Starting phenix.real_space_refine on Sat Mar 16 13:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u23_20616/03_2024/6u23_20616_neut.pdb" } resolution = 3.49 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= -0.001 sd= 0.186 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 400 5.16 5 C 46384 2.51 5 N 12496 2.21 5 O 14192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 575": "NH1" <-> "NH2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 205": "NH1" <-> "NH2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 575": "NH1" <-> "NH2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 205": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 575": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 205": "NH1" <-> "NH2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 575": "NH1" <-> "NH2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 205": "NH1" <-> "NH2" Residue "H ARG 257": "NH1" <-> "NH2" Residue "H TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 444": "NH1" <-> "NH2" Residue "H ARG 575": "NH1" <-> "NH2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 118": "NH1" <-> "NH2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I ARG 205": "NH1" <-> "NH2" Residue "I ARG 257": "NH1" <-> "NH2" Residue "I TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 444": "NH1" <-> "NH2" Residue "I ARG 575": "NH1" <-> "NH2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 205": "NH1" <-> "NH2" Residue "J ARG 257": "NH1" <-> "NH2" Residue "J TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 444": "NH1" <-> "NH2" Residue "J ARG 575": "NH1" <-> "NH2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ARG 136": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "K ARG 257": "NH1" <-> "NH2" Residue "K TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 444": "NH1" <-> "NH2" Residue "K ARG 575": "NH1" <-> "NH2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L ARG 205": "NH1" <-> "NH2" Residue "L ARG 257": "NH1" <-> "NH2" Residue "L TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 444": "NH1" <-> "NH2" Residue "L ARG 575": "NH1" <-> "NH2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 205": "NH1" <-> "NH2" Residue "M ARG 257": "NH1" <-> "NH2" Residue "M TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 444": "NH1" <-> "NH2" Residue "M ARG 575": "NH1" <-> "NH2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "N ARG 205": "NH1" <-> "NH2" Residue "N ARG 257": "NH1" <-> "NH2" Residue "N TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 444": "NH1" <-> "NH2" Residue "N ARG 575": "NH1" <-> "NH2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O ARG 205": "NH1" <-> "NH2" Residue "O ARG 257": "NH1" <-> "NH2" Residue "O TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 444": "NH1" <-> "NH2" Residue "O ARG 575": "NH1" <-> "NH2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "P ARG 136": "NH1" <-> "NH2" Residue "P ARG 205": "NH1" <-> "NH2" Residue "P ARG 257": "NH1" <-> "NH2" Residue "P TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 444": "NH1" <-> "NH2" Residue "P ARG 575": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 73472 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "N" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4536 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 551} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 27.72, per 1000 atoms: 0.38 Number of scatterers: 73472 At special positions: 0 Unit cell: (239.8, 240.9, 106.7, 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 400 16.00 O 14192 8.00 N 12496 7.00 C 46384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=112, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 368 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS B 517 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 368 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 496 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 555 " distance=2.03 Simple disulfide: pdb=" SG CYS C 540 " - pdb=" SG CYS C 560 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 53 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 352 " distance=2.03 Simple disulfide: pdb=" SG CYS D 368 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 517 " - pdb=" SG CYS D 555 " distance=2.03 Simple disulfide: pdb=" SG CYS D 540 " - pdb=" SG CYS D 560 " distance=2.03 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 53 " distance=2.03 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 368 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 496 " distance=2.03 Simple disulfide: pdb=" SG CYS E 517 " - pdb=" SG CYS E 555 " distance=2.03 Simple disulfide: pdb=" SG CYS E 540 " - pdb=" SG CYS E 560 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 53 " distance=2.03 Simple disulfide: pdb=" SG CYS F 333 " - pdb=" SG CYS F 352 " distance=2.03 Simple disulfide: pdb=" SG CYS F 368 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 418 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 517 " - pdb=" SG CYS F 555 " distance=2.03 Simple disulfide: pdb=" SG CYS F 540 " - pdb=" SG CYS F 560 " distance=2.03 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 53 " distance=2.03 Simple disulfide: pdb=" SG CYS G 333 " - pdb=" SG CYS G 352 " distance=2.03 Simple disulfide: pdb=" SG CYS G 368 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 496 " distance=2.03 Simple disulfide: pdb=" SG CYS G 517 " - pdb=" SG CYS G 555 " distance=2.03 Simple disulfide: pdb=" SG CYS G 540 " - pdb=" SG CYS G 560 " distance=2.03 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 53 " distance=2.03 Simple disulfide: pdb=" SG CYS H 333 " - pdb=" SG CYS H 352 " distance=2.03 Simple disulfide: pdb=" SG CYS H 368 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 418 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 480 " - pdb=" SG CYS H 496 " distance=2.03 Simple disulfide: pdb=" SG CYS H 517 " - pdb=" SG CYS H 555 " distance=2.03 Simple disulfide: pdb=" SG CYS H 540 " - pdb=" SG CYS H 560 " distance=2.03 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 53 " distance=2.03 Simple disulfide: pdb=" SG CYS I 333 " - pdb=" SG CYS I 352 " distance=2.03 Simple disulfide: pdb=" SG CYS I 368 " - pdb=" SG CYS I 380 " distance=2.03 Simple disulfide: pdb=" SG CYS I 418 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 496 " distance=2.03 Simple disulfide: pdb=" SG CYS I 517 " - pdb=" SG CYS I 555 " distance=2.03 Simple disulfide: pdb=" SG CYS I 540 " - pdb=" SG CYS I 560 " distance=2.03 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 53 " distance=2.03 Simple disulfide: pdb=" SG CYS J 333 " - pdb=" SG CYS J 352 " distance=2.03 Simple disulfide: pdb=" SG CYS J 368 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 418 " - pdb=" SG CYS J 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 496 " distance=2.03 Simple disulfide: pdb=" SG CYS J 517 " - pdb=" SG CYS J 555 " distance=2.03 Simple disulfide: pdb=" SG CYS J 540 " - pdb=" SG CYS J 560 " distance=2.03 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 53 " distance=2.03 Simple disulfide: pdb=" SG CYS K 333 " - pdb=" SG CYS K 352 " distance=2.03 Simple disulfide: pdb=" SG CYS K 368 " - pdb=" SG CYS K 380 " distance=2.03 Simple disulfide: pdb=" SG CYS K 418 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 496 " distance=2.03 Simple disulfide: pdb=" SG CYS K 517 " - pdb=" SG CYS K 555 " distance=2.03 Simple disulfide: pdb=" SG CYS K 540 " - pdb=" SG CYS K 560 " distance=2.03 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 53 " distance=2.03 Simple disulfide: pdb=" SG CYS L 333 " - pdb=" SG CYS L 352 " distance=2.03 Simple disulfide: pdb=" SG CYS L 368 " - pdb=" SG CYS L 380 " distance=2.03 Simple disulfide: pdb=" SG CYS L 418 " - pdb=" SG CYS L 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 480 " - pdb=" SG CYS L 496 " distance=2.03 Simple disulfide: pdb=" SG CYS L 517 " - pdb=" SG CYS L 555 " distance=2.03 Simple disulfide: pdb=" SG CYS L 540 " - pdb=" SG CYS L 560 " distance=2.03 Simple disulfide: pdb=" SG CYS M 17 " - pdb=" SG CYS M 53 " distance=2.03 Simple disulfide: pdb=" SG CYS M 333 " - pdb=" SG CYS M 352 " distance=2.03 Simple disulfide: pdb=" SG CYS M 368 " - pdb=" SG CYS M 380 " distance=2.03 Simple disulfide: pdb=" SG CYS M 418 " - pdb=" SG CYS M 432 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 496 " distance=2.03 Simple disulfide: pdb=" SG CYS M 517 " - pdb=" SG CYS M 555 " distance=2.03 Simple disulfide: pdb=" SG CYS M 540 " - pdb=" SG CYS M 560 " distance=2.03 Simple disulfide: pdb=" SG CYS N 17 " - pdb=" SG CYS N 53 " distance=2.03 Simple disulfide: pdb=" SG CYS N 333 " - pdb=" SG CYS N 352 " distance=2.03 Simple disulfide: pdb=" SG CYS N 368 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 418 " - pdb=" SG CYS N 432 " distance=2.03 Simple disulfide: pdb=" SG CYS N 480 " - pdb=" SG CYS N 496 " distance=2.03 Simple disulfide: pdb=" SG CYS N 517 " - pdb=" SG CYS N 555 " distance=2.03 Simple disulfide: pdb=" SG CYS N 540 " - pdb=" SG CYS N 560 " distance=2.03 Simple disulfide: pdb=" SG CYS O 17 " - pdb=" SG CYS O 53 " distance=2.03 Simple disulfide: pdb=" SG CYS O 333 " - pdb=" SG CYS O 352 " distance=2.03 Simple disulfide: pdb=" SG CYS O 368 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 418 " - pdb=" SG CYS O 432 " distance=2.03 Simple disulfide: pdb=" SG CYS O 480 " - pdb=" SG CYS O 496 " distance=2.03 Simple disulfide: pdb=" SG CYS O 517 " - pdb=" SG CYS O 555 " distance=2.03 Simple disulfide: pdb=" SG CYS O 540 " - pdb=" SG CYS O 560 " distance=2.03 Simple disulfide: pdb=" SG CYS P 17 " - pdb=" SG CYS P 53 " distance=2.03 Simple disulfide: pdb=" SG CYS P 333 " - pdb=" SG CYS P 352 " distance=2.03 Simple disulfide: pdb=" SG CYS P 368 " - pdb=" SG CYS P 380 " distance=2.03 Simple disulfide: pdb=" SG CYS P 418 " - pdb=" SG CYS P 432 " distance=2.03 Simple disulfide: pdb=" SG CYS P 480 " - pdb=" SG CYS P 496 " distance=2.03 Simple disulfide: pdb=" SG CYS P 517 " - pdb=" SG CYS P 555 " distance=2.03 Simple disulfide: pdb=" SG CYS P 540 " - pdb=" SG CYS P 560 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG Q 1 " - " ASN A 168 " " NAG R 1 " - " ASN A 252 " " NAG S 1 " - " ASN B 168 " " NAG T 1 " - " ASN B 252 " " NAG U 1 " - " ASN C 168 " " NAG V 1 " - " ASN C 252 " " NAG W 1 " - " ASN D 168 " " NAG X 1 " - " ASN D 252 " " NAG Y 1 " - " ASN E 168 " " NAG Z 1 " - " ASN E 252 " " NAG a 1 " - " ASN F 168 " " NAG b 1 " - " ASN F 252 " " NAG c 1 " - " ASN G 168 " " NAG d 1 " - " ASN G 252 " " NAG e 1 " - " ASN H 168 " " NAG f 1 " - " ASN H 252 " " NAG g 1 " - " ASN I 168 " " NAG h 1 " - " ASN I 252 " " NAG i 1 " - " ASN J 168 " " NAG j 1 " - " ASN J 252 " " NAG k 1 " - " ASN K 168 " " NAG l 1 " - " ASN K 252 " " NAG m 1 " - " ASN L 168 " " NAG n 1 " - " ASN L 252 " " NAG o 1 " - " ASN M 168 " " NAG p 1 " - " ASN M 252 " " NAG q 1 " - " ASN N 168 " " NAG r 1 " - " ASN N 252 " " NAG s 1 " - " ASN O 168 " " NAG t 1 " - " ASN O 252 " " NAG u 1 " - " ASN P 168 " " NAG v 1 " - " ASN P 252 " Time building additional restraints: 22.07 Conformation dependent library (CDL) restraints added in 9.6 seconds 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17408 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 167 sheets defined 21.1% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.643A pdb=" N ASN A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 212' Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.946A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 212' Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS C 17 " --> pdb=" O GLY C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 212' Processing helix chain 'C' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 294 through 297 Processing helix chain 'C' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL C 310 " --> pdb=" O PRO C 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.643A pdb=" N ASN D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 212 removed outlier: 3.948A pdb=" N GLN D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 212' Processing helix chain 'D' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 212' Processing helix chain 'E' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 312 " --> pdb=" O PRO E 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER F 212 " --> pdb=" O PHE F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 212' Processing helix chain 'F' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 222 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN F 228 " --> pdb=" O GLY F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL F 310 " --> pdb=" O PRO F 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS F 312 " --> pdb=" O PRO F 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 625 Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP G 211 " --> pdb=" O SER G 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER G 212 " --> pdb=" O PHE G 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 206 through 212' Processing helix chain 'G' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN G 228 " --> pdb=" O GLY G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL G 310 " --> pdb=" O PRO G 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 312 " --> pdb=" O PRO G 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 620 through 625 Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.906A pdb=" N CYS H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 Processing helix chain 'H' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU H 157 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP H 211 " --> pdb=" O SER H 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER H 212 " --> pdb=" O PHE H 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 206 through 212' Processing helix chain 'H' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN H 228 " --> pdb=" O GLY H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 294 through 297 Processing helix chain 'H' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL H 310 " --> pdb=" O PRO H 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 311 " --> pdb=" O GLY H 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS H 312 " --> pdb=" O PRO H 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 620 through 625 Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'I' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU I 157 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 206 through 212' Processing helix chain 'I' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN I 228 " --> pdb=" O GLY I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 294 through 297 Processing helix chain 'I' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL I 310 " --> pdb=" O PRO I 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS I 312 " --> pdb=" O PRO I 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 315 " --> pdb=" O LYS I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 625 Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET J 119 " --> pdb=" O GLU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP J 211 " --> pdb=" O SER J 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER J 212 " --> pdb=" O PHE J 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 206 through 212' Processing helix chain 'J' and resid 215 through 233 removed outlier: 3.519A pdb=" N ALA J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN J 228 " --> pdb=" O GLY J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 276 Processing helix chain 'J' and resid 294 through 297 Processing helix chain 'J' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL J 310 " --> pdb=" O PRO J 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS J 311 " --> pdb=" O GLY J 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS J 312 " --> pdb=" O PRO J 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS J 315 " --> pdb=" O LYS J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 625 Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 113 through 125 removed outlier: 3.640A pdb=" N MET K 119 " --> pdb=" O GLU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU K 157 " --> pdb=" O GLY K 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE K 161 " --> pdb=" O GLU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN K 183 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 212 removed outlier: 3.946A pdb=" N GLN K 210 " --> pdb=" O ALA K 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP K 211 " --> pdb=" O SER K 207 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER K 212 " --> pdb=" O PHE K 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 206 through 212' Processing helix chain 'K' and resid 215 through 233 removed outlier: 3.521A pdb=" N ALA K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 222 " --> pdb=" O ALA K 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN K 228 " --> pdb=" O GLY K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 294 through 297 Processing helix chain 'K' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL K 310 " --> pdb=" O PRO K 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS K 311 " --> pdb=" O GLY K 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS K 312 " --> pdb=" O PRO K 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS K 315 " --> pdb=" O LYS K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 620 through 625 Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 100 Processing helix chain 'L' and resid 113 through 125 removed outlier: 3.640A pdb=" N MET L 119 " --> pdb=" O GLU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE L 161 " --> pdb=" O GLU L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 212 removed outlier: 3.946A pdb=" N GLN L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP L 211 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER L 212 " --> pdb=" O PHE L 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 212' Processing helix chain 'L' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER L 222 " --> pdb=" O ALA L 218 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 Processing helix chain 'L' and resid 294 through 297 Processing helix chain 'L' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL L 310 " --> pdb=" O PRO L 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS L 311 " --> pdb=" O GLY L 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS L 312 " --> pdb=" O PRO L 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS L 315 " --> pdb=" O LYS L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 620 through 625 Processing helix chain 'M' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 100 Processing helix chain 'M' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 166 removed outlier: 3.639A pdb=" N GLU M 157 " --> pdb=" O GLY M 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE M 161 " --> pdb=" O GLU M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 185 removed outlier: 3.643A pdb=" N ASN M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP M 211 " --> pdb=" O SER M 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER M 212 " --> pdb=" O PHE M 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 206 through 212' Processing helix chain 'M' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER M 222 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN M 228 " --> pdb=" O GLY M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 276 Processing helix chain 'M' and resid 294 through 297 Processing helix chain 'M' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS M 311 " --> pdb=" O GLY M 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS M 312 " --> pdb=" O PRO M 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS M 315 " --> pdb=" O LYS M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 620 through 625 Processing helix chain 'N' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS N 17 " --> pdb=" O GLY N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 100 Processing helix chain 'N' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET N 119 " --> pdb=" O GLU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU N 157 " --> pdb=" O GLY N 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE N 161 " --> pdb=" O GLU N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 212 removed outlier: 3.946A pdb=" N GLN N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP N 211 " --> pdb=" O SER N 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER N 212 " --> pdb=" O PHE N 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 206 through 212' Processing helix chain 'N' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN N 228 " --> pdb=" O GLY N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 276 Processing helix chain 'N' and resid 294 through 297 Processing helix chain 'N' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL N 310 " --> pdb=" O PRO N 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS N 311 " --> pdb=" O GLY N 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS N 312 " --> pdb=" O PRO N 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS N 315 " --> pdb=" O LYS N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 620 through 625 Processing helix chain 'O' and resid 13 through 22 removed outlier: 3.907A pdb=" N CYS O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 100 Processing helix chain 'O' and resid 113 through 125 removed outlier: 3.640A pdb=" N MET O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU O 157 " --> pdb=" O GLY O 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE O 161 " --> pdb=" O GLU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.644A pdb=" N ASN O 183 " --> pdb=" O LEU O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP O 211 " --> pdb=" O SER O 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER O 212 " --> pdb=" O PHE O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 206 through 212' Processing helix chain 'O' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA O 221 " --> pdb=" O SER O 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER O 222 " --> pdb=" O ALA O 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN O 228 " --> pdb=" O GLY O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 294 through 297 Processing helix chain 'O' and resid 306 through 327 removed outlier: 3.618A pdb=" N VAL O 310 " --> pdb=" O PRO O 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS O 311 " --> pdb=" O GLY O 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 312 " --> pdb=" O PRO O 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS O 315 " --> pdb=" O LYS O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 625 Processing helix chain 'P' and resid 13 through 22 removed outlier: 3.908A pdb=" N CYS P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 Processing helix chain 'P' and resid 113 through 125 removed outlier: 3.641A pdb=" N MET P 119 " --> pdb=" O GLU P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 166 removed outlier: 3.640A pdb=" N GLU P 157 " --> pdb=" O GLY P 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE P 161 " --> pdb=" O GLU P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 185 removed outlier: 3.643A pdb=" N ASN P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 212 removed outlier: 3.947A pdb=" N GLN P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP P 211 " --> pdb=" O SER P 207 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER P 212 " --> pdb=" O PHE P 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 206 through 212' Processing helix chain 'P' and resid 215 through 233 removed outlier: 3.520A pdb=" N ALA P 221 " --> pdb=" O SER P 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER P 222 " --> pdb=" O ALA P 218 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN P 228 " --> pdb=" O GLY P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 276 Processing helix chain 'P' and resid 294 through 297 Processing helix chain 'P' and resid 306 through 327 removed outlier: 3.619A pdb=" N VAL P 310 " --> pdb=" O PRO P 306 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS P 311 " --> pdb=" O GLY P 307 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS P 312 " --> pdb=" O PRO P 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS P 315 " --> pdb=" O LYS P 311 " (cutoff:3.500A) Processing helix chain 'P' and resid 620 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL A 40 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA A 194 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 141 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 192 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS A 143 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR A 190 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 187 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 189 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 290 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER A 191 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG A 288 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP A 193 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR A 130 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 199 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL A 258 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU A 201 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 256 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 203 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'P' and resid 613 through 615 removed outlier: 4.007A pdb=" N ARG P 602 " --> pdb=" O ASN P 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL P 593 " --> pdb=" O LYS P 606 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ASP A 434 " --> pdb=" O VAL P 593 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL P 595 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N PHE A 436 " --> pdb=" O VAL P 595 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN P 597 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N VAL A 438 " --> pdb=" O ASN P 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP A 447 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.654A pdb=" N TRP A 447 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 437 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 413 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 407 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 407 through 414 removed outlier: 3.618A pdb=" N GLN A 407 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 413 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 437 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 417 through 418 removed outlier: 8.206A pdb=" N ASP A 434 " --> pdb=" O VAL P 593 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL P 595 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N PHE A 436 " --> pdb=" O VAL P 595 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN P 597 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N VAL A 438 " --> pdb=" O ASN P 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL P 593 " --> pdb=" O LYS P 606 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG P 602 " --> pdb=" O ASN P 597 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY A 464 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 466 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS A 560 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE A 514 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 558 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 557 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG A 602 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 593 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS B 432 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 594 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 434 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP B 447 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP B 447 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 437 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 413 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 407 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 407 through 414 removed outlier: 3.617A pdb=" N GLN B 407 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 413 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 437 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 417 through 418 removed outlier: 6.277A pdb=" N CYS B 432 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 594 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 434 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 593 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 602 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL B 40 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA B 194 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 141 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 192 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS B 143 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR B 190 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B 187 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 189 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 290 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER B 191 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG B 288 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 193 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 258 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU B 201 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B 256 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS B 203 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AC3, first strand: chain 'B' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY B 464 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 466 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 511 through 515 removed outlier: 5.391A pdb=" N CYS B 560 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B 514 " --> pdb=" O SER B 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 558 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 557 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG B 602 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 593 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 591 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP C 434 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL B 593 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 12.966A pdb=" N PHE C 436 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N VAL B 595 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 14.104A pdb=" N VAL C 438 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N ASN B 597 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 15.394A pdb=" N LYS C 440 " --> pdb=" O ASN B 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP C 447 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP C 447 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 437 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 413 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 407 " --> pdb=" O PHE C 443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 414 removed outlier: 3.617A pdb=" N GLN C 407 " --> pdb=" O PHE C 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 413 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 437 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 417 through 418 removed outlier: 6.493A pdb=" N ASN B 591 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP C 434 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL B 593 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 12.966A pdb=" N PHE C 436 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N VAL B 595 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 14.104A pdb=" N VAL C 438 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N ASN B 597 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 15.394A pdb=" N LYS C 440 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 593 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 602 " --> pdb=" O ASN B 597 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL C 40 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA C 194 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 141 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 192 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS C 143 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR C 190 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS C 187 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 189 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 290 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER C 191 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG C 288 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP C 193 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR C 130 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 199 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 258 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU C 201 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 256 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS C 203 " --> pdb=" O THR C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 331 through 332 Processing sheet with id=AD5, first strand: chain 'C' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY C 464 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 466 " --> pdb=" O LYS C 494 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS C 560 " --> pdb=" O GLY C 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE C 514 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER C 558 " --> pdb=" O PHE C 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 557 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG C 602 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 593 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN C 591 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP D 434 " --> pdb=" O ASN C 591 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 593 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N PHE D 436 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL C 595 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 14.245A pdb=" N VAL D 438 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ASN C 597 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 15.552A pdb=" N LYS D 440 " --> pdb=" O ASN C 597 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP D 447 " --> pdb=" O VAL D 402 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP D 447 " --> pdb=" O VAL D 402 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 437 " --> pdb=" O TYR D 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 413 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 407 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 407 through 414 removed outlier: 3.618A pdb=" N GLN D 407 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 413 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 437 " --> pdb=" O TYR D 413 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 417 through 418 removed outlier: 6.576A pdb=" N ASN C 591 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP D 434 " --> pdb=" O ASN C 591 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 593 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N PHE D 436 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL C 595 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 14.245A pdb=" N VAL D 438 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ASN C 597 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 15.552A pdb=" N LYS D 440 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 593 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 602 " --> pdb=" O ASN C 597 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL D 40 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA D 194 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR D 141 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 192 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS D 143 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR D 190 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS D 187 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 189 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY D 290 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER D 191 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG D 288 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP D 193 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.623A pdb=" N THR D 130 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 199 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL D 258 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU D 201 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 256 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS D 203 " --> pdb=" O THR D 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AE7, first strand: chain 'D' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY D 464 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 466 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS D 560 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE D 514 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER D 558 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 557 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG D 602 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 593 " --> pdb=" O LYS D 606 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN D 591 " --> pdb=" O CYS E 432 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP E 434 " --> pdb=" O ASN D 591 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL D 593 " --> pdb=" O ASP E 434 " (cutoff:3.500A) removed outlier: 13.194A pdb=" N PHE E 436 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N VAL D 595 " --> pdb=" O PHE E 436 " (cutoff:3.500A) removed outlier: 14.348A pdb=" N VAL E 438 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 12.432A pdb=" N ASN D 597 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 15.661A pdb=" N LYS E 440 " --> pdb=" O ASN D 597 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP E 447 " --> pdb=" O VAL E 402 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP E 447 " --> pdb=" O VAL E 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN E 437 " --> pdb=" O TYR E 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR E 413 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 407 " --> pdb=" O PHE E 443 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 407 through 414 removed outlier: 3.618A pdb=" N GLN E 407 " --> pdb=" O PHE E 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR E 413 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN E 437 " --> pdb=" O TYR E 413 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 417 through 418 removed outlier: 6.650A pdb=" N ASN D 591 " --> pdb=" O CYS E 432 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP E 434 " --> pdb=" O ASN D 591 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL D 593 " --> pdb=" O ASP E 434 " (cutoff:3.500A) removed outlier: 13.194A pdb=" N PHE E 436 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N VAL D 595 " --> pdb=" O PHE E 436 " (cutoff:3.500A) removed outlier: 14.348A pdb=" N VAL E 438 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 12.432A pdb=" N ASN D 597 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 15.661A pdb=" N LYS E 440 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 593 " --> pdb=" O LYS D 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG D 602 " --> pdb=" O ASN D 597 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL E 40 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA E 194 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR E 141 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 192 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS E 143 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR E 190 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS E 187 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR E 189 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY E 290 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 191 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG E 288 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP E 193 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR E 130 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 199 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 258 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU E 201 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER E 256 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS E 203 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=AF9, first strand: chain 'E' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY E 464 " --> pdb=" O CYS E 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 466 " --> pdb=" O LYS E 494 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 511 through 515 removed outlier: 5.393A pdb=" N CYS E 560 " --> pdb=" O GLY E 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE E 514 " --> pdb=" O SER E 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 558 " --> pdb=" O PHE E 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 557 " --> pdb=" O ALA E 549 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG E 602 " --> pdb=" O ASN E 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 593 " --> pdb=" O LYS E 606 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS F 432 " --> pdb=" O THR E 592 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 594 " --> pdb=" O CYS F 432 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F 434 " --> pdb=" O ILE E 594 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP F 447 " --> pdb=" O VAL F 402 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP F 447 " --> pdb=" O VAL F 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN F 437 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 413 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN F 407 " --> pdb=" O PHE F 443 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 407 through 414 removed outlier: 3.617A pdb=" N GLN F 407 " --> pdb=" O PHE F 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 413 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN F 437 " --> pdb=" O TYR F 413 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 417 through 418 removed outlier: 6.276A pdb=" N CYS F 432 " --> pdb=" O THR E 592 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 594 " --> pdb=" O CYS F 432 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F 434 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 593 " --> pdb=" O LYS E 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 602 " --> pdb=" O ASN E 597 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL F 40 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA F 194 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR F 141 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 192 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS F 143 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR F 190 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS F 187 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR F 189 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY F 290 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER F 191 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG F 288 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP F 193 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR F 130 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 199 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL F 258 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU F 201 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER F 256 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS F 203 " --> pdb=" O THR F 254 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AH2, first strand: chain 'F' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY F 464 " --> pdb=" O CYS F 496 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 466 " --> pdb=" O LYS F 494 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS F 560 " --> pdb=" O GLY F 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE F 514 " --> pdb=" O SER F 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER F 558 " --> pdb=" O PHE F 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 557 " --> pdb=" O ALA F 549 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG F 602 " --> pdb=" O ASN F 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 593 " --> pdb=" O LYS F 606 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN F 591 " --> pdb=" O CYS G 432 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP G 434 " --> pdb=" O ASN F 591 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL F 593 " --> pdb=" O ASP G 434 " (cutoff:3.500A) removed outlier: 12.967A pdb=" N PHE G 436 " --> pdb=" O VAL F 593 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N VAL F 595 " --> pdb=" O PHE G 436 " (cutoff:3.500A) removed outlier: 14.104A pdb=" N VAL G 438 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N ASN F 597 " --> pdb=" O VAL G 438 " (cutoff:3.500A) removed outlier: 15.395A pdb=" N LYS G 440 " --> pdb=" O ASN F 597 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP G 447 " --> pdb=" O VAL G 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP G 447 " --> pdb=" O VAL G 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN G 437 " --> pdb=" O TYR G 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 413 " --> pdb=" O GLN G 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 407 " --> pdb=" O PHE G 443 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 407 through 414 removed outlier: 3.617A pdb=" N GLN G 407 " --> pdb=" O PHE G 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 413 " --> pdb=" O GLN G 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN G 437 " --> pdb=" O TYR G 413 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 417 through 418 removed outlier: 6.494A pdb=" N ASN F 591 " --> pdb=" O CYS G 432 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP G 434 " --> pdb=" O ASN F 591 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL F 593 " --> pdb=" O ASP G 434 " (cutoff:3.500A) removed outlier: 12.967A pdb=" N PHE G 436 " --> pdb=" O VAL F 593 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N VAL F 595 " --> pdb=" O PHE G 436 " (cutoff:3.500A) removed outlier: 14.104A pdb=" N VAL G 438 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 12.180A pdb=" N ASN F 597 " --> pdb=" O VAL G 438 " (cutoff:3.500A) removed outlier: 15.395A pdb=" N LYS G 440 " --> pdb=" O ASN F 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 593 " --> pdb=" O LYS F 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG F 602 " --> pdb=" O ASN F 597 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL G 40 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA G 194 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR G 141 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL G 192 " --> pdb=" O THR G 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS G 143 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR G 190 " --> pdb=" O LYS G 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS G 187 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR G 189 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY G 290 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER G 191 " --> pdb=" O ARG G 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG G 288 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP G 193 " --> pdb=" O ILE G 286 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR G 130 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE G 199 " --> pdb=" O VAL G 258 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL G 258 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU G 201 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER G 256 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS G 203 " --> pdb=" O THR G 254 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AI4, first strand: chain 'G' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY G 464 " --> pdb=" O CYS G 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 466 " --> pdb=" O LYS G 494 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 511 through 515 removed outlier: 5.393A pdb=" N CYS G 560 " --> pdb=" O GLY G 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE G 514 " --> pdb=" O SER G 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER G 558 " --> pdb=" O PHE G 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G 557 " --> pdb=" O ALA G 549 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG G 602 " --> pdb=" O ASN G 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL G 593 " --> pdb=" O LYS G 606 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN G 591 " --> pdb=" O CYS H 432 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP H 434 " --> pdb=" O ASN G 591 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL G 593 " --> pdb=" O ASP H 434 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N PHE H 436 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL G 595 " --> pdb=" O PHE H 436 " (cutoff:3.500A) removed outlier: 14.245A pdb=" N VAL H 438 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N ASN G 597 " --> pdb=" O VAL H 438 " (cutoff:3.500A) removed outlier: 15.553A pdb=" N LYS H 440 " --> pdb=" O ASN G 597 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP H 447 " --> pdb=" O VAL H 402 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 401 through 402 removed outlier: 3.654A pdb=" N TRP H 447 " --> pdb=" O VAL H 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 437 " --> pdb=" O TYR H 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 413 " --> pdb=" O GLN H 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 407 " --> pdb=" O PHE H 443 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 407 through 414 removed outlier: 3.618A pdb=" N GLN H 407 " --> pdb=" O PHE H 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 413 " --> pdb=" O GLN H 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 437 " --> pdb=" O TYR H 413 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 417 through 418 removed outlier: 6.577A pdb=" N ASN G 591 " --> pdb=" O CYS H 432 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP H 434 " --> pdb=" O ASN G 591 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL G 593 " --> pdb=" O ASP H 434 " (cutoff:3.500A) removed outlier: 13.091A pdb=" N PHE H 436 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL G 595 " --> pdb=" O PHE H 436 " (cutoff:3.500A) removed outlier: 14.245A pdb=" N VAL H 438 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N ASN G 597 " --> pdb=" O VAL H 438 " (cutoff:3.500A) removed outlier: 15.553A pdb=" N LYS H 440 " --> pdb=" O ASN G 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL G 593 " --> pdb=" O LYS G 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG G 602 " --> pdb=" O ASN G 597 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL H 40 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA H 194 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR H 141 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL H 192 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS H 143 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR H 190 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS H 187 " --> pdb=" O PRO H 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR H 189 " --> pdb=" O GLY H 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY H 290 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER H 191 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG H 288 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP H 193 " --> pdb=" O ILE H 286 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR H 130 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE H 199 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL H 258 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU H 201 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER H 256 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS H 203 " --> pdb=" O THR H 254 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AJ6, first strand: chain 'H' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY H 464 " --> pdb=" O CYS H 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE H 466 " --> pdb=" O LYS H 494 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS H 560 " --> pdb=" O GLY H 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE H 514 " --> pdb=" O SER H 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER H 558 " --> pdb=" O PHE H 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL H 557 " --> pdb=" O ALA H 549 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 591 through 592 removed outlier: 7.344A pdb=" N ASN H 591 " --> pdb=" O CYS I 432 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 594 through 597 removed outlier: 4.007A pdb=" N ARG H 602 " --> pdb=" O ASN H 597 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL I 40 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA I 194 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR I 141 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL I 192 " --> pdb=" O THR I 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS I 143 " --> pdb=" O THR I 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR I 190 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS I 187 " --> pdb=" O PRO I 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR I 189 " --> pdb=" O GLY I 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY I 290 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER I 191 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG I 288 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP I 193 " --> pdb=" O ILE I 286 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR I 130 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE I 199 " --> pdb=" O VAL I 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL I 258 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU I 201 " --> pdb=" O SER I 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER I 256 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS I 203 " --> pdb=" O THR I 254 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 331 through 332 Processing sheet with id=AK5, first strand: chain 'I' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP I 447 " --> pdb=" O VAL I 402 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'I' and resid 364 through 368 removed outlier: 3.713A pdb=" N GLN I 437 " --> pdb=" O TYR I 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR I 413 " --> pdb=" O GLN I 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN I 407 " --> pdb=" O PHE I 443 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'I' and resid 464 through 466 removed outlier: 3.971A pdb=" N GLY I 464 " --> pdb=" O CYS I 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE I 466 " --> pdb=" O LYS I 494 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'I' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS I 560 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE I 514 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 558 " --> pdb=" O PHE I 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL I 557 " --> pdb=" O ALA I 549 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 613 through 615 removed outlier: 4.007A pdb=" N ARG I 602 " --> pdb=" O ASN I 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL I 593 " --> pdb=" O LYS I 606 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN I 591 " --> pdb=" O CYS J 432 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP J 434 " --> pdb=" O ASN I 591 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL I 593 " --> pdb=" O ASP J 434 " (cutoff:3.500A) removed outlier: 13.082A pdb=" N PHE J 436 " --> pdb=" O VAL I 593 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL I 595 " --> pdb=" O PHE J 436 " (cutoff:3.500A) removed outlier: 14.227A pdb=" N VAL J 438 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 12.301A pdb=" N ASN I 597 " --> pdb=" O VAL J 438 " (cutoff:3.500A) removed outlier: 15.513A pdb=" N LYS J 440 " --> pdb=" O ASN I 597 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP J 447 " --> pdb=" O VAL J 402 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'J' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP J 447 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN J 437 " --> pdb=" O TYR J 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR J 413 " --> pdb=" O GLN J 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN J 407 " --> pdb=" O PHE J 443 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'J' and resid 407 through 414 removed outlier: 3.618A pdb=" N GLN J 407 " --> pdb=" O PHE J 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR J 413 " --> pdb=" O GLN J 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN J 437 " --> pdb=" O TYR J 413 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 417 through 418 removed outlier: 6.680A pdb=" N ASN I 591 " --> pdb=" O CYS J 432 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP J 434 " --> pdb=" O ASN I 591 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL I 593 " --> pdb=" O ASP J 434 " (cutoff:3.500A) removed outlier: 13.082A pdb=" N PHE J 436 " --> pdb=" O VAL I 593 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL I 595 " --> pdb=" O PHE J 436 " (cutoff:3.500A) removed outlier: 14.227A pdb=" N VAL J 438 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 12.301A pdb=" N ASN I 597 " --> pdb=" O VAL J 438 " (cutoff:3.500A) removed outlier: 15.513A pdb=" N LYS J 440 " --> pdb=" O ASN I 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL I 593 " --> pdb=" O LYS I 606 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG I 602 " --> pdb=" O ASN I 597 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL J 40 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA J 194 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR J 141 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL J 192 " --> pdb=" O THR J 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS J 143 " --> pdb=" O THR J 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR J 190 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS J 187 " --> pdb=" O PRO J 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR J 189 " --> pdb=" O GLY J 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY J 290 " --> pdb=" O THR J 189 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER J 191 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG J 288 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP J 193 " --> pdb=" O ILE J 286 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR J 130 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE J 199 " --> pdb=" O VAL J 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL J 258 " --> pdb=" O ILE J 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU J 201 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER J 256 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS J 203 " --> pdb=" O THR J 254 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 331 through 332 Processing sheet with id=AL9, first strand: chain 'J' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY J 464 " --> pdb=" O CYS J 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE J 466 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'J' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS J 560 " --> pdb=" O GLY J 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE J 514 " --> pdb=" O SER J 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER J 558 " --> pdb=" O PHE J 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL J 557 " --> pdb=" O ALA J 549 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG J 602 " --> pdb=" O ASN J 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL J 593 " --> pdb=" O LYS J 606 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN J 591 " --> pdb=" O CYS K 432 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP K 434 " --> pdb=" O ASN J 591 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL J 593 " --> pdb=" O ASP K 434 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N PHE K 436 " --> pdb=" O VAL J 593 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N VAL J 595 " --> pdb=" O PHE K 436 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL K 438 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N ASN J 597 " --> pdb=" O VAL K 438 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N LYS K 440 " --> pdb=" O ASN J 597 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP K 447 " --> pdb=" O VAL K 402 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'K' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP K 447 " --> pdb=" O VAL K 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 437 " --> pdb=" O TYR K 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 413 " --> pdb=" O GLN K 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN K 407 " --> pdb=" O PHE K 443 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'K' and resid 407 through 414 removed outlier: 3.617A pdb=" N GLN K 407 " --> pdb=" O PHE K 443 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 413 " --> pdb=" O GLN K 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 437 " --> pdb=" O TYR K 413 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'K' and resid 417 through 418 removed outlier: 6.608A pdb=" N ASN J 591 " --> pdb=" O CYS K 432 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP K 434 " --> pdb=" O ASN J 591 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL J 593 " --> pdb=" O ASP K 434 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N PHE K 436 " --> pdb=" O VAL J 593 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N VAL J 595 " --> pdb=" O PHE K 436 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL K 438 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N ASN J 597 " --> pdb=" O VAL K 438 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N LYS K 440 " --> pdb=" O ASN J 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL J 593 " --> pdb=" O LYS J 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG J 602 " --> pdb=" O ASN J 597 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL K 40 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA K 194 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR K 141 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 192 " --> pdb=" O THR K 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS K 143 " --> pdb=" O THR K 190 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR K 190 " --> pdb=" O LYS K 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS K 187 " --> pdb=" O PRO K 292 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 189 " --> pdb=" O GLY K 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY K 290 " --> pdb=" O THR K 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER K 191 " --> pdb=" O ARG K 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG K 288 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP K 193 " --> pdb=" O ILE K 286 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR K 130 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE K 199 " --> pdb=" O VAL K 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL K 258 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU K 201 " --> pdb=" O SER K 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER K 256 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS K 203 " --> pdb=" O THR K 254 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AN2, first strand: chain 'K' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY K 464 " --> pdb=" O CYS K 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE K 466 " --> pdb=" O LYS K 494 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS K 560 " --> pdb=" O GLY K 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE K 514 " --> pdb=" O SER K 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER K 558 " --> pdb=" O PHE K 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 557 " --> pdb=" O ALA K 549 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'K' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG K 602 " --> pdb=" O ASN K 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL K 593 " --> pdb=" O LYS K 606 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS L 432 " --> pdb=" O THR K 592 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE K 594 " --> pdb=" O CYS L 432 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP L 434 " --> pdb=" O ILE K 594 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'L' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP L 447 " --> pdb=" O VAL L 402 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'L' and resid 401 through 402 removed outlier: 3.653A pdb=" N TRP L 447 " --> pdb=" O VAL L 402 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN L 437 " --> pdb=" O TYR L 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR L 413 " --> pdb=" O GLN L 437 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN L 407 " --> pdb=" O PHE L 443 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'L' and resid 407 through 414 removed outlier: 3.619A pdb=" N GLN L 407 " --> pdb=" O PHE L 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR L 413 " --> pdb=" O GLN L 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN L 437 " --> pdb=" O TYR L 413 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L' and resid 417 through 418 removed outlier: 6.179A pdb=" N CYS L 432 " --> pdb=" O THR K 592 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE K 594 " --> pdb=" O CYS L 432 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP L 434 " --> pdb=" O ILE K 594 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL K 593 " --> pdb=" O LYS K 606 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG K 602 " --> pdb=" O ASN K 597 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'L' and resid 33 through 35 removed outlier: 3.637A pdb=" N VAL L 40 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA L 194 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR L 141 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL L 192 " --> pdb=" O THR L 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS L 143 " --> pdb=" O THR L 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR L 190 " --> pdb=" O LYS L 143 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS L 187 " --> pdb=" O PRO L 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR L 189 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY L 290 " --> pdb=" O THR L 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER L 191 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG L 288 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP L 193 " --> pdb=" O ILE L 286 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'L' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR L 130 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE L 199 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL L 258 " --> pdb=" O ILE L 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU L 201 " --> pdb=" O SER L 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER L 256 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS L 203 " --> pdb=" O THR L 254 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'L' and resid 331 through 332 Processing sheet with id=AO4, first strand: chain 'L' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY L 464 " --> pdb=" O CYS L 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE L 466 " --> pdb=" O LYS L 494 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'L' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS L 560 " --> pdb=" O GLY L 512 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE L 514 " --> pdb=" O SER L 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER L 558 " --> pdb=" O PHE L 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 557 " --> pdb=" O ALA L 549 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'L' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG L 602 " --> pdb=" O ASN L 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL L 593 " --> pdb=" O LYS L 606 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N CYS M 432 " --> pdb=" O THR L 592 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE L 594 " --> pdb=" O CYS M 432 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP M 434 " --> pdb=" O ILE L 594 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'M' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL M 40 " --> pdb=" O ASP M 35 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'M' and resid 67 through 71 removed outlier: 6.692A pdb=" N ALA M 194 " --> pdb=" O VAL M 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR M 141 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL M 192 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS M 143 " --> pdb=" O THR M 190 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR M 190 " --> pdb=" O LYS M 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS M 187 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR M 189 " --> pdb=" O GLY M 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY M 290 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER M 191 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG M 288 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP M 193 " --> pdb=" O ILE M 286 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'M' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR M 130 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE M 199 " --> pdb=" O VAL M 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL M 258 " --> pdb=" O ILE M 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU M 201 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER M 256 " --> pdb=" O GLU M 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS M 203 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'M' and resid 331 through 332 Processing sheet with id=AP2, first strand: chain 'M' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP M 447 " --> pdb=" O VAL M 402 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'M' and resid 364 through 368 removed outlier: 3.713A pdb=" N GLN M 437 " --> pdb=" O TYR M 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR M 413 " --> pdb=" O GLN M 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN M 407 " --> pdb=" O PHE M 443 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY M 464 " --> pdb=" O CYS M 496 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE M 466 " --> pdb=" O LYS M 494 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 511 through 515 removed outlier: 5.391A pdb=" N CYS M 560 " --> pdb=" O GLY M 512 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE M 514 " --> pdb=" O SER M 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER M 558 " --> pdb=" O PHE M 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL M 557 " --> pdb=" O ALA M 549 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG M 602 " --> pdb=" O ASN M 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL M 593 " --> pdb=" O LYS M 606 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN M 591 " --> pdb=" O CYS N 432 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASP N 434 " --> pdb=" O ASN M 591 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL M 593 " --> pdb=" O ASP N 434 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'N' and resid 33 through 35 removed outlier: 3.638A pdb=" N VAL N 40 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'N' and resid 67 through 71 removed outlier: 6.693A pdb=" N ALA N 194 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR N 141 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL N 192 " --> pdb=" O THR N 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS N 143 " --> pdb=" O THR N 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR N 190 " --> pdb=" O LYS N 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS N 187 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR N 189 " --> pdb=" O GLY N 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY N 290 " --> pdb=" O THR N 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER N 191 " --> pdb=" O ARG N 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG N 288 " --> pdb=" O SER N 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP N 193 " --> pdb=" O ILE N 286 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'N' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR N 130 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE N 199 " --> pdb=" O VAL N 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL N 258 " --> pdb=" O ILE N 199 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU N 201 " --> pdb=" O SER N 256 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER N 256 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS N 203 " --> pdb=" O THR N 254 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'N' and resid 331 through 332 Processing sheet with id=AQ2, first strand: chain 'N' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP N 447 " --> pdb=" O VAL N 402 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'N' and resid 364 through 368 removed outlier: 3.713A pdb=" N GLN N 437 " --> pdb=" O TYR N 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR N 413 " --> pdb=" O GLN N 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN N 407 " --> pdb=" O PHE N 443 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'N' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY N 464 " --> pdb=" O CYS N 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE N 466 " --> pdb=" O LYS N 494 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'N' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS N 560 " --> pdb=" O GLY N 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE N 514 " --> pdb=" O SER N 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER N 558 " --> pdb=" O PHE N 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL N 557 " --> pdb=" O ALA N 549 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'N' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG N 602 " --> pdb=" O ASN N 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL N 593 " --> pdb=" O LYS N 606 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS O 432 " --> pdb=" O THR N 592 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE N 594 " --> pdb=" O CYS O 432 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP O 434 " --> pdb=" O ILE N 594 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'O' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL O 40 " --> pdb=" O ASP O 35 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'O' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA O 194 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR O 141 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL O 192 " --> pdb=" O THR O 141 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS O 143 " --> pdb=" O THR O 190 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR O 190 " --> pdb=" O LYS O 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS O 187 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR O 189 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY O 290 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER O 191 " --> pdb=" O ARG O 288 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG O 288 " --> pdb=" O SER O 191 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP O 193 " --> pdb=" O ILE O 286 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'O' and resid 82 through 84 removed outlier: 3.624A pdb=" N THR O 130 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE O 199 " --> pdb=" O VAL O 258 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL O 258 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU O 201 " --> pdb=" O SER O 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER O 256 " --> pdb=" O GLU O 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS O 203 " --> pdb=" O THR O 254 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'O' and resid 331 through 332 Processing sheet with id=AR2, first strand: chain 'O' and resid 364 through 368 removed outlier: 3.653A pdb=" N TRP O 447 " --> pdb=" O VAL O 402 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'O' and resid 364 through 368 removed outlier: 3.713A pdb=" N GLN O 437 " --> pdb=" O TYR O 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR O 413 " --> pdb=" O GLN O 437 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN O 407 " --> pdb=" O PHE O 443 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'O' and resid 464 through 466 removed outlier: 3.969A pdb=" N GLY O 464 " --> pdb=" O CYS O 496 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE O 466 " --> pdb=" O LYS O 494 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'O' and resid 511 through 515 removed outlier: 5.392A pdb=" N CYS O 560 " --> pdb=" O GLY O 512 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE O 514 " --> pdb=" O SER O 558 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER O 558 " --> pdb=" O PHE O 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL O 557 " --> pdb=" O ALA O 549 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'O' and resid 613 through 615 removed outlier: 4.006A pdb=" N ARG O 602 " --> pdb=" O ASN O 597 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL O 593 " --> pdb=" O LYS O 606 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS P 432 " --> pdb=" O THR O 592 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE O 594 " --> pdb=" O CYS P 432 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP P 434 " --> pdb=" O ILE O 594 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'P' and resid 33 through 35 removed outlier: 3.636A pdb=" N VAL P 40 " --> pdb=" O ASP P 35 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'P' and resid 67 through 71 removed outlier: 6.694A pdb=" N ALA P 194 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR P 141 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL P 192 " --> pdb=" O THR P 141 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS P 143 " --> pdb=" O THR P 190 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR P 190 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS P 187 " --> pdb=" O PRO P 292 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR P 189 " --> pdb=" O GLY P 290 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY P 290 " --> pdb=" O THR P 189 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER P 191 " --> pdb=" O ARG P 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG P 288 " --> pdb=" O SER P 191 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP P 193 " --> pdb=" O ILE P 286 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'P' and resid 82 through 84 removed outlier: 3.625A pdb=" N THR P 130 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE P 199 " --> pdb=" O VAL P 258 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL P 258 " --> pdb=" O ILE P 199 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU P 201 " --> pdb=" O SER P 256 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER P 256 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS P 203 " --> pdb=" O THR P 254 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'P' and resid 331 through 332 Processing sheet with id=AS2, first strand: chain 'P' and resid 364 through 368 removed outlier: 3.654A pdb=" N TRP P 447 " --> pdb=" O VAL P 402 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'P' and resid 364 through 368 removed outlier: 3.713A pdb=" N GLN P 437 " --> pdb=" O TYR P 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR P 413 " --> pdb=" O GLN P 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN P 407 " --> pdb=" O PHE P 443 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'P' and resid 464 through 466 removed outlier: 3.970A pdb=" N GLY P 464 " --> pdb=" O CYS P 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE P 466 " --> pdb=" O LYS P 494 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'P' and resid 511 through 515 removed outlier: 5.391A pdb=" N CYS P 560 " --> pdb=" O GLY P 512 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE P 514 " --> pdb=" O SER P 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER P 558 " --> pdb=" O PHE P 514 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL P 557 " --> pdb=" O ALA P 549 " (cutoff:3.500A) 2044 hydrogen bonds defined for protein. 5763 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: 34.55 Time building geometry restraints manager: 24.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23757 1.34 - 1.46: 17432 1.46 - 1.58: 33291 1.58 - 1.71: 0 1.71 - 1.83: 560 Bond restraints: 75040 Sorted by residual: bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C1 NAG l 2 " pdb=" O5 NAG l 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C1 NAG h 2 " pdb=" O5 NAG h 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.10e+00 ... (remaining 75035 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 2435 106.38 - 113.31: 40164 113.31 - 120.23: 27253 120.23 - 127.16: 31190 127.16 - 134.08: 830 Bond angle restraints: 101872 Sorted by residual: angle pdb=" C LYS C 386 " pdb=" N ASN C 387 " pdb=" CA ASN C 387 " ideal model delta sigma weight residual 120.83 127.78 -6.95 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C LYS I 386 " pdb=" N ASN I 387 " pdb=" CA ASN I 387 " ideal model delta sigma weight residual 120.83 127.75 -6.92 1.43e+00 4.89e-01 2.34e+01 angle pdb=" C LYS E 386 " pdb=" N ASN E 387 " pdb=" CA ASN E 387 " ideal model delta sigma weight residual 120.83 127.74 -6.91 1.43e+00 4.89e-01 2.34e+01 angle pdb=" C LYS F 386 " pdb=" N ASN F 387 " pdb=" CA ASN F 387 " ideal model delta sigma weight residual 120.83 127.74 -6.91 1.43e+00 4.89e-01 2.34e+01 angle pdb=" C LYS N 386 " pdb=" N ASN N 387 " pdb=" CA ASN N 387 " ideal model delta sigma weight residual 120.83 127.74 -6.91 1.43e+00 4.89e-01 2.34e+01 ... (remaining 101867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 43312 15.72 - 31.44: 2075 31.44 - 47.16: 581 47.16 - 62.88: 80 62.88 - 78.60: 48 Dihedral angle restraints: 46096 sinusoidal: 19136 harmonic: 26960 Sorted by residual: dihedral pdb=" CA VAL B 135 " pdb=" C VAL B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta harmonic sigma weight residual 180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA VAL F 135 " pdb=" C VAL F 135 " pdb=" N ARG F 136 " pdb=" CA ARG F 136 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA VAL A 135 " pdb=" C VAL A 135 " pdb=" N ARG A 136 " pdb=" CA ARG A 136 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 46093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 6676 0.041 - 0.082: 3474 0.082 - 0.124: 956 0.124 - 0.165: 446 0.165 - 0.206: 80 Chirality restraints: 11632 Sorted by residual: chirality pdb=" CB ILE G 594 " pdb=" CA ILE G 594 " pdb=" CG1 ILE G 594 " pdb=" CG2 ILE G 594 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE D 594 " pdb=" CA ILE D 594 " pdb=" CG1 ILE D 594 " pdb=" CG2 ILE D 594 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE M 594 " pdb=" CA ILE M 594 " pdb=" CG1 ILE M 594 " pdb=" CG2 ILE M 594 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 11629 not shown) Planarity restraints: 13232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS G 403 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C HIS G 403 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS G 403 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU G 404 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS O 403 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C HIS O 403 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS O 403 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU O 404 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS I 403 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C HIS I 403 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS I 403 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU I 404 " -0.013 2.00e-02 2.50e+03 ... (remaining 13229 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1406 2.67 - 3.23: 64385 3.23 - 3.78: 107301 3.78 - 4.34: 151004 4.34 - 4.90: 250025 Nonbonded interactions: 574121 Sorted by model distance: nonbonded pdb=" OD2 ASP D 58 " pdb=" OH TYR D 140 " model vdw 2.111 2.440 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR A 140 " model vdw 2.112 2.440 nonbonded pdb=" OD2 ASP E 58 " pdb=" OH TYR E 140 " model vdw 2.112 2.440 nonbonded pdb=" OD2 ASP K 58 " pdb=" OH TYR K 140 " model vdw 2.112 2.440 nonbonded pdb=" OD2 ASP I 58 " pdb=" OH TYR I 140 " model vdw 2.112 2.440 ... (remaining 574116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain '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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = 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' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.830 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 155.090 Find NCS groups from input model: 4.200 Set up NCS constraints: 1.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.007 0.078 75040 Z= 0.467 Angle : 0.935 9.201 101872 Z= 0.510 Chirality : 0.056 0.206 11632 Planarity : 0.008 0.055 13200 Dihedral : 10.418 78.603 28352 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.39 % Allowed : 3.74 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.07), residues: 9168 helix: -4.53 (0.04), residues: 2128 sheet: -2.93 (0.09), residues: 2112 loop : -2.27 (0.08), residues: 4928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 275 HIS 0.010 0.003 HIS M 419 PHE 0.024 0.003 PHE L 327 TYR 0.029 0.003 TYR E 324 ARG 0.010 0.001 ARG O 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1179 time to evaluate : 6.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.7748 (mmt) cc_final: 0.7442 (mmp) REVERT: B 469 LYS cc_start: 0.8492 (mttm) cc_final: 0.8274 (mppt) REVERT: B 625 MET cc_start: 0.7523 (mtt) cc_final: 0.7139 (ttt) REVERT: C 300 ASN cc_start: 0.8524 (t0) cc_final: 0.8246 (t0) REVERT: C 301 MET cc_start: 0.8852 (mmt) cc_final: 0.8524 (mmt) REVERT: C 409 HIS cc_start: 0.7398 (t70) cc_final: 0.6886 (t70) REVERT: C 474 MET cc_start: 0.8339 (mmm) cc_final: 0.8113 (mmm) REVERT: C 585 MET cc_start: 0.7677 (mmt) cc_final: 0.7420 (mmp) REVERT: D 300 ASN cc_start: 0.8376 (t0) cc_final: 0.8169 (t0) REVERT: D 402 VAL cc_start: 0.6259 (m) cc_final: 0.6057 (p) REVERT: D 565 LEU cc_start: 0.8247 (tp) cc_final: 0.8035 (tp) REVERT: D 625 MET cc_start: 0.7070 (mtt) cc_final: 0.6862 (mtt) REVERT: E 36 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8179 (t0) REVERT: E 409 HIS cc_start: 0.7308 (t70) cc_final: 0.7103 (t70) REVERT: F 371 LEU cc_start: 0.6213 (tm) cc_final: 0.5989 (tt) REVERT: F 474 MET cc_start: 0.8350 (mmm) cc_final: 0.8135 (mmm) REVERT: F 476 ASN cc_start: 0.8765 (t0) cc_final: 0.8509 (t160) REVERT: G 300 ASN cc_start: 0.8375 (t0) cc_final: 0.8165 (t0) REVERT: G 301 MET cc_start: 0.8636 (mmt) cc_final: 0.8367 (mmt) REVERT: G 357 THR cc_start: 0.7859 (m) cc_final: 0.7441 (p) REVERT: G 371 LEU cc_start: 0.6484 (tm) cc_final: 0.5298 (pp) REVERT: G 585 MET cc_start: 0.7580 (mmt) cc_final: 0.7355 (mmp) REVERT: G 625 MET cc_start: 0.7115 (mtt) cc_final: 0.6868 (mtt) REVERT: H 402 VAL cc_start: 0.6186 (m) cc_final: 0.5970 (p) REVERT: H 625 MET cc_start: 0.7241 (mtt) cc_final: 0.6765 (mtt) REVERT: J 625 MET cc_start: 0.7209 (mtt) cc_final: 0.6980 (ttt) REVERT: K 301 MET cc_start: 0.8839 (mmt) cc_final: 0.8568 (mmt) REVERT: K 416 LEU cc_start: 0.7335 (tp) cc_final: 0.7022 (tp) REVERT: K 585 MET cc_start: 0.7662 (mmt) cc_final: 0.7158 (mmp) REVERT: L 402 VAL cc_start: 0.6955 (m) cc_final: 0.6668 (p) REVERT: L 625 MET cc_start: 0.7485 (mtt) cc_final: 0.7165 (mtt) REVERT: N 84 LEU cc_start: 0.6618 (pt) cc_final: 0.6097 (pp) REVERT: O 84 LEU cc_start: 0.6428 (pt) cc_final: 0.5981 (pp) REVERT: O 148 LEU cc_start: 0.7863 (tp) cc_final: 0.7389 (tp) REVERT: P 84 LEU cc_start: 0.6882 (pt) cc_final: 0.6377 (pp) outliers start: 32 outliers final: 0 residues processed: 1195 average time/residue: 0.7538 time to fit residues: 1510.0049 Evaluate side-chains 622 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 621 time to evaluate : 6.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 783 optimal weight: 0.8980 chunk 703 optimal weight: 7.9990 chunk 390 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 474 optimal weight: 1.9990 chunk 375 optimal weight: 2.9990 chunk 727 optimal weight: 0.9980 chunk 281 optimal weight: 0.5980 chunk 442 optimal weight: 0.5980 chunk 541 optimal weight: 4.9990 chunk 842 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN A 370 GLN A 414 ASN A 476 ASN A 612 GLN B 187 HIS B 228 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 370 GLN B 414 ASN B 476 ASN C 36 ASN C 187 HIS C 255 ASN C 281 ASN C 370 GLN C 414 ASN C 476 ASN D 36 ASN D 187 HIS D 228 GLN D 255 ASN D 370 GLN D 414 ASN D 437 GLN D 476 ASN E 15 GLN E 19 ASN E 36 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN E 370 GLN E 414 ASN E 437 GLN E 476 ASN F 15 GLN F 19 ASN F 36 ASN F 187 HIS ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 370 GLN F 414 ASN F 547 HIS G 36 ASN G 187 HIS ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 370 GLN G 409 HIS G 414 ASN G 437 GLN G 476 ASN H 15 GLN H 19 ASN H 36 ASN H 187 HIS H 228 GLN H 255 ASN H 370 GLN H 414 ASN H 437 GLN H 476 ASN I 187 HIS I 255 ASN I 281 ASN I 370 GLN I 407 GLN I 414 ASN I 476 ASN I 612 GLN J 15 GLN J 19 ASN J 187 HIS J 228 GLN J 255 ASN J 281 ASN J 328 ASN J 370 GLN J 414 ASN K 109 ASN K 187 HIS K 255 ASN K 328 ASN K 370 GLN K 414 ASN K 492 ASN L 15 GLN L 19 ASN L 187 HIS ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 370 GLN L 409 HIS L 414 ASN L 476 ASN M 187 HIS M 228 GLN M 255 ASN M 370 GLN M 407 GLN M 547 HIS N 15 GLN N 19 ASN N 187 HIS N 228 GLN N 281 ASN N 358 ASN N 370 GLN N 414 ASN N 476 ASN N 547 HIS N 612 GLN O 187 HIS O 228 GLN O 255 ASN O 370 GLN O 414 ASN O 476 ASN O 547 HIS O 612 GLN P 187 HIS P 228 GLN P 255 ASN P 370 GLN P 547 HIS P 612 GLN Total number of N/Q/H flips: 123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75040 Z= 0.184 Angle : 0.611 11.287 101872 Z= 0.324 Chirality : 0.044 0.175 11632 Planarity : 0.005 0.043 13200 Dihedral : 7.136 56.799 11266 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.44 % Allowed : 7.37 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.08), residues: 9168 helix: -2.61 (0.09), residues: 2112 sheet: -2.42 (0.10), residues: 1936 loop : -1.73 (0.08), residues: 5120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 447 HIS 0.008 0.001 HIS K 419 PHE 0.022 0.002 PHE D 514 TYR 0.025 0.002 TYR M 365 ARG 0.005 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 726 time to evaluate : 6.318 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: A 46 MET cc_start: 0.8838 (mmt) cc_final: 0.8586 (mmt) REVERT: A 469 LYS cc_start: 0.8104 (mppt) cc_final: 0.7593 (mptt) REVERT: A 585 MET cc_start: 0.7722 (mmt) cc_final: 0.7363 (mmp) REVERT: B 60 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: B 281 ASN cc_start: 0.8665 (m-40) cc_final: 0.8463 (m-40) REVERT: B 625 MET cc_start: 0.7392 (mtt) cc_final: 0.7132 (ttt) REVERT: C 84 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6622 (pp) REVERT: C 156 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7660 (mtmm) REVERT: C 300 ASN cc_start: 0.8524 (t0) cc_final: 0.8257 (t0) REVERT: C 301 MET cc_start: 0.8891 (mmt) cc_final: 0.8508 (mmt) REVERT: D 281 ASN cc_start: 0.8547 (m-40) cc_final: 0.8330 (m-40) REVERT: D 301 MET cc_start: 0.8757 (mmp) cc_final: 0.8492 (mmp) REVERT: G 300 ASN cc_start: 0.8400 (t0) cc_final: 0.8184 (t0) REVERT: G 301 MET cc_start: 0.8734 (mmt) cc_final: 0.8373 (mmt) REVERT: G 357 THR cc_start: 0.7955 (m) cc_final: 0.7669 (p) REVERT: G 371 LEU cc_start: 0.6639 (tm) cc_final: 0.6360 (tt) REVERT: G 437 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7206 (mm110) REVERT: H 46 MET cc_start: 0.8719 (mmt) cc_final: 0.8292 (mmt) REVERT: H 625 MET cc_start: 0.7149 (mtt) cc_final: 0.6810 (mtt) REVERT: I 84 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6884 (pp) REVERT: J 625 MET cc_start: 0.7356 (mtt) cc_final: 0.7029 (ttt) REVERT: K 585 MET cc_start: 0.7748 (mmt) cc_final: 0.7510 (mmp) REVERT: L 301 MET cc_start: 0.8624 (mmp) cc_final: 0.8285 (mmp) REVERT: L 625 MET cc_start: 0.7407 (mtt) cc_final: 0.7175 (mtt) REVERT: N 84 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6568 (pp) REVERT: N 315 LYS cc_start: 0.8566 (tppt) cc_final: 0.8277 (tptm) REVERT: O 84 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6302 (pp) REVERT: O 315 LYS cc_start: 0.8614 (tppt) cc_final: 0.8179 (tptm) REVERT: P 46 MET cc_start: 0.8800 (mmt) cc_final: 0.8549 (mmt) REVERT: P 84 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6815 (pp) REVERT: P 102 LEU cc_start: 0.7931 (mt) cc_final: 0.7669 (mp) REVERT: P 443 PHE cc_start: 0.4957 (p90) cc_final: 0.4674 (p90) outliers start: 117 outliers final: 68 residues processed: 797 average time/residue: 0.6656 time to fit residues: 914.1948 Evaluate side-chains 664 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 589 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 105 PHE Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 36 ASN Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 437 GLN Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 585 MET Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 304 ASP Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 585 MET Chi-restraints excluded: chain L residue 593 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 446 PHE Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 446 PHE Chi-restraints excluded: chain P residue 581 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 468 optimal weight: 6.9990 chunk 261 optimal weight: 0.3980 chunk 701 optimal weight: 3.9990 chunk 573 optimal weight: 10.0000 chunk 232 optimal weight: 0.5980 chunk 844 optimal weight: 5.9990 chunk 912 optimal weight: 20.0000 chunk 751 optimal weight: 0.8980 chunk 837 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 677 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 255 ASN B 612 GLN C 281 ASN C 328 ASN C 409 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN D 203 HIS D 612 GLN E 187 HIS E 407 GLN E 476 ASN F 437 GLN F 612 GLN G 437 GLN ** G 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 612 GLN H 203 HIS H 409 HIS H 612 GLN I 228 GLN ** K 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 612 GLN L 203 HIS L 612 GLN ** M 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 GLN M 478 GLN N 328 ASN O 109 ASN O 203 HIS O 228 GLN O 419 HIS P 109 ASN P 203 HIS ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 75040 Z= 0.249 Angle : 0.592 9.139 101872 Z= 0.312 Chirality : 0.045 0.188 11632 Planarity : 0.005 0.042 13200 Dihedral : 6.700 58.712 11264 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.89 % Allowed : 8.87 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.08), residues: 9168 helix: -1.46 (0.11), residues: 2112 sheet: -2.16 (0.10), residues: 1952 loop : -1.44 (0.08), residues: 5104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 447 HIS 0.009 0.002 HIS J 419 PHE 0.019 0.002 PHE P 68 TYR 0.025 0.002 TYR A 365 ARG 0.005 0.001 ARG P 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 656 time to evaluate : 6.151 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: A 469 LYS cc_start: 0.8116 (mppt) cc_final: 0.7614 (mptt) REVERT: A 585 MET cc_start: 0.7755 (mmt) cc_final: 0.7429 (mmp) REVERT: B 60 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: B 371 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6870 (tt) REVERT: B 625 MET cc_start: 0.7438 (mtt) cc_final: 0.7162 (ttt) REVERT: C 156 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7743 (mtmm) REVERT: C 300 ASN cc_start: 0.8467 (t0) cc_final: 0.8204 (t0) REVERT: C 301 MET cc_start: 0.8915 (mmt) cc_final: 0.8537 (mmt) REVERT: C 371 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6801 (tt) REVERT: C 409 HIS cc_start: 0.7642 (t-90) cc_final: 0.6476 (t70) REVERT: D 156 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7959 (mtmm) REVERT: D 371 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6128 (tt) REVERT: D 384 GLU cc_start: 0.6628 (tp30) cc_final: 0.6107 (mm-30) REVERT: E 300 ASN cc_start: 0.8345 (t0) cc_final: 0.8069 (t0) REVERT: E 371 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5894 (tt) REVERT: E 386 LYS cc_start: 0.2961 (mmtt) cc_final: 0.2488 (mmmt) REVERT: F 371 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6166 (tt) REVERT: G 300 ASN cc_start: 0.8424 (t0) cc_final: 0.8191 (t0) REVERT: G 301 MET cc_start: 0.8797 (mmt) cc_final: 0.8410 (mmt) REVERT: G 357 THR cc_start: 0.7971 (m) cc_final: 0.7702 (p) REVERT: G 371 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6339 (tt) REVERT: H 46 MET cc_start: 0.8757 (mmt) cc_final: 0.8399 (mmt) REVERT: H 357 THR cc_start: 0.7931 (m) cc_final: 0.7652 (p) REVERT: H 625 MET cc_start: 0.7192 (mtt) cc_final: 0.6841 (mtt) REVERT: I 493 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6313 (pt) REVERT: I 539 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8343 (pttt) REVERT: J 493 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7120 (pt) REVERT: J 625 MET cc_start: 0.7498 (mtt) cc_final: 0.7164 (ttt) REVERT: K 371 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.5926 (pp) REVERT: K 493 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7283 (pt) REVERT: L 41 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7944 (p0) REVERT: L 301 MET cc_start: 0.8588 (mmp) cc_final: 0.8289 (mmp) REVERT: L 371 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6216 (tt) REVERT: N 84 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6732 (pp) REVERT: N 315 LYS cc_start: 0.8608 (tppt) cc_final: 0.8305 (tppp) REVERT: N 493 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6041 (pt) REVERT: O 84 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6439 (pp) REVERT: P 84 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6705 (pp) REVERT: P 102 LEU cc_start: 0.7845 (mt) cc_final: 0.7623 (mp) outliers start: 154 outliers final: 79 residues processed: 752 average time/residue: 0.6688 time to fit residues: 865.1297 Evaluate side-chains 685 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 588 time to evaluate : 6.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 539 LYS Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 585 MET Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 304 ASP Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 585 MET Chi-restraints excluded: chain L residue 593 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 357 THR Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 446 PHE Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain M residue 597 ASN Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 446 PHE Chi-restraints excluded: chain N residue 493 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 446 PHE Chi-restraints excluded: chain P residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 834 optimal weight: 6.9990 chunk 634 optimal weight: 0.5980 chunk 438 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 566 optimal weight: 9.9990 chunk 847 optimal weight: 8.9990 chunk 897 optimal weight: 2.9990 chunk 442 optimal weight: 0.2980 chunk 803 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 409 HIS A 476 ASN B 109 ASN C 109 ASN C 203 HIS C 281 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN E 407 GLN G 109 ASN G 203 HIS G 478 GLN ** G 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 409 HIS I 109 ASN I 547 HIS J 109 ASN J 476 ASN K 203 HIS K 407 GLN K 492 ASN L 19 ASN L 255 ASN L 409 HIS M 109 ASN M 407 GLN N 109 ASN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN P 476 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 75040 Z= 0.169 Angle : 0.549 10.341 101872 Z= 0.282 Chirality : 0.043 0.172 11632 Planarity : 0.004 0.039 13200 Dihedral : 6.225 56.820 11264 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.88 % Allowed : 9.81 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.08), residues: 9168 helix: -0.77 (0.11), residues: 2112 sheet: -1.86 (0.11), residues: 1936 loop : -1.26 (0.08), residues: 5120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 613 HIS 0.008 0.001 HIS A 409 PHE 0.027 0.002 PHE O 507 TYR 0.021 0.001 TYR I 365 ARG 0.006 0.000 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 667 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 LYS cc_start: 0.8072 (mppt) cc_final: 0.7616 (mptt) REVERT: A 585 MET cc_start: 0.7713 (mmt) cc_final: 0.7481 (mmp) REVERT: B 60 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: B 474 MET cc_start: 0.8286 (mmm) cc_final: 0.8021 (mmm) REVERT: B 625 MET cc_start: 0.7451 (mtt) cc_final: 0.7169 (tmm) REVERT: C 84 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6583 (pp) REVERT: C 156 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7669 (mtmm) REVERT: C 300 ASN cc_start: 0.8424 (t0) cc_final: 0.8202 (t0) REVERT: C 371 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6846 (tt) REVERT: C 567 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8102 (p) REVERT: D 119 MET cc_start: 0.7781 (ttp) cc_final: 0.7540 (tmm) REVERT: D 156 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7829 (mtpp) REVERT: D 301 MET cc_start: 0.8721 (mmp) cc_final: 0.8459 (mmt) REVERT: D 371 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6255 (tt) REVERT: D 514 PHE cc_start: 0.8201 (m-80) cc_final: 0.7999 (m-80) REVERT: E 163 ASP cc_start: 0.7552 (m-30) cc_final: 0.7343 (m-30) REVERT: E 300 ASN cc_start: 0.8342 (t0) cc_final: 0.8112 (t0) REVERT: E 371 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6257 (tt) REVERT: E 386 LYS cc_start: 0.3122 (mmtt) cc_final: 0.2653 (mmmt) REVERT: G 84 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6552 (pp) REVERT: G 156 LYS cc_start: 0.8251 (ttpt) cc_final: 0.8039 (mtmm) REVERT: G 357 THR cc_start: 0.7945 (m) cc_final: 0.7745 (p) REVERT: H 104 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8110 (mt) REVERT: H 357 THR cc_start: 0.7951 (m) cc_final: 0.7708 (p) REVERT: H 625 MET cc_start: 0.7322 (mtt) cc_final: 0.7071 (mtt) REVERT: I 84 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6307 (pp) REVERT: J 493 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7227 (pt) REVERT: J 625 MET cc_start: 0.7525 (mtt) cc_final: 0.7219 (ttt) REVERT: K 156 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7669 (mtpp) REVERT: K 493 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7250 (pt) REVERT: L 371 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6473 (tt) REVERT: L 419 HIS cc_start: 0.5940 (m-70) cc_final: 0.5693 (m-70) REVERT: M 315 LYS cc_start: 0.8318 (tppt) cc_final: 0.8019 (tptm) REVERT: N 84 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6748 (pp) REVERT: N 315 LYS cc_start: 0.8533 (tppt) cc_final: 0.8235 (tppp) REVERT: O 84 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6489 (pp) REVERT: P 84 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6676 (pp) REVERT: P 104 LEU cc_start: 0.8688 (mt) cc_final: 0.7731 (mp) outliers start: 153 outliers final: 78 residues processed: 768 average time/residue: 0.6597 time to fit residues: 877.5325 Evaluate side-chains 685 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 592 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 585 MET Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 438 VAL Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain M residue 597 ASN Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 105 PHE Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 595 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 404 LEU Chi-restraints excluded: chain O residue 446 PHE Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 404 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 747 optimal weight: 7.9990 chunk 509 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 667 optimal weight: 0.0980 chunk 370 optimal weight: 0.7980 chunk 765 optimal weight: 4.9990 chunk 620 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 458 optimal weight: 0.0980 chunk 805 optimal weight: 5.9990 chunk 226 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 547 HIS B 547 HIS C 228 GLN C 281 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 HIS D 547 HIS E 109 ASN E 407 GLN E 476 ASN G 228 GLN G 478 GLN G 547 HIS H 476 ASN H 547 HIS I 228 GLN J 476 ASN J 547 HIS J 612 GLN K 407 GLN K 547 HIS L 409 HIS L 547 HIS ** M 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 GLN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 75040 Z= 0.122 Angle : 0.512 11.245 101872 Z= 0.259 Chirality : 0.041 0.177 11632 Planarity : 0.004 0.037 13200 Dihedral : 5.763 54.686 11264 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.73 % Allowed : 10.40 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.09), residues: 9168 helix: -0.10 (0.12), residues: 2096 sheet: -1.61 (0.11), residues: 1936 loop : -1.11 (0.08), residues: 5136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 447 HIS 0.026 0.001 HIS G 409 PHE 0.019 0.001 PHE L 514 TYR 0.015 0.001 TYR J 365 ARG 0.004 0.000 ARG E 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 672 time to evaluate : 6.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6214 (pp) REVERT: A 134 GLN cc_start: 0.8325 (tt0) cc_final: 0.8122 (tt0) REVERT: A 148 LEU cc_start: 0.8157 (tp) cc_final: 0.7926 (mt) REVERT: A 469 LYS cc_start: 0.8155 (mppt) cc_final: 0.7620 (mptt) REVERT: A 585 MET cc_start: 0.7683 (mmt) cc_final: 0.7483 (mmp) REVERT: B 625 MET cc_start: 0.7393 (mtt) cc_final: 0.7152 (tmm) REVERT: C 84 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6488 (pp) REVERT: C 156 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7649 (mtmm) REVERT: C 301 MET cc_start: 0.8962 (mmt) cc_final: 0.8523 (mmt) REVERT: C 371 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6870 (tt) REVERT: D 156 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7803 (mtpp) REVERT: D 371 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6456 (tt) REVERT: D 384 GLU cc_start: 0.6829 (tp30) cc_final: 0.6136 (mm-30) REVERT: D 407 GLN cc_start: 0.6951 (tp40) cc_final: 0.6690 (tp40) REVERT: E 163 ASP cc_start: 0.7552 (m-30) cc_final: 0.7326 (m-30) REVERT: E 300 ASN cc_start: 0.8334 (t0) cc_final: 0.8101 (t0) REVERT: E 371 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6543 (tt) REVERT: E 386 LYS cc_start: 0.3088 (mmtt) cc_final: 0.2552 (mmmt) REVERT: F 46 MET cc_start: 0.8655 (mmt) cc_final: 0.8305 (mmt) REVERT: F 371 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6491 (tt) REVERT: F 625 MET cc_start: 0.7361 (mtt) cc_final: 0.7132 (tmm) REVERT: G 84 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6482 (pp) REVERT: G 301 MET cc_start: 0.8850 (mmt) cc_final: 0.8516 (mmt) REVERT: G 371 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6488 (tt) REVERT: G 519 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8089 (p) REVERT: H 84 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6092 (pp) REVERT: H 104 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7897 (mt) REVERT: H 625 MET cc_start: 0.7170 (mtt) cc_final: 0.6900 (mtt) REVERT: I 84 LEU cc_start: 0.7341 (pt) cc_final: 0.6492 (pp) REVERT: I 301 MET cc_start: 0.8750 (mmt) cc_final: 0.8359 (mmt) REVERT: J 84 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6641 (pp) REVERT: J 493 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7203 (pt) REVERT: J 625 MET cc_start: 0.7504 (mtt) cc_final: 0.7241 (ttt) REVERT: K 84 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6761 (pp) REVERT: K 156 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7605 (mtpp) REVERT: K 300 ASN cc_start: 0.8412 (t0) cc_final: 0.8177 (t0) REVERT: K 493 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7198 (pt) REVERT: L 156 LYS cc_start: 0.8247 (mtpt) cc_final: 0.8000 (mtmm) REVERT: L 371 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6749 (tt) REVERT: M 84 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6199 (pp) REVERT: M 134 GLN cc_start: 0.8371 (tt0) cc_final: 0.8170 (tt0) REVERT: N 84 LEU cc_start: 0.7138 (pt) cc_final: 0.6716 (pp) REVERT: N 315 LYS cc_start: 0.8497 (tppt) cc_final: 0.8219 (tppp) REVERT: O 84 LEU cc_start: 0.6889 (pt) cc_final: 0.6387 (pp) REVERT: O 104 LEU cc_start: 0.8349 (tp) cc_final: 0.8105 (mp) REVERT: P 84 LEU cc_start: 0.7200 (pt) cc_final: 0.6717 (pp) REVERT: P 104 LEU cc_start: 0.8701 (mt) cc_final: 0.8398 (mt) REVERT: P 301 MET cc_start: 0.8660 (mmt) cc_final: 0.8344 (mmt) outliers start: 141 outliers final: 76 residues processed: 761 average time/residue: 0.6712 time to fit residues: 877.1957 Evaluate side-chains 691 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 598 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 304 ASP Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 357 THR Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 105 PHE Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 595 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 404 LEU Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 467 SER Chi-restraints excluded: chain P residue 581 ARG Chi-restraints excluded: chain P residue 597 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 301 optimal weight: 6.9990 chunk 807 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 526 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 897 optimal weight: 3.9990 chunk 745 optimal weight: 2.9990 chunk 415 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 471 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 547 HIS B 385 GLN B 547 HIS C 547 HIS D 134 GLN D 547 HIS E 80 ASN E 134 GLN E 407 GLN F 109 ASN F 547 HIS G 547 HIS H 547 HIS J 385 GLN J 437 GLN J 547 HIS K 547 HIS L 134 GLN L 547 HIS M 328 ASN M 407 GLN N 228 GLN N 547 HIS P 228 GLN P 437 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 75040 Z= 0.375 Angle : 0.639 11.503 101872 Z= 0.331 Chirality : 0.047 0.177 11632 Planarity : 0.005 0.045 13200 Dihedral : 6.409 59.987 11264 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.45 % Allowed : 10.54 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.08), residues: 9168 helix: -0.02 (0.12), residues: 1904 sheet: -1.78 (0.11), residues: 1968 loop : -1.22 (0.08), residues: 5296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 447 HIS 0.015 0.002 HIS I 415 PHE 0.020 0.002 PHE C 296 TYR 0.022 0.002 TYR N 50 ARG 0.009 0.001 ARG J 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 617 time to evaluate : 6.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.7821 (mmt) cc_final: 0.7520 (mmp) REVERT: B 625 MET cc_start: 0.7530 (mtt) cc_final: 0.7237 (tmm) REVERT: C 156 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7824 (mtpp) REVERT: C 301 MET cc_start: 0.8940 (mmt) cc_final: 0.8493 (mmm) REVERT: C 371 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6796 (tt) REVERT: D 41 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 156 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7962 (mtpp) REVERT: D 371 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6396 (tt) REVERT: D 384 GLU cc_start: 0.6681 (tp30) cc_final: 0.6137 (mm-30) REVERT: D 407 GLN cc_start: 0.7049 (tp40) cc_final: 0.6697 (tp40) REVERT: E 163 ASP cc_start: 0.7808 (m-30) cc_final: 0.7092 (m-30) REVERT: E 371 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6562 (tt) REVERT: E 386 LYS cc_start: 0.3228 (mmtt) cc_final: 0.2713 (mmmt) REVERT: E 567 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7921 (p) REVERT: F 371 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6339 (tt) REVERT: G 156 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7979 (mtmm) REVERT: G 301 MET cc_start: 0.8906 (mmt) cc_final: 0.8442 (mmm) REVERT: G 371 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6660 (tt) REVERT: H 104 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8182 (mt) REVERT: H 172 MET cc_start: 0.7973 (tpt) cc_final: 0.7561 (tpt) REVERT: H 407 GLN cc_start: 0.6704 (tp40) cc_final: 0.6350 (tp40) REVERT: H 625 MET cc_start: 0.7240 (mtt) cc_final: 0.6927 (mtt) REVERT: I 301 MET cc_start: 0.8897 (mmt) cc_final: 0.8626 (mmt) REVERT: J 474 MET cc_start: 0.8628 (mmm) cc_final: 0.8367 (mmm) REVERT: J 493 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7263 (pt) REVERT: J 625 MET cc_start: 0.7597 (mtt) cc_final: 0.7249 (ttt) REVERT: K 300 ASN cc_start: 0.8457 (t0) cc_final: 0.8246 (t0) REVERT: K 493 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (pt) REVERT: L 41 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (p0) REVERT: L 156 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8085 (mtmm) REVERT: L 371 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6406 (tt) REVERT: L 384 GLU cc_start: 0.6467 (tp30) cc_final: 0.5857 (mm-30) REVERT: M 172 MET cc_start: 0.7907 (tpt) cc_final: 0.7380 (tpt) REVERT: M 387 ASN cc_start: 0.3687 (OUTLIER) cc_final: 0.3313 (m110) REVERT: N 315 LYS cc_start: 0.8633 (tppt) cc_final: 0.8364 (tppp) REVERT: N 469 LYS cc_start: 0.8603 (mttm) cc_final: 0.8314 (mppt) REVERT: O 84 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6582 (pp) REVERT: O 104 LEU cc_start: 0.8613 (tp) cc_final: 0.8282 (mp) REVERT: O 469 LYS cc_start: 0.8480 (mttm) cc_final: 0.8162 (mppt) REVERT: P 104 LEU cc_start: 0.8769 (mt) cc_final: 0.8452 (mt) outliers start: 199 outliers final: 113 residues processed: 754 average time/residue: 0.6563 time to fit residues: 854.0079 Evaluate side-chains 720 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 593 time to evaluate : 6.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 565 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 304 ASP Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 594 ILE Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 432 CYS Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 357 THR Chi-restraints excluded: chain M residue 387 ASN Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 438 VAL Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain O residue 597 ASN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 865 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 511 optimal weight: 7.9990 chunk 655 optimal weight: 4.9990 chunk 508 optimal weight: 2.9990 chunk 755 optimal weight: 1.9990 chunk 501 optimal weight: 5.9990 chunk 894 optimal weight: 3.9990 chunk 559 optimal weight: 7.9990 chunk 545 optimal weight: 6.9990 chunk 412 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN C 281 ASN C 476 ASN E 407 GLN G 478 GLN I 409 HIS K 281 ASN K 409 HIS L 109 ASN L 228 GLN M 80 ASN M 407 GLN M 409 HIS M 476 ASN O 281 ASN O 409 HIS O 587 GLN P 437 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 75040 Z= 0.249 Angle : 0.577 12.503 101872 Z= 0.297 Chirality : 0.044 0.227 11632 Planarity : 0.004 0.042 13200 Dihedral : 6.285 58.663 11264 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.33 % Allowed : 11.13 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 9168 helix: 0.03 (0.12), residues: 2000 sheet: -1.74 (0.11), residues: 1968 loop : -1.14 (0.08), residues: 5200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.006 0.001 HIS J 409 PHE 0.017 0.002 PHE P 443 TYR 0.014 0.002 TYR M 365 ARG 0.010 0.001 ARG K 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 625 time to evaluate : 6.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.7790 (mmt) cc_final: 0.7559 (mmp) REVERT: C 156 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7761 (mtpp) REVERT: C 301 MET cc_start: 0.8872 (mmt) cc_final: 0.8372 (mmm) REVERT: C 371 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6794 (tt) REVERT: C 409 HIS cc_start: 0.7557 (t-90) cc_final: 0.7345 (t-90) REVERT: C 567 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (p) REVERT: D 41 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7948 (p0) REVERT: D 156 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7835 (mtpp) REVERT: D 371 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6420 (tt) REVERT: D 384 GLU cc_start: 0.6647 (tp30) cc_final: 0.5991 (mm-30) REVERT: D 407 GLN cc_start: 0.6912 (tp40) cc_final: 0.6603 (tp40) REVERT: E 41 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7888 (p0) REVERT: E 163 ASP cc_start: 0.7719 (m-30) cc_final: 0.7011 (m-30) REVERT: E 371 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6573 (tt) REVERT: G 301 MET cc_start: 0.8931 (mmt) cc_final: 0.8453 (mmm) REVERT: H 104 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8064 (mt) REVERT: H 625 MET cc_start: 0.7239 (mtt) cc_final: 0.6951 (mtt) REVERT: I 301 MET cc_start: 0.8930 (mmt) cc_final: 0.8710 (mmt) REVERT: J 493 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7528 (pt) REVERT: J 625 MET cc_start: 0.7576 (mtt) cc_final: 0.7237 (ttt) REVERT: K 493 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7034 (pt) REVERT: K 615 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8673 (tt) REVERT: L 41 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7928 (p0) REVERT: L 156 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7884 (mtpp) REVERT: L 371 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6815 (tt) REVERT: L 384 GLU cc_start: 0.6425 (tp30) cc_final: 0.5602 (mm-30) REVERT: M 102 LEU cc_start: 0.7995 (mt) cc_final: 0.7663 (mp) REVERT: N 315 LYS cc_start: 0.8546 (tppt) cc_final: 0.8285 (tppp) REVERT: N 469 LYS cc_start: 0.8631 (mttm) cc_final: 0.8424 (mppt) REVERT: O 84 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6654 (pp) REVERT: O 469 LYS cc_start: 0.8591 (mttm) cc_final: 0.8331 (mppt) REVERT: P 104 LEU cc_start: 0.8661 (mt) cc_final: 0.8264 (mt) REVERT: P 281 ASN cc_start: 0.8794 (m-40) cc_final: 0.8471 (m110) outliers start: 189 outliers final: 125 residues processed: 757 average time/residue: 0.6661 time to fit residues: 872.3219 Evaluate side-chains 730 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 592 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 380 CYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 594 ILE Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 615 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 432 CYS Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 357 THR Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 438 VAL Chi-restraints excluded: chain M residue 598 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 408 ILE Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 597 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 553 optimal weight: 4.9990 chunk 357 optimal weight: 0.5980 chunk 534 optimal weight: 0.8980 chunk 269 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 173 optimal weight: 20.0000 chunk 568 optimal weight: 6.9990 chunk 609 optimal weight: 0.7980 chunk 442 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 703 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN C 281 ASN D 476 ASN E 407 GLN G 478 GLN K 36 ASN K 281 ASN L 36 ASN M 407 GLN O 281 ASN P 409 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 75040 Z= 0.140 Angle : 0.534 13.124 101872 Z= 0.267 Chirality : 0.042 0.177 11632 Planarity : 0.004 0.044 13200 Dihedral : 5.855 55.266 11264 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.04 % Allowed : 11.65 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.09), residues: 9168 helix: 0.51 (0.12), residues: 1984 sheet: -1.54 (0.11), residues: 1936 loop : -1.06 (0.08), residues: 5248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 447 HIS 0.006 0.001 HIS J 409 PHE 0.016 0.001 PHE P 443 TYR 0.015 0.001 TYR P 365 ARG 0.008 0.000 ARG K 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 650 time to evaluate : 6.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7939 (p) REVERT: C 84 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6609 (pp) REVERT: C 156 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7693 (mtpp) REVERT: C 301 MET cc_start: 0.8955 (mmt) cc_final: 0.8506 (mmm) REVERT: C 587 GLN cc_start: 0.7518 (tp40) cc_final: 0.7220 (tp40) REVERT: D 156 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7756 (mtpp) REVERT: D 371 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6439 (tt) REVERT: D 384 GLU cc_start: 0.6494 (tp30) cc_final: 0.5835 (mm-30) REVERT: D 407 GLN cc_start: 0.6832 (tp40) cc_final: 0.6522 (tp40) REVERT: E 163 ASP cc_start: 0.7607 (m-30) cc_final: 0.6872 (m-30) REVERT: E 386 LYS cc_start: 0.3172 (mmtt) cc_final: 0.2586 (mmmt) REVERT: G 84 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6590 (pp) REVERT: G 301 MET cc_start: 0.8876 (mmt) cc_final: 0.8434 (mmm) REVERT: H 84 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6113 (pp) REVERT: H 104 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8026 (mt) REVERT: H 300 ASN cc_start: 0.8500 (t0) cc_final: 0.8242 (t0) REVERT: H 625 MET cc_start: 0.7227 (mtt) cc_final: 0.6960 (mtt) REVERT: I 84 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6526 (pp) REVERT: I 614 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7696 (ttp-110) REVERT: J 493 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7500 (pt) REVERT: J 625 MET cc_start: 0.7624 (mtt) cc_final: 0.7290 (ttt) REVERT: K 84 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6697 (pp) REVERT: K 493 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7043 (pt) REVERT: L 156 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7793 (mtpp) REVERT: L 371 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6783 (tt) REVERT: L 384 GLU cc_start: 0.6389 (tp30) cc_final: 0.5701 (mm-30) REVERT: M 102 LEU cc_start: 0.7836 (mt) cc_final: 0.7521 (mp) REVERT: N 84 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6868 (pp) REVERT: N 315 LYS cc_start: 0.8502 (tppt) cc_final: 0.8270 (tppp) REVERT: N 600 ASN cc_start: 0.8046 (p0) cc_final: 0.7842 (p0) REVERT: O 84 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6590 (pp) REVERT: O 469 LYS cc_start: 0.8580 (mttm) cc_final: 0.8324 (mppt) REVERT: P 84 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6330 (pp) REVERT: P 104 LEU cc_start: 0.8640 (mt) cc_final: 0.8210 (mt) REVERT: P 281 ASN cc_start: 0.8784 (m-40) cc_final: 0.8482 (m110) REVERT: P 301 MET cc_start: 0.8735 (mmt) cc_final: 0.8340 (mmt) outliers start: 166 outliers final: 109 residues processed: 748 average time/residue: 0.6664 time to fit residues: 860.8118 Evaluate side-chains 736 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 613 time to evaluate : 6.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain H residue 42 MET Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 380 CYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 432 CYS Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 565 LEU Chi-restraints excluded: chain N residue 597 ASN Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 404 LEU Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain O residue 597 ASN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 581 ARG Chi-restraints excluded: chain P residue 597 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 813 optimal weight: 0.5980 chunk 856 optimal weight: 0.4980 chunk 781 optimal weight: 3.9990 chunk 833 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 chunk 363 optimal weight: 1.9990 chunk 654 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 753 optimal weight: 0.4980 chunk 788 optimal weight: 20.0000 chunk 830 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 281 ASN L 36 ASN M 407 GLN M 587 GLN O 281 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 75040 Z= 0.207 Angle : 0.560 13.141 101872 Z= 0.281 Chirality : 0.043 0.171 11632 Planarity : 0.004 0.043 13200 Dihedral : 5.941 57.077 11264 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.96 % Allowed : 11.88 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.09), residues: 9168 helix: 0.47 (0.12), residues: 2000 sheet: -1.54 (0.11), residues: 1952 loop : -1.04 (0.08), residues: 5216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 447 HIS 0.007 0.001 HIS G 409 PHE 0.018 0.002 PHE H 68 TYR 0.014 0.001 TYR P 365 ARG 0.008 0.000 ARG K 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 629 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 84 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.5824 (pp) REVERT: C 156 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7740 (mtpp) REVERT: C 301 MET cc_start: 0.8882 (mmt) cc_final: 0.8422 (mmm) REVERT: C 587 GLN cc_start: 0.7545 (tp40) cc_final: 0.7266 (tp40) REVERT: D 41 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7761 (p0) REVERT: D 156 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7792 (mtpp) REVERT: D 371 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6390 (tt) REVERT: D 407 GLN cc_start: 0.6858 (tp40) cc_final: 0.6531 (tp40) REVERT: E 41 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7786 (p0) REVERT: E 163 ASP cc_start: 0.7692 (m-30) cc_final: 0.6999 (m-30) REVERT: G 84 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.5809 (pp) REVERT: G 301 MET cc_start: 0.8881 (mmt) cc_final: 0.8448 (mmm) REVERT: H 104 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8051 (mt) REVERT: H 625 MET cc_start: 0.7231 (mtt) cc_final: 0.6970 (mtt) REVERT: I 614 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7676 (ttp-110) REVERT: J 493 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7521 (pt) REVERT: J 625 MET cc_start: 0.7629 (mtt) cc_final: 0.7296 (ttt) REVERT: K 84 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6707 (pp) REVERT: K 493 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7012 (pt) REVERT: L 156 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7826 (mtpp) REVERT: L 371 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6910 (tt) REVERT: M 102 LEU cc_start: 0.7840 (mt) cc_final: 0.7544 (mp) REVERT: N 84 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6850 (pp) REVERT: N 104 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8292 (mt) REVERT: N 315 LYS cc_start: 0.8546 (tppt) cc_final: 0.8307 (tppp) REVERT: N 567 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8104 (p) REVERT: O 84 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6649 (pp) REVERT: O 171 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7451 (ptm160) REVERT: O 469 LYS cc_start: 0.8623 (mttm) cc_final: 0.8349 (mppt) REVERT: P 84 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6288 (pp) REVERT: P 104 LEU cc_start: 0.8664 (mt) cc_final: 0.8215 (mt) REVERT: P 281 ASN cc_start: 0.8798 (m-40) cc_final: 0.8495 (m110) outliers start: 159 outliers final: 118 residues processed: 725 average time/residue: 0.6659 time to fit residues: 832.9620 Evaluate side-chains 756 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 621 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 565 LEU Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 380 CYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 42 MET Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 432 CYS Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 489 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 565 LEU Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 597 ASN Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 171 ARG Chi-restraints excluded: chain O residue 404 LEU Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain O residue 597 ASN Chi-restraints excluded: chain P residue 42 MET Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 565 LEU Chi-restraints excluded: chain P residue 581 ARG Chi-restraints excluded: chain P residue 597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 547 optimal weight: 0.9990 chunk 881 optimal weight: 5.9990 chunk 537 optimal weight: 3.9990 chunk 418 optimal weight: 3.9990 chunk 612 optimal weight: 1.9990 chunk 924 optimal weight: 20.0000 chunk 850 optimal weight: 20.0000 chunk 736 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 568 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 385 GLN I 80 ASN K 15 GLN K 19 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN L 36 ASN M 407 GLN M 547 HIS O 281 ASN O 409 HIS O 547 HIS ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 547 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 75040 Z= 0.392 Angle : 0.666 13.203 101872 Z= 0.343 Chirality : 0.048 0.189 11632 Planarity : 0.005 0.054 13200 Dihedral : 6.524 59.989 11264 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.96 % Allowed : 11.96 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.08), residues: 9168 helix: -0.02 (0.12), residues: 1984 sheet: -1.65 (0.11), residues: 1968 loop : -1.27 (0.08), residues: 5216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 34 HIS 0.009 0.002 HIS F 187 PHE 0.020 0.002 PHE B 68 TYR 0.024 0.002 TYR N 50 ARG 0.010 0.001 ARG C 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 593 time to evaluate : 6.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7828 (mtpp) REVERT: C 587 GLN cc_start: 0.7700 (tp40) cc_final: 0.7459 (tp40) REVERT: D 41 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (p0) REVERT: D 156 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7879 (mtpp) REVERT: D 371 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6387 (tt) REVERT: D 384 GLU cc_start: 0.6567 (tp30) cc_final: 0.5871 (mm-30) REVERT: D 407 GLN cc_start: 0.6960 (tp40) cc_final: 0.6591 (tp40) REVERT: E 41 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (p0) REVERT: E 163 ASP cc_start: 0.7815 (m-30) cc_final: 0.7287 (m-30) REVERT: H 104 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8099 (mt) REVERT: I 172 MET cc_start: 0.7864 (tpt) cc_final: 0.7571 (tpt) REVERT: I 614 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7670 (ttp-110) REVERT: J 493 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7543 (pt) REVERT: J 625 MET cc_start: 0.7720 (mtt) cc_final: 0.7322 (ttt) REVERT: K 493 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7088 (pt) REVERT: L 41 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7909 (p0) REVERT: L 156 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7927 (mtpp) REVERT: L 371 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6775 (tt) REVERT: L 384 GLU cc_start: 0.6464 (tp30) cc_final: 0.5645 (mm-30) REVERT: N 104 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8244 (mt) REVERT: N 315 LYS cc_start: 0.8618 (tppt) cc_final: 0.8370 (tppp) REVERT: N 597 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7179 (p0) REVERT: O 171 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7522 (ptm160) REVERT: O 597 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7295 (p0) REVERT: P 104 LEU cc_start: 0.8672 (mt) cc_final: 0.8269 (mt) REVERT: P 281 ASN cc_start: 0.8750 (m-40) cc_final: 0.8500 (m110) outliers start: 159 outliers final: 123 residues processed: 692 average time/residue: 0.6736 time to fit residues: 805.0087 Evaluate side-chains 713 residues out of total 8240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 578 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 519 VAL Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 489 LEU Chi-restraints excluded: chain G residue 594 ILE Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain H residue 489 LEU Chi-restraints excluded: chain H residue 519 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 565 LEU Chi-restraints excluded: chain I residue 597 ASN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 380 CYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 519 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 371 LEU Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 432 CYS Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 489 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 594 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 404 LEU Chi-restraints excluded: chain M residue 434 ASP Chi-restraints excluded: chain M residue 470 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 565 LEU Chi-restraints excluded: chain N residue 597 ASN Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 171 ARG Chi-restraints excluded: chain O residue 210 GLN Chi-restraints excluded: chain O residue 246 THR Chi-restraints excluded: chain O residue 404 LEU Chi-restraints excluded: chain O residue 434 ASP Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 595 VAL Chi-restraints excluded: chain O residue 597 ASN Chi-restraints excluded: chain P residue 42 MET Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 404 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 928 random chunks: chunk 584 optimal weight: 0.0980 chunk 784 optimal weight: 0.9990 chunk 225 optimal weight: 0.4980 chunk 678 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 204 optimal weight: 0.6980 chunk 737 optimal weight: 7.9990 chunk 308 optimal weight: 0.0770 chunk 757 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 281 ASN ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN G 478 GLN I 409 HIS K 80 ASN K 281 ASN K 407 GLN L 36 ASN M 407 GLN N 80 ASN O 80 ASN O 281 ASN O 476 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116562 restraints weight = 101840.528| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.74 r_work: 0.3105 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 75040 Z= 0.131 Angle : 0.553 14.181 101872 Z= 0.275 Chirality : 0.042 0.179 11632 Planarity : 0.004 0.057 13200 Dihedral : 5.953 55.614 11264 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.51 % Allowed : 12.45 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.09), residues: 9168 helix: 0.46 (0.12), residues: 2064 sheet: -1.47 (0.11), residues: 1936 loop : -1.08 (0.08), residues: 5168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 34 HIS 0.007 0.001 HIS G 409 PHE 0.030 0.001 PHE I 235 TYR 0.014 0.001 TYR P 365 ARG 0.009 0.000 ARG K 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15482.69 seconds wall clock time: 273 minutes 40.90 seconds (16420.90 seconds total)