 427 GLN J 204 HIS J 451 GLN 5 17 GLN 5 51 GLN 5 59 ASN L 204 HIS ** L 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 431 GLN L 451 GLN 6 51 GLN 6 53 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 59766 Z= 0.318 Angle : 0.638 9.513 80838 Z= 0.350 Chirality : 0.048 0.166 8670 Planarity : 0.005 0.042 10620 Dihedral : 5.186 43.318 7968 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.16 % Allowed : 13.94 % Favored : 83.90 % 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: 0.56 (0.10), residues: 7158 helix: 1.64 (0.09), residues: 3216 sheet: 0.43 (0.15), residues: 1008 loop : -1.09 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 1 28 HIS 0.005 0.001 HIS g 17 PHE 0.018 0.002 PHE a 31 TYR 0.015 0.002 TYR B 206 ARG 0.004 0.001 ARG K 175 *********************** 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 1214 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1077 time to evaluate : 5.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 79 residues processed: 1134 average time/residue: 1.5012 time to fit residues: 2153.0138 Evaluate side-chains 1131 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1052 time to evaluate : 5.252 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 42 residues processed: 40 average time/residue: 0.7523 time to fit residues: 52.9445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 135 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 685 optimal weight: 5.9990 chunk 568 optimal weight: 0.9980 chunk 317 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 359 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN B 451 GLN 1 51 GLN 1 59 ASN D 398 ASN D 451 GLN D 465 ASN 2 51 GLN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 431 GLN H 451 GLN H 465 ASN 4 51 GLN 4 53 GLN 4 59 ASN I 345 GLN J 451 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 59766 Z= 0.166 Angle : 0.533 9.547 80838 Z= 0.289 Chirality : 0.043 0.145 8670 Planarity : 0.004 0.040 10620 Dihedral : 4.848 40.343 7968 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.56 % Allowed : 15.17 % Favored : 83.27 % 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: 0.88 (0.10), residues: 7158 helix: 1.99 (0.09), residues: 3180 sheet: 0.43 (0.15), residues: 1074 loop : -0.96 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.002 0.001 HIS l 17 PHE 0.012 0.001 PHE i 31 TYR 0.013 0.001 TYR D 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 1189 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1090 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 51 residues processed: 1142 average time/residue: 1.4930 time to fit residues: 2164.5985 Evaluate side-chains 1121 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1070 time to evaluate : 5.243 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 51 outliers final: 41 residues processed: 14 average time/residue: 1.0110 time to fit residues: 26.6960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 390 optimal weight: 7.9990 chunk 500 optimal weight: 3.9990 chunk 387 optimal weight: 10.0000 chunk 576 optimal weight: 4.9990 chunk 382 optimal weight: 6.9990 chunk 682 optimal weight: 0.4980 chunk 427 optimal weight: 9.9990 chunk 416 optimal weight: 0.7980 chunk 315 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 431 GLN H 451 GLN 4 51 GLN 4 59 ASN I 427 GLN J 451 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2966 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= 0.186 Angle : 0.545 8.827 80838 Z= 0.296 Chirality : 0.044 0.151 8670 Planarity : 0.004 0.040 10620 Dihedral : 4.803 38.764 7968 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.58 % Allowed : 15.28 % Favored : 83.14 % 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: 2.06 (0.09), residues: 3180 sheet: 0.45 (0.15), residues: 1062 loop : -0.96 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 28 HIS 0.003 0.001 HIS e 17 PHE 0.014 0.001 PHE c 31 TYR 0.013 0.001 TYR H 186 ARG 0.002 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 1178 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1078 time to evaluate : 5.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 61 residues processed: 1126 average time/residue: 1.4594 time to fit residues: 2090.0389 Evaluate side-chains 1131 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1070 time to evaluate : 6.536 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 41 residues processed: 23 average time/residue: 0.9315 time to fit residues: 37.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 407 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 433 optimal weight: 0.8980 chunk 464 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 536 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 3 59 ASN H 365 ASN H 431 GLN H 451 GLN 4 51 GLN 4 59 ASN I 349 ASN J 451 GLN 5 51 GLN L 225 ASN L 398 ASN L 451 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 59766 Z= 0.152 Angle : 0.516 8.755 80838 Z= 0.279 Chirality : 0.043 0.149 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.650 37.244 7968 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.34 % Allowed : 15.63 % Favored : 83.03 % 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: 1.04 (0.10), residues: 7158 helix: 2.17 (0.09), residues: 3180 sheet: 0.23 (0.15), residues: 1110 loop : -0.83 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.002 0.001 HIS k 17 PHE 0.012 0.001 PHE i 31 TYR 0.012 0.001 TYR B 186 ARG 0.002 0.000 ARG L 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 1163 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1078 time to evaluate : 5.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 51 residues processed: 1127 average time/residue: 1.4461 time to fit residues: 2080.9484 Evaluate side-chains 1117 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1066 time to evaluate : 5.254 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 13 average time/residue: 1.1030 time to fit residues: 26.7981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 3.9990 chunk 653 optimal weight: 9.9990 chunk 596 optimal weight: 8.9990 chunk 635 optimal weight: 0.9990 chunk 382 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 499 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 574 optimal weight: 6.9990 chunk 601 optimal weight: 1.9990 chunk 633 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 D 465 ASN 2 51 GLN 2 59 ASN F 398 ASN F 451 GLN 3 51 GLN 3 53 GLN H 431 GLN H 451 GLN 4 51 GLN 4 59 ASN I 427 GLN 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 59766 Z= 0.265 Angle : 0.601 9.084 80838 Z= 0.329 Chirality : 0.046 0.160 8670 Planarity : 0.005 0.040 10620 Dihedral : 4.941 37.435 7968 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.34 % Allowed : 15.80 % 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: 0.86 (0.10), residues: 7158 helix: 1.94 (0.09), residues: 3192 sheet: 0.56 (0.15), residues: 1008 loop : -0.99 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 88 HIS 0.004 0.001 HIS i 17 PHE 0.017 0.002 PHE a 31 TYR 0.015 0.001 TYR B 206 ARG 0.004 0.000 ARG L 227 *********************** 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 1146 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1061 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 54 residues processed: 1109 average time/residue: 1.4641 time to fit residues: 2068.1309 Evaluate side-chains 1108 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1054 time to evaluate : 5.276 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 40 residues processed: 15 average time/residue: 1.0766 time to fit residues: 29.1039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 5.9990 chunk 672 optimal weight: 2.9990 chunk 410 optimal weight: 0.9990 chunk 318 optimal weight: 0.0060 chunk 467 optimal weight: 2.9990 chunk 705 optimal weight: 3.9990 chunk 649 optimal weight: 4.9990 chunk 561 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 433 optimal weight: 3.9990 chunk 344 optimal weight: 0.0000 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN B 451 GLN 1 51 GLN 1 59 ASN C 349 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 H 431 GLN H 451 GLN H 465 ASN ** 4 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 51 GLN 4 53 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: 0.8254 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 59766 Z= 0.149 Angle : 0.514 9.184 80838 Z= 0.277 Chirality : 0.043 0.155 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.640 35.346 7968 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.90 % Allowed : 16.34 % Favored : 82.77 % 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: 1.07 (0.10), residues: 7158 helix: 2.19 (0.09), residues: 3180 sheet: 0.25 (0.15), residues: 1110 loop : -0.80 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 28 HIS 0.003 0.001 HIS d 17 PHE 0.010 0.001 PHE i 31 TYR 0.012 0.001 TYR H 186 ARG 0.002 0.000 ARG f 98 ********************** 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 1138 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1081 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 42 residues processed: 1125 average time/residue: 1.4885 time to fit residues: 2139.5844 Evaluate side-chains 1108 residues out of total 6384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1066 time to evaluate : 5.273 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 37 residues processed: 6 average time/residue: 1.0658 time to fit residues: 16.0263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 0.0470 chunk 598 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 517 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 562 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 577 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN F 451 GLN 3 17 GLN 3 51 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117361 restraints weight = 63950.024| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.48 r_work: 0.3077 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3109 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= 0.149 Angle : 0.510 8.324 80838 Z= 0.275 Chirality : 0.043 0.154 8670 Planarity : 0.004 0.039 10620 Dihedral : 4.533 34.606 7968 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.04 % Allowed : 16.37 % Favored : 82.59 % 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: 1.18 (0.10), residues: 7158 helix: 2.28 (0.09), residues: 3180 sheet: 0.31 (0.15), residues: 1110 loop : -0.76 (0.11), residues: 2868 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 I 467 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: 28417.11 seconds wall clock time: 490 minutes 29.17 seconds (29429.17 seconds total)