Starting phenix.real_space_refine on Sun Feb 18 01:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2j_20620/02_2024/6u2j_20620_neut.pdb" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 45360 2.51 5 N 12256 2.21 5 O 13728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" 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 ARG 444": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 71744 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "H" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "I" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "J" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "K" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "O" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "P" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4442 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 542} Chain breaks: 6 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 28.83, per 1000 atoms: 0.40 Number of scatterers: 71744 At special positions: 0 Unit cell: (240.62, 240.62, 106, 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 13728 8.00 N 12256 7.00 C 45360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 496 " distance=2.03 Simple disulfide: pdb=" SG CYS C 540 " - pdb=" SG CYS C 560 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 540 " - pdb=" SG CYS D 560 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 496 " distance=2.03 Simple disulfide: pdb=" SG CYS E 540 " - pdb=" SG CYS E 560 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 540 " - pdb=" SG CYS F 560 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 496 " distance=2.03 Simple disulfide: pdb=" SG CYS G 540 " - pdb=" SG CYS G 560 " distance=2.03 Simple disulfide: pdb=" SG CYS H 480 " - pdb=" SG CYS H 496 " distance=2.03 Simple disulfide: pdb=" SG CYS H 540 " - pdb=" SG CYS H 560 " distance=2.03 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 496 " distance=2.03 Simple disulfide: pdb=" SG CYS I 540 " - pdb=" SG CYS I 560 " distance=2.03 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 496 " distance=2.03 Simple disulfide: pdb=" SG CYS J 540 " - pdb=" SG CYS J 560 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 496 " distance=2.03 Simple disulfide: pdb=" SG CYS K 540 " - pdb=" SG CYS K 560 " distance=2.03 Simple disulfide: pdb=" SG CYS L 480 " - pdb=" SG CYS L 496 " distance=2.03 Simple disulfide: pdb=" SG CYS L 540 " - pdb=" SG CYS L 560 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 496 " distance=2.03 Simple disulfide: pdb=" SG CYS M 540 " - pdb=" SG CYS M 560 " distance=2.03 Simple disulfide: pdb=" SG CYS N 480 " - pdb=" SG CYS N 496 " distance=2.03 Simple disulfide: pdb=" SG CYS N 540 " - pdb=" SG CYS N 560 " distance=2.03 Simple disulfide: pdb=" SG CYS O 480 " - pdb=" SG CYS O 496 " distance=2.03 Simple disulfide: pdb=" SG CYS O 540 " - pdb=" SG CYS O 560 " distance=2.03 Simple disulfide: pdb=" SG CYS P 480 " - pdb=" SG CYS P 496 " 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-ASN " NAG A 701 " - " ASN A 168 " " NAG B 701 " - " ASN B 168 " " NAG C 701 " - " ASN C 168 " " NAG D 701 " - " ASN D 168 " " NAG E 701 " - " ASN E 168 " " NAG F 701 " - " ASN F 168 " " NAG G 701 " - " ASN G 168 " " NAG H 701 " - " ASN H 168 " " NAG I 701 " - " ASN I 168 " " NAG J 701 " - " ASN J 168 " " NAG K 701 " - " ASN K 168 " " NAG L 701 " - " ASN L 168 " " NAG M 701 " - " ASN M 168 " " NAG N 701 " - " ASN N 168 " " NAG O 701 " - " ASN O 168 " " NAG P 701 " - " ASN P 168 " " NAG Q 1 " - " ASN A 252 " " NAG R 1 " - " ASN B 252 " " NAG S 1 " - " ASN C 252 " " NAG T 1 " - " ASN D 252 " " NAG U 1 " - " ASN E 252 " " NAG V 1 " - " ASN F 252 " " NAG W 1 " - " ASN G 252 " " NAG X 1 " - " ASN H 252 " " NAG Y 1 " - " ASN I 252 " " NAG Z 1 " - " ASN J 252 " " NAG a 1 " - " ASN K 252 " " NAG b 1 " - " ASN L 252 " " NAG c 1 " - " ASN M 252 " " NAG d 1 " - " ASN N 252 " " NAG e 1 " - " ASN O 252 " " NAG f 1 " - " ASN P 252 " Time building additional restraints: 22.68 Conformation dependent library (CDL) restraints added in 10.3 seconds 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17152 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 128 sheets defined 26.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.058A pdb=" N ASP A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 306 through 327 removed outlier: 3.606A pdb=" N VAL A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 617 through 629 removed outlier: 3.770A pdb=" N ARG A 622 " --> pdb=" O PRO A 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 210' Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.664A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.625A pdb=" N GLY B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG B 506 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 508 " --> pdb=" O SER B 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 508' Processing helix chain 'B' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG B 622 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.058A pdb=" N ASP C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 185 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 210' Processing helix chain 'C' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 297 Processing helix chain 'C' and resid 306 through 327 removed outlier: 3.606A pdb=" N VAL C 310 " --> pdb=" O PRO C 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 507 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 503 through 508' Processing helix chain 'C' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG C 622 " --> pdb=" O PRO C 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 185 Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 210' Processing helix chain 'D' and resid 215 through 233 removed outlier: 3.662A pdb=" N ALA D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 306 through 327 removed outlier: 3.606A pdb=" N VAL D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG D 506 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 507 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 508 " --> pdb=" O SER D 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG D 622 " --> pdb=" O PRO D 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL D 627 " --> pdb=" O ARG D 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.058A pdb=" N ASP E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 185 Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 210' Processing helix chain 'E' and resid 215 through 233 removed outlier: 3.664A pdb=" N ALA E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.676A pdb=" N LYS E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 306 through 327 removed outlier: 3.606A pdb=" N VAL E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.994A pdb=" N ARG E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 507 " --> pdb=" O GLY E 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 508 " --> pdb=" O SER E 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 508' Processing helix chain 'E' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG E 622 " --> pdb=" O PRO E 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL E 627 " --> pdb=" O ARG E 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.058A pdb=" N ASP F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 185 Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 210' Processing helix chain 'F' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS F 247 " --> pdb=" O ASN F 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER F 248 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL F 310 " --> pdb=" O PRO F 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE F 507 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 508 " --> pdb=" O SER F 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG F 622 " --> pdb=" O PRO F 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL F 627 " --> pdb=" O ARG F 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 185 Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 206 through 210' Processing helix chain 'G' and resid 215 through 233 removed outlier: 3.664A pdb=" N ALA G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 removed outlier: 3.676A pdb=" N LYS G 247 " --> pdb=" O ASN G 243 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY G 278 " --> pdb=" O ALA G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL G 310 " --> pdb=" O PRO G 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 508 removed outlier: 3.994A pdb=" N ARG G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE G 507 " --> pdb=" O GLY G 504 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA G 508 " --> pdb=" O SER G 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 508' Processing helix chain 'G' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG G 622 " --> pdb=" O PRO G 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.059A pdb=" N ASP H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 185 Processing helix chain 'H' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 206 through 210' Processing helix chain 'H' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS H 247 " --> pdb=" O ASN H 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER H 248 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER H 251 " --> pdb=" O LYS H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 278 removed outlier: 3.625A pdb=" N GLY H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 297 Processing helix chain 'H' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL H 310 " --> pdb=" O PRO H 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS H 311 " --> pdb=" O GLY H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.994A pdb=" N ARG H 506 " --> pdb=" O LEU H 503 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 507 " --> pdb=" O GLY H 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 508 " --> pdb=" O SER H 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 508' Processing helix chain 'H' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG H 622 " --> pdb=" O PRO H 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL H 627 " --> pdb=" O ARG H 623 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 185 Processing helix chain 'I' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 206 through 210' Processing helix chain 'I' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS I 247 " --> pdb=" O ASN I 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER I 248 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER I 251 " --> pdb=" O LYS I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY I 278 " --> pdb=" O ALA I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 297 Processing helix chain 'I' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL I 310 " --> pdb=" O PRO I 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 508 removed outlier: 3.994A pdb=" N ARG I 506 " --> pdb=" O LEU I 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE I 507 " --> pdb=" O GLY I 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA I 508 " --> pdb=" O SER I 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 503 through 508' Processing helix chain 'I' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG I 622 " --> pdb=" O PRO I 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL I 627 " --> pdb=" O ARG I 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.059A pdb=" N ASP J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 185 Processing helix chain 'J' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 206 through 210' Processing helix chain 'J' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS J 247 " --> pdb=" O ASN J 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER J 248 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER J 251 " --> pdb=" O LYS J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY J 278 " --> pdb=" O ALA J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 297 Processing helix chain 'J' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL J 310 " --> pdb=" O PRO J 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS J 311 " --> pdb=" O GLY J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 503 through 508 removed outlier: 3.994A pdb=" N ARG J 506 " --> pdb=" O LEU J 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE J 507 " --> pdb=" O GLY J 504 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA J 508 " --> pdb=" O SER J 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 503 through 508' Processing helix chain 'J' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG J 622 " --> pdb=" O PRO J 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL J 627 " --> pdb=" O ARG J 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.057A pdb=" N ASP K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE K 161 " --> pdb=" O GLU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 185 Processing helix chain 'K' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN K 210 " --> pdb=" O ALA K 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 206 through 210' Processing helix chain 'K' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS K 247 " --> pdb=" O ASN K 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER K 248 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER K 251 " --> pdb=" O LYS K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY K 278 " --> pdb=" O ALA K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 297 Processing helix chain 'K' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL K 310 " --> pdb=" O PRO K 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS K 311 " --> pdb=" O GLY K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG K 506 " --> pdb=" O LEU K 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE K 507 " --> pdb=" O GLY K 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 508 " --> pdb=" O SER K 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 503 through 508' Processing helix chain 'K' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG K 622 " --> pdb=" O PRO K 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL K 627 " --> pdb=" O ARG K 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE L 161 " --> pdb=" O GLU L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 185 Processing helix chain 'L' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 210' Processing helix chain 'L' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS L 247 " --> pdb=" O ASN L 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER L 248 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER L 251 " --> pdb=" O LYS L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY L 278 " --> pdb=" O ALA L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 297 Processing helix chain 'L' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL L 310 " --> pdb=" O PRO L 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS L 311 " --> pdb=" O GLY L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG L 506 " --> pdb=" O LEU L 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE L 507 " --> pdb=" O GLY L 504 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA L 508 " --> pdb=" O SER L 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 503 through 508' Processing helix chain 'L' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG L 622 " --> pdb=" O PRO L 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL L 627 " --> pdb=" O ARG L 623 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.057A pdb=" N ASP M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE M 161 " --> pdb=" O GLU M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 185 Processing helix chain 'M' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 206 through 210' Processing helix chain 'M' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 252 removed outlier: 3.677A pdb=" N LYS M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER M 248 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY M 278 " --> pdb=" O ALA M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 297 Processing helix chain 'M' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 311 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG M 506 " --> pdb=" O LEU M 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE M 507 " --> pdb=" O GLY M 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 508 " --> pdb=" O SER M 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 503 through 508' Processing helix chain 'M' and resid 617 through 629 removed outlier: 3.769A pdb=" N ARG M 622 " --> pdb=" O PRO M 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL M 627 " --> pdb=" O ARG M 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 22 removed outlier: 3.735A 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 126 removed outlier: 4.058A pdb=" N ASP N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE N 161 " --> pdb=" O GLU N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 185 Processing helix chain 'N' and resid 206 through 210 removed outlier: 3.936A pdb=" N GLN N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 206 through 210' Processing helix chain 'N' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 252 removed outlier: 3.676A pdb=" N LYS N 247 " --> pdb=" O ASN N 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER N 248 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER N 251 " --> pdb=" O LYS N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 278 removed outlier: 3.627A pdb=" N GLY N 278 " --> pdb=" O ALA N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 297 Processing helix chain 'N' and resid 306 through 327 removed outlier: 3.606A pdb=" N VAL N 310 " --> pdb=" O PRO N 306 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS N 311 " --> pdb=" O GLY N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG N 506 " --> pdb=" O LEU N 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE N 507 " --> pdb=" O GLY N 504 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA N 508 " --> pdb=" O SER N 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 503 through 508' Processing helix chain 'N' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG N 622 " --> pdb=" O PRO N 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL N 627 " --> pdb=" O ARG N 623 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 167 removed outlier: 3.651A pdb=" N ILE O 161 " --> pdb=" O GLU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 185 Processing helix chain 'O' and resid 206 through 210 removed outlier: 3.937A pdb=" N GLN O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 206 through 210' Processing helix chain 'O' and resid 215 through 233 removed outlier: 3.663A pdb=" N ALA O 221 " --> pdb=" O SER O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 252 removed outlier: 3.676A pdb=" N LYS O 247 " --> pdb=" O ASN O 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER O 248 " --> pdb=" O VAL O 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 278 removed outlier: 3.626A pdb=" N GLY O 278 " --> pdb=" O ALA O 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 297 Processing helix chain 'O' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL O 310 " --> pdb=" O PRO O 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS O 311 " --> pdb=" O GLY O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG O 506 " --> pdb=" O LEU O 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE O 507 " --> pdb=" O GLY O 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA O 508 " --> pdb=" O SER O 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 503 through 508' Processing helix chain 'O' and resid 617 through 629 removed outlier: 3.768A pdb=" N ARG O 622 " --> pdb=" O PRO O 618 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL O 627 " --> pdb=" O ARG O 623 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 22 removed outlier: 3.734A 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 126 removed outlier: 4.058A pdb=" N ASP P 126 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 167 removed outlier: 3.650A pdb=" N ILE P 161 " --> pdb=" O GLU P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 185 Processing helix chain 'P' and resid 206 through 210 removed outlier: 3.935A pdb=" N GLN P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 206 through 210' Processing helix chain 'P' and resid 215 through 233 removed outlier: 3.664A pdb=" N ALA P 221 " --> pdb=" O SER P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 252 removed outlier: 3.676A pdb=" N LYS P 247 " --> pdb=" O ASN P 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER P 248 " --> pdb=" O VAL P 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER P 251 " --> pdb=" O LYS P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 278 removed outlier: 3.627A pdb=" N GLY P 278 " --> pdb=" O ALA P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 297 Processing helix chain 'P' and resid 306 through 327 removed outlier: 3.607A pdb=" N VAL P 310 " --> pdb=" O PRO P 306 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS P 311 " --> pdb=" O GLY P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 503 through 508 removed outlier: 3.995A pdb=" N ARG P 506 " --> pdb=" O LEU P 503 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE P 507 " --> pdb=" O GLY P 504 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA P 508 " --> pdb=" O SER P 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 503 through 508' Processing helix chain 'P' and resid 617 through 629 removed outlier: 3.770A pdb=" N ARG P 622 " --> pdb=" O PRO P 618 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL P 627 " --> pdb=" O ARG P 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY A 43 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP A 35 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP A 41 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 194 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR B 141 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 192 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS B 143 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR B 190 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS B 187 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 189 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 290 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER B 191 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG B 288 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP B 193 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP B 193 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG B 288 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER B 191 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 290 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 189 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS B 187 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 197 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B 260 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 258 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU B 201 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 256 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS B 203 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE A 68 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE A 144 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 70 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 142 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN A 72 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 140 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 78 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN A 134 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 130 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR A 130 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 194 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR A 141 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 192 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A 143 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR A 190 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS A 187 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 189 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY A 290 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 191 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 288 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A 193 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP A 193 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 288 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 191 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY A 290 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 189 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS A 187 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 197 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER A 260 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 199 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 258 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU A 201 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 256 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS A 203 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE P 68 " --> pdb=" O ILE P 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE P 144 " --> pdb=" O PHE P 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE P 70 " --> pdb=" O VAL P 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL P 142 " --> pdb=" O ILE P 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN P 72 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR P 140 " --> pdb=" O GLN P 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU P 78 " --> pdb=" O GLN P 134 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN P 134 " --> pdb=" O GLU P 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR P 130 " --> pdb=" O LEU P 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR P 130 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA P 194 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR P 141 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL P 192 " --> pdb=" O THR P 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS P 143 " --> pdb=" O THR P 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR P 190 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS P 187 " --> pdb=" O PRO P 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR P 189 " --> pdb=" O GLY P 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY P 290 " --> pdb=" O THR P 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER P 191 " --> pdb=" O ARG P 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG P 288 " --> pdb=" O SER P 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP P 193 " --> pdb=" O ILE P 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP P 193 " --> pdb=" O ILE P 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG P 288 " --> pdb=" O SER P 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER P 191 " --> pdb=" O ARG P 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY P 290 " --> pdb=" O THR P 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR P 189 " --> pdb=" O GLY P 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS P 187 " --> pdb=" O PRO P 292 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA P 197 " --> pdb=" O SER P 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER P 260 " --> pdb=" O ALA P 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE P 199 " --> pdb=" O VAL P 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL P 258 " --> pdb=" O ILE P 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU P 201 " --> pdb=" O SER P 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER P 256 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS P 203 " --> pdb=" O THR P 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE O 68 " --> pdb=" O ILE O 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE O 144 " --> pdb=" O PHE O 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE O 70 " --> pdb=" O VAL O 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL O 142 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN O 72 " --> pdb=" O TYR O 140 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR O 140 " --> pdb=" O GLN O 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU O 78 " --> pdb=" O GLN O 134 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN O 134 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR O 130 " --> pdb=" O LEU O 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR O 130 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA O 194 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR O 141 " --> pdb=" O VAL O 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL O 192 " --> pdb=" O THR O 141 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS O 143 " --> pdb=" O THR O 190 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR O 190 " --> pdb=" O LYS O 143 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS O 187 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR O 189 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY O 290 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER O 191 " --> pdb=" O ARG O 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG O 288 " --> pdb=" O SER O 191 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP O 193 " --> pdb=" O ILE O 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 284 through 292 removed outlier: 6.581A pdb=" N ASP O 193 " --> pdb=" O ILE O 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG O 288 " --> pdb=" O SER O 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER O 191 " --> pdb=" O ARG O 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY O 290 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR O 189 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS O 187 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA O 197 " --> pdb=" O SER O 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER O 260 " --> pdb=" O ALA O 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE O 199 " --> pdb=" O VAL O 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL O 258 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU O 201 " --> pdb=" O SER O 256 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER O 256 " --> pdb=" O GLU O 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS O 203 " --> pdb=" O THR O 254 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE N 68 " --> pdb=" O ILE N 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE N 144 " --> pdb=" O PHE N 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE N 70 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL N 142 " --> pdb=" O ILE N 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN N 72 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR N 140 " --> pdb=" O GLN N 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU N 78 " --> pdb=" O GLN N 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN N 134 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR N 130 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR N 130 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA N 194 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR N 141 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL N 192 " --> pdb=" O THR N 141 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS N 143 " --> pdb=" O THR N 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR N 190 " --> pdb=" O LYS N 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS N 187 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR N 189 " --> pdb=" O GLY N 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY N 290 " --> pdb=" O THR N 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER N 191 " --> pdb=" O ARG N 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG N 288 " --> pdb=" O SER N 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP N 193 " --> pdb=" O ILE N 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP N 193 " --> pdb=" O ILE N 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG N 288 " --> pdb=" O SER N 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER N 191 " --> pdb=" O ARG N 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY N 290 " --> pdb=" O THR N 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR N 189 " --> pdb=" O GLY N 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS N 187 " --> pdb=" O PRO N 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA N 197 " --> pdb=" O SER N 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER N 260 " --> pdb=" O ALA N 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE N 199 " --> pdb=" O VAL N 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL N 258 " --> pdb=" O ILE N 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU N 201 " --> pdb=" O SER N 256 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER N 256 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS N 203 " --> pdb=" O THR N 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE M 68 " --> pdb=" O ILE M 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE M 144 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE M 70 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL M 142 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN M 72 " --> pdb=" O TYR M 140 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR M 140 " --> pdb=" O GLN M 72 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU M 78 " --> pdb=" O GLN M 134 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN M 134 " --> pdb=" O GLU M 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR M 130 " --> pdb=" O LEU M 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR M 130 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA M 194 " --> pdb=" O VAL M 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR M 141 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL M 192 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS M 143 " --> pdb=" O THR M 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR M 190 " --> pdb=" O LYS M 143 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS M 187 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR M 189 " --> pdb=" O GLY M 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY M 290 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER M 191 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG M 288 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP M 193 " --> pdb=" O ILE M 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP M 193 " --> pdb=" O ILE M 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG M 288 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER M 191 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY M 290 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR M 189 " --> pdb=" O GLY M 290 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS M 187 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA M 197 " --> pdb=" O SER M 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER M 260 " --> pdb=" O ALA M 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE M 199 " --> pdb=" O VAL M 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL M 258 " --> pdb=" O ILE M 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU M 201 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER M 256 " --> pdb=" O GLU M 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS M 203 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE L 68 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE L 144 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE L 70 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL L 142 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN L 72 " --> pdb=" O TYR L 140 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR L 140 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU L 78 " --> pdb=" O GLN L 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN L 134 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 130 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR L 130 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA L 194 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR L 141 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL L 192 " --> pdb=" O THR L 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS L 143 " --> pdb=" O THR L 190 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR L 190 " --> pdb=" O LYS L 143 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS L 187 " --> pdb=" O PRO L 292 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR L 189 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY L 290 " --> pdb=" O THR L 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER L 191 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG L 288 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP L 193 " --> pdb=" O ILE L 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 284 through 292 removed outlier: 6.583A pdb=" N ASP L 193 " --> pdb=" O ILE L 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG L 288 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER L 191 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY L 290 " --> pdb=" O THR L 189 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR L 189 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS L 187 " --> pdb=" O PRO L 292 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA L 197 " --> pdb=" O SER L 260 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER L 260 " --> pdb=" O ALA L 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE L 199 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL L 258 " --> pdb=" O ILE L 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU L 201 " --> pdb=" O SER L 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER L 256 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS L 203 " --> pdb=" O THR L 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE K 68 " --> pdb=" O ILE K 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE K 144 " --> pdb=" O PHE K 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE K 70 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL K 142 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN K 72 " --> pdb=" O TYR K 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR K 140 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU K 78 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN K 134 " --> pdb=" O GLU K 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR K 130 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR K 130 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA K 194 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR K 141 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL K 192 " --> pdb=" O THR K 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS K 143 " --> pdb=" O THR K 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR K 190 " --> pdb=" O LYS K 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS K 187 " --> pdb=" O PRO K 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR K 189 " --> pdb=" O GLY K 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY K 290 " --> pdb=" O THR K 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER K 191 " --> pdb=" O ARG K 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG K 288 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP K 193 " --> pdb=" O ILE K 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 284 through 292 removed outlier: 6.581A pdb=" N ASP K 193 " --> pdb=" O ILE K 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG K 288 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER K 191 " --> pdb=" O ARG K 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY K 290 " --> pdb=" O THR K 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR K 189 " --> pdb=" O GLY K 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS K 187 " --> pdb=" O PRO K 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA K 197 " --> pdb=" O SER K 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER K 260 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE K 199 " --> pdb=" O VAL K 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL K 258 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU K 201 " --> pdb=" O SER K 256 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER K 256 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS K 203 " --> pdb=" O THR K 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE J 68 " --> pdb=" O ILE J 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE J 144 " --> pdb=" O PHE J 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE J 70 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL J 142 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN J 72 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR J 140 " --> pdb=" O GLN J 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU J 78 " --> pdb=" O GLN J 134 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN J 134 " --> pdb=" O GLU J 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR J 130 " --> pdb=" O LEU J 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR J 130 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA J 194 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR J 141 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 192 " --> pdb=" O THR J 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS J 143 " --> pdb=" O THR J 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR J 190 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS J 187 " --> pdb=" O PRO J 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR J 189 " --> pdb=" O GLY J 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY J 290 " --> pdb=" O THR J 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER J 191 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG J 288 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP J 193 " --> pdb=" O ILE J 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 284 through 292 removed outlier: 6.581A pdb=" N ASP J 193 " --> pdb=" O ILE J 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG J 288 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER J 191 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY J 290 " --> pdb=" O THR J 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR J 189 " --> pdb=" O GLY J 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS J 187 " --> pdb=" O PRO J 292 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA J 197 " --> pdb=" O SER J 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER J 260 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE J 199 " --> pdb=" O VAL J 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL J 258 " --> pdb=" O ILE J 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU J 201 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER J 256 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS J 203 " --> pdb=" O THR J 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE I 68 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE I 144 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE I 70 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL I 142 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN I 72 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR I 140 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU I 78 " --> pdb=" O GLN I 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN I 134 " --> pdb=" O GLU I 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR I 130 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR I 130 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA I 194 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR I 141 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL I 192 " --> pdb=" O THR I 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS I 143 " --> pdb=" O THR I 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR I 190 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS I 187 " --> pdb=" O PRO I 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR I 189 " --> pdb=" O GLY I 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY I 290 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER I 191 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG I 288 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP I 193 " --> pdb=" O ILE I 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP I 193 " --> pdb=" O ILE I 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG I 288 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER I 191 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY I 290 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR I 189 " --> pdb=" O GLY I 290 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS I 187 " --> pdb=" O PRO I 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA I 197 " --> pdb=" O SER I 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER I 260 " --> pdb=" O ALA I 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE I 199 " --> pdb=" O VAL I 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL I 258 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU I 201 " --> pdb=" O SER I 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER I 256 " --> pdb=" O GLU I 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS I 203 " --> pdb=" O THR I 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE H 68 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE H 144 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE H 70 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL H 142 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN H 72 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR H 140 " --> pdb=" O GLN H 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU H 78 " --> pdb=" O GLN H 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN H 134 " --> pdb=" O GLU H 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR H 130 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR H 130 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA H 194 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR H 141 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL H 192 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS H 143 " --> pdb=" O THR H 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR H 190 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS H 187 " --> pdb=" O PRO H 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR H 189 " --> pdb=" O GLY H 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY H 290 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER H 191 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG H 288 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP H 193 " --> pdb=" O ILE H 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 284 through 292 removed outlier: 6.581A pdb=" N ASP H 193 " --> pdb=" O ILE H 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG H 288 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER H 191 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY H 290 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR H 189 " --> pdb=" O GLY H 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS H 187 " --> pdb=" O PRO H 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA H 197 " --> pdb=" O SER H 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER H 260 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE H 199 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL H 258 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU H 201 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER H 256 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS H 203 " --> pdb=" O THR H 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE G 68 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE G 144 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE G 70 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL G 142 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN G 72 " --> pdb=" O TYR G 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR G 140 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU G 78 " --> pdb=" O GLN G 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN G 134 " --> pdb=" O GLU G 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR G 130 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR G 130 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA G 194 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR G 141 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL G 192 " --> pdb=" O THR G 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS G 143 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N THR G 190 " --> pdb=" O LYS G 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS G 187 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR G 189 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY G 290 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER G 191 " --> pdb=" O ARG G 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG G 288 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP G 193 " --> pdb=" O ILE G 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 284 through 292 removed outlier: 6.581A pdb=" N ASP G 193 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG G 288 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER G 191 " --> pdb=" O ARG G 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY G 290 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR G 189 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS G 187 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA G 197 " --> pdb=" O SER G 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER G 260 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE G 199 " --> pdb=" O VAL G 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL G 258 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU G 201 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER G 256 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS G 203 " --> pdb=" O THR G 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 68 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE F 144 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE F 70 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL F 142 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN F 72 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR F 140 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 78 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN F 134 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR F 130 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.707A pdb=" N THR F 130 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA F 194 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR F 141 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL F 192 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS F 143 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR F 190 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS F 187 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR F 189 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY F 290 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER F 191 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG F 288 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP F 193 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP F 193 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG F 288 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER F 191 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY F 290 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR F 189 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS F 187 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA F 197 " --> pdb=" O SER F 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER F 260 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 199 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL F 258 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU F 201 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER F 256 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS F 203 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE E 68 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE E 144 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE E 70 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL E 142 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN E 72 " --> pdb=" O TYR E 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR E 140 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 78 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN E 134 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 130 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR E 130 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA E 194 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR E 141 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL E 192 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS E 143 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR E 190 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS E 187 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 189 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 290 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER E 191 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 288 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP E 193 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP E 193 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 288 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER E 191 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 290 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 189 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS E 187 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA E 197 " --> pdb=" O SER E 260 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER E 260 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 199 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL E 258 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU E 201 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER E 256 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS E 203 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE D 68 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE D 144 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE D 70 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL D 142 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN D 72 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR D 140 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 78 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN D 134 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 130 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR D 130 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA D 194 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR D 141 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 192 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS D 143 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR D 190 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS D 187 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR D 189 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY D 290 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER D 191 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG D 288 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP D 193 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP D 193 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG D 288 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER D 191 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY D 290 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR D 189 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS D 187 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA D 197 " --> pdb=" O SER D 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER D 260 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 199 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL D 258 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU D 201 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER D 256 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS D 203 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 68 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE C 144 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE C 70 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL C 142 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN C 72 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR C 140 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 78 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN C 134 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 130 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.706A pdb=" N THR C 130 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 194 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 141 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 192 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS C 143 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR C 190 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS C 187 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR C 189 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 290 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 191 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG C 288 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP C 193 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 284 through 292 removed outlier: 6.582A pdb=" N ASP C 193 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG C 288 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 191 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 290 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR C 189 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS C 187 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA C 197 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER C 260 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 199 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 258 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU C 201 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C 256 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS C 203 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE B 68 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE B 144 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 70 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL B 142 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN B 72 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 140 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 78 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN B 134 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AD8, first strand: chain 'A' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR A 365 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 431 " --> pdb=" O HIS A 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS A 419 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 407 through 414 removed outlier: 4.260A pdb=" N GLN A 407 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 443 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N CYS A 432 " --> pdb=" O VAL P 593 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL P 595 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP A 434 " --> pdb=" O VAL P 595 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASN P 597 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 436 " --> pdb=" O ASN P 597 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG P 602 " --> pdb=" O ASN P 597 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 485 through 488 Processing sheet with id=AE2, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY A 513 " --> pdb=" O CYS A 560 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG A 602 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP B 434 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 595 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 436 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN A 597 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL B 438 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 443 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B 407 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR B 365 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 431 " --> pdb=" O HIS B 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 419 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY B 43 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP B 35 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP B 41 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AE7, first strand: chain 'B' and resid 485 through 488 Processing sheet with id=AE8, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY B 513 " --> pdb=" O CYS B 560 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG B 602 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP C 434 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL B 595 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE C 436 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN B 597 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL C 438 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 443 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN C 407 " --> pdb=" O PHE C 443 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR C 365 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C 431 " --> pdb=" O HIS C 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS C 419 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY C 43 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP C 35 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP C 41 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 331 through 332 Processing sheet with id=AF4, first strand: chain 'C' and resid 485 through 488 Processing sheet with id=AF5, first strand: chain 'C' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY C 513 " --> pdb=" O CYS C 560 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG C 602 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP D 434 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL C 595 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE D 436 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN C 597 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL D 438 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE D 443 " --> pdb=" O GLN D 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN D 407 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR D 365 " --> pdb=" O PHE D 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL D 431 " --> pdb=" O HIS D 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS D 419 " --> pdb=" O VAL D 431 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY D 43 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP D 35 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP D 41 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AG1, first strand: chain 'D' and resid 485 through 488 Processing sheet with id=AG2, first strand: chain 'D' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY D 513 " --> pdb=" O CYS D 560 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 602 through 605 removed outlier: 3.858A pdb=" N ARG D 602 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS E 432 " --> pdb=" O THR D 592 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 594 " --> pdb=" O CYS E 432 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 443 " --> pdb=" O GLN E 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN E 407 " --> pdb=" O PHE E 443 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR E 365 " --> pdb=" O PHE E 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 431 " --> pdb=" O HIS E 419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS E 419 " --> pdb=" O VAL E 431 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY E 43 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP E 35 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP E 41 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=AG7, first strand: chain 'E' and resid 485 through 488 Processing sheet with id=AG8, first strand: chain 'E' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY E 513 " --> pdb=" O CYS E 560 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG E 602 " --> pdb=" O ASN E 597 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN E 591 " --> pdb=" O CYS F 432 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP F 434 " --> pdb=" O ASN E 591 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL E 593 " --> pdb=" O ASP F 434 " (cutoff:3.500A) removed outlier: 12.533A pdb=" N PHE F 436 " --> pdb=" O VAL E 593 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL E 595 " --> pdb=" O PHE F 436 " (cutoff:3.500A) removed outlier: 13.895A pdb=" N VAL F 438 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 12.108A pdb=" N ASN E 597 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 14.704A pdb=" N LYS F 440 " --> pdb=" O ASN E 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 443 " --> pdb=" O GLN F 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN F 407 " --> pdb=" O PHE F 443 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR F 365 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL F 431 " --> pdb=" O HIS F 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS F 419 " --> pdb=" O VAL F 431 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 32 through 35 removed outlier: 4.615A pdb=" N GLY F 43 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP F 35 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP F 41 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AH4, first strand: chain 'F' and resid 485 through 488 Processing sheet with id=AH5, first strand: chain 'F' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY F 513 " --> pdb=" O CYS F 560 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 602 through 605 removed outlier: 3.858A pdb=" N ARG F 602 " --> pdb=" O ASN F 597 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N CYS G 432 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 594 " --> pdb=" O CYS G 432 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE G 443 " --> pdb=" O GLN G 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN G 407 " --> pdb=" O PHE G 443 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR G 365 " --> pdb=" O PHE G 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL G 431 " --> pdb=" O HIS G 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS G 419 " --> pdb=" O VAL G 431 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY G 43 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP G 35 " --> pdb=" O ASP G 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP G 41 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AI1, first strand: chain 'G' and resid 485 through 488 Processing sheet with id=AI2, first strand: chain 'G' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY G 513 " --> pdb=" O CYS G 560 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG G 602 " --> pdb=" O ASN G 597 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN G 591 " --> pdb=" O CYS H 432 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP H 434 " --> pdb=" O ASN G 591 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL G 593 " --> pdb=" O ASP H 434 " (cutoff:3.500A) removed outlier: 12.473A pdb=" N PHE H 436 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N VAL G 595 " --> pdb=" O PHE H 436 " (cutoff:3.500A) removed outlier: 13.820A pdb=" N VAL H 438 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 12.027A pdb=" N ASN G 597 " --> pdb=" O VAL H 438 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N LYS H 440 " --> pdb=" O ASN G 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE H 443 " --> pdb=" O GLN H 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN H 407 " --> pdb=" O PHE H 443 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR H 365 " --> pdb=" O PHE H 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL H 431 " --> pdb=" O HIS H 419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS H 419 " --> pdb=" O VAL H 431 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY H 43 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP H 35 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP H 41 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AI7, first strand: chain 'H' and resid 485 through 488 Processing sheet with id=AI8, first strand: chain 'H' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY H 513 " --> pdb=" O CYS H 560 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG H 602 " --> pdb=" O ASN H 597 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP I 434 " --> pdb=" O VAL H 593 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL H 595 " --> pdb=" O ASP I 434 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE I 436 " --> pdb=" O VAL H 595 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN H 597 " --> pdb=" O PHE I 436 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL I 438 " --> pdb=" O ASN H 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE I 443 " --> pdb=" O GLN I 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN I 407 " --> pdb=" O PHE I 443 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR I 365 " --> pdb=" O PHE I 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL I 431 " --> pdb=" O HIS I 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS I 419 " --> pdb=" O VAL I 431 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY I 43 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP I 35 " --> pdb=" O ASP I 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP I 41 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 331 through 332 Processing sheet with id=AJ4, first strand: chain 'I' and resid 485 through 488 Processing sheet with id=AJ5, first strand: chain 'I' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY I 513 " --> pdb=" O CYS I 560 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG I 602 " --> pdb=" O ASN I 597 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN I 591 " --> pdb=" O CYS J 432 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP J 434 " --> pdb=" O ASN I 591 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL I 593 " --> pdb=" O ASP J 434 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N PHE J 436 " --> pdb=" O VAL I 593 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N VAL I 595 " --> pdb=" O PHE J 436 " (cutoff:3.500A) removed outlier: 13.843A pdb=" N VAL J 438 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASN I 597 " --> pdb=" O VAL J 438 " (cutoff:3.500A) removed outlier: 14.623A pdb=" N LYS J 440 " --> pdb=" O ASN I 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE J 443 " --> pdb=" O GLN J 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN J 407 " --> pdb=" O PHE J 443 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'J' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR J 365 " --> pdb=" O PHE J 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL J 431 " --> pdb=" O HIS J 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS J 419 " --> pdb=" O VAL J 431 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY J 43 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP J 35 " --> pdb=" O ASP J 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP J 41 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'J' and resid 331 through 332 Processing sheet with id=AK1, first strand: chain 'J' and resid 485 through 488 Processing sheet with id=AK2, first strand: chain 'J' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY J 513 " --> pdb=" O CYS J 560 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG J 602 " --> pdb=" O ASN J 597 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP K 434 " --> pdb=" O VAL J 593 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL J 595 " --> pdb=" O ASP K 434 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE K 436 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN J 597 " --> pdb=" O PHE K 436 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N VAL K 438 " --> pdb=" O ASN J 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE K 443 " --> pdb=" O GLN K 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN K 407 " --> pdb=" O PHE K 443 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'K' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR K 365 " --> pdb=" O PHE K 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL K 431 " --> pdb=" O HIS K 419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS K 419 " --> pdb=" O VAL K 431 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'K' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY K 43 " --> pdb=" O GLY K 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP K 35 " --> pdb=" O ASP K 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP K 41 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AK7, first strand: chain 'K' and resid 485 through 488 Processing sheet with id=AK8, first strand: chain 'K' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY K 513 " --> pdb=" O CYS K 560 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG K 602 " --> pdb=" O ASN K 597 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP L 434 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL K 595 " --> pdb=" O ASP L 434 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE L 436 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN K 597 " --> pdb=" O PHE L 436 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N VAL L 438 " --> pdb=" O ASN K 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE L 443 " --> pdb=" O GLN L 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN L 407 " --> pdb=" O PHE L 443 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'L' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR L 365 " --> pdb=" O PHE L 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL L 431 " --> pdb=" O HIS L 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS L 419 " --> pdb=" O VAL L 431 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY L 43 " --> pdb=" O GLY L 33 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP L 35 " --> pdb=" O ASP L 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP L 41 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'L' and resid 331 through 332 Processing sheet with id=AL4, first strand: chain 'L' and resid 485 through 488 Processing sheet with id=AL5, first strand: chain 'L' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY L 513 " --> pdb=" O CYS L 560 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'L' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG L 602 " --> pdb=" O ASN L 597 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP M 434 " --> pdb=" O VAL L 593 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL L 595 " --> pdb=" O ASP M 434 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE M 436 " --> pdb=" O VAL L 595 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN L 597 " --> pdb=" O PHE M 436 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL M 438 " --> pdb=" O ASN L 597 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE M 443 " --> pdb=" O GLN M 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN M 407 " --> pdb=" O PHE M 443 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'M' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR M 365 " --> pdb=" O PHE M 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL M 431 " --> pdb=" O HIS M 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS M 419 " --> pdb=" O VAL M 431 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY M 43 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP M 35 " --> pdb=" O ASP M 41 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP M 41 " --> pdb=" O ASP M 35 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'M' and resid 331 through 332 Processing sheet with id=AM1, first strand: chain 'M' and resid 485 through 488 Processing sheet with id=AM2, first strand: chain 'M' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY M 513 " --> pdb=" O CYS M 560 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'M' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG M 602 " --> pdb=" O ASN M 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP N 434 " --> pdb=" O VAL M 593 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL M 595 " --> pdb=" O ASP N 434 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE N 436 " --> pdb=" O VAL M 595 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN M 597 " --> pdb=" O PHE N 436 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N VAL N 438 " --> pdb=" O ASN M 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE N 443 " --> pdb=" O GLN N 407 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN N 407 " --> pdb=" O PHE N 443 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR N 365 " --> pdb=" O PHE N 446 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL N 431 " --> pdb=" O HIS N 419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS N 419 " --> pdb=" O VAL N 431 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY N 43 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP N 35 " --> pdb=" O ASP N 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP N 41 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'N' and resid 331 through 332 Processing sheet with id=AM7, first strand: chain 'N' and resid 485 through 488 Processing sheet with id=AM8, first strand: chain 'N' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY N 513 " --> pdb=" O CYS N 560 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'N' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG N 602 " --> pdb=" O ASN N 597 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP O 434 " --> pdb=" O VAL N 593 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL N 595 " --> pdb=" O ASP O 434 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE O 436 " --> pdb=" O VAL N 595 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN N 597 " --> pdb=" O PHE O 436 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL O 438 " --> pdb=" O ASN N 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE O 443 " --> pdb=" O GLN O 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN O 407 " --> pdb=" O PHE O 443 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'O' and resid 364 through 369 removed outlier: 3.516A pdb=" N TYR O 365 " --> pdb=" O PHE O 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL O 431 " --> pdb=" O HIS O 419 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS O 419 " --> pdb=" O VAL O 431 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'O' and resid 32 through 35 removed outlier: 4.616A pdb=" N GLY O 43 " --> pdb=" O GLY O 33 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP O 35 " --> pdb=" O ASP O 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP O 41 " --> pdb=" O ASP O 35 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'O' and resid 331 through 332 Processing sheet with id=AN4, first strand: chain 'O' and resid 485 through 488 Processing sheet with id=AN5, first strand: chain 'O' and resid 513 through 515 removed outlier: 4.174A pdb=" N GLY O 513 " --> pdb=" O CYS O 560 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'O' and resid 602 through 605 removed outlier: 3.859A pdb=" N ARG O 602 " --> pdb=" O ASN O 597 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP P 434 " --> pdb=" O VAL O 593 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL O 595 " --> pdb=" O ASP P 434 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE P 436 " --> pdb=" O VAL O 595 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN O 597 " --> pdb=" O PHE P 436 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL P 438 " --> pdb=" O ASN O 597 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE P 443 " --> pdb=" O GLN P 407 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN P 407 " --> pdb=" O PHE P 443 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'P' and resid 364 through 369 removed outlier: 3.515A pdb=" N TYR P 365 " --> pdb=" O PHE P 446 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL P 431 " --> pdb=" O HIS P 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS P 419 " --> pdb=" O VAL P 431 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'P' and resid 32 through 35 removed outlier: 4.617A pdb=" N GLY P 43 " --> pdb=" O GLY P 33 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP P 35 " --> pdb=" O ASP P 41 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP P 41 " --> pdb=" O ASP P 35 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'P' and resid 331 through 332 Processing sheet with id=AO1, first strand: chain 'P' and resid 485 through 488 Processing sheet with id=AO2, first strand: chain 'P' and resid 513 through 515 removed outlier: 4.173A pdb=" N GLY P 513 " --> pdb=" O CYS P 560 " (cutoff:3.500A) 2362 hydrogen bonds defined for protein. 6654 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: 29.53 Time building geometry restraints manager: 25.13 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: 22366 1.34 - 1.45: 12399 1.45 - 1.57: 37907 1.57 - 1.69: 0 1.69 - 1.81: 560 Bond restraints: 73232 Sorted by residual: bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 ... (remaining 73227 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 1712 105.68 - 112.78: 37991 112.78 - 119.89: 24943 119.89 - 127.00: 33852 127.00 - 134.10: 862 Bond angle restraints: 99360 Sorted by residual: angle pdb=" C SER M 92 " pdb=" N SER M 93 " pdb=" CA SER M 93 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C SER N 92 " pdb=" N SER N 93 " pdb=" CA SER N 93 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C SER J 92 " pdb=" N SER J 93 " pdb=" CA SER J 93 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C SER G 92 " pdb=" N SER G 93 " pdb=" CA SER G 93 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C SER L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 ... (remaining 99355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 42224 16.11 - 32.23: 1664 32.23 - 48.34: 432 48.34 - 64.46: 96 64.46 - 80.57: 32 Dihedral angle restraints: 44448 sinusoidal: 17936 harmonic: 26512 Sorted by residual: dihedral pdb=" CA PRO M 573 " pdb=" C PRO M 573 " pdb=" N ALA M 574 " pdb=" CA ALA M 574 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO H 573 " pdb=" C PRO H 573 " pdb=" N ALA H 574 " pdb=" CA ALA H 574 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PRO O 573 " pdb=" C PRO O 573 " pdb=" N ALA O 574 " pdb=" CA ALA O 574 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 44445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 6952 0.043 - 0.086: 3094 0.086 - 0.129: 987 0.129 - 0.172: 271 0.172 - 0.214: 72 Chirality restraints: 11376 Sorted by residual: chirality pdb=" CB ILE C 67 " pdb=" CA ILE C 67 " pdb=" CG1 ILE C 67 " pdb=" CG2 ILE C 67 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE E 67 " pdb=" CA ILE E 67 " pdb=" CG1 ILE E 67 " pdb=" CG2 ILE E 67 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 11373 not shown) Planarity restraints: 12880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 231 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C VAL C 231 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL C 231 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN C 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 231 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C VAL P 231 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL P 231 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN P 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 231 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C VAL G 231 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL G 231 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 232 " -0.016 2.00e-02 2.50e+03 ... (remaining 12877 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 22766 2.84 - 3.35: 61526 3.35 - 3.87: 118345 3.87 - 4.38: 137245 4.38 - 4.90: 234831 Nonbonded interactions: 574713 Sorted by model distance: nonbonded pdb=" NE2 GLN M 366 " pdb=" O LEU M 489 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN D 366 " pdb=" O LEU D 489 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN E 366 " pdb=" O LEU E 489 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN B 366 " pdb=" O LEU B 489 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN K 366 " pdb=" O LEU K 489 " model vdw 2.320 2.520 ... (remaining 574708 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.090 Extract box with map and model: 15.380 Check model and map are aligned: 0.860 Set scattering table: 0.540 Process input model: 152.690 Find NCS groups from input model: 4.300 Set up NCS constraints: 0.990 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: 0.020 Load rotamer database and sin/cos tables:9.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 0.056 73232 Z= 0.440 Angle : 0.899 9.730 99360 Z= 0.481 Chirality : 0.056 0.214 11376 Planarity : 0.007 0.055 12848 Dihedral : 10.396 80.571 27200 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.41 % Allowed : 3.56 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % 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: -3.36 (0.07), residues: 8976 helix: -3.68 (0.05), residues: 2064 sheet: -0.91 (0.11), residues: 1984 loop : -2.15 (0.07), residues: 4928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP G 275 HIS 0.012 0.003 HIS B 203 PHE 0.030 0.004 PHE C 393 TYR 0.027 0.003 TYR I 324 ARG 0.013 0.002 ARG K 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1540 time to evaluate : 6.427 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 THR cc_start: 0.8025 (m) cc_final: 0.7623 (p) REVERT: C 471 ILE cc_start: 0.8323 (pt) cc_final: 0.8108 (pt) REVERT: D 160 ASP cc_start: 0.7634 (m-30) cc_final: 0.7325 (m-30) REVERT: D 334 THR cc_start: 0.8000 (m) cc_final: 0.7541 (p) REVERT: E 334 THR cc_start: 0.7418 (m) cc_final: 0.6903 (p) REVERT: E 348 ASP cc_start: 0.8641 (t0) cc_final: 0.8438 (t70) REVERT: G 334 THR cc_start: 0.7340 (m) cc_final: 0.6976 (p) REVERT: G 433 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7135 (tm-30) REVERT: G 591 ASN cc_start: 0.7828 (m110) cc_final: 0.7498 (p0) REVERT: H 156 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7696 (tmmt) REVERT: H 471 ILE cc_start: 0.8567 (pt) cc_final: 0.8345 (pp) REVERT: H 614 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7827 (tmm-80) REVERT: I 334 THR cc_start: 0.7426 (m) cc_final: 0.6973 (p) REVERT: I 591 ASN cc_start: 0.7854 (m110) cc_final: 0.7512 (p0) REVERT: J 209 LEU cc_start: 0.7923 (tp) cc_final: 0.7685 (tp) REVERT: J 334 THR cc_start: 0.7746 (m) cc_final: 0.7398 (p) REVERT: K 334 THR cc_start: 0.7964 (m) cc_final: 0.7579 (p) REVERT: L 301 MET cc_start: 0.8878 (mmt) cc_final: 0.8306 (mmt) REVERT: L 334 THR cc_start: 0.8027 (m) cc_final: 0.7587 (p) REVERT: L 434 ASP cc_start: 0.8238 (p0) cc_final: 0.7908 (p0) REVERT: M 433 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7302 (tm-30) REVERT: N 46 MET cc_start: 0.8169 (mmt) cc_final: 0.7857 (mmt) REVERT: N 334 THR cc_start: 0.8121 (m) cc_final: 0.7727 (p) REVERT: N 433 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7433 (tm-30) REVERT: O 172 MET cc_start: 0.8298 (tpt) cc_final: 0.8062 (tpt) REVERT: O 433 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7639 (tm-30) REVERT: P 433 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7353 (tm-30) REVERT: P 434 ASP cc_start: 0.8191 (p0) cc_final: 0.7695 (p0) outliers start: 32 outliers final: 4 residues processed: 1567 average time/residue: 1.5351 time to fit residues: 3141.6712 Evaluate side-chains 834 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 830 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain H residue 393 PHE Chi-restraints excluded: chain L residue 393 PHE Chi-restraints excluded: chain P residue 393 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 0.2980 chunk 691 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 466 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 714 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 434 optimal weight: 6.9990 chunk 532 optimal weight: 0.7980 chunk 828 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 76 ASN A 109 ASN A 167 ASN A 187 HIS A 203 HIS A 277 GLN A 340 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 437 GLN A 476 ASN A 478 GLN A 556 GLN A 587 GLN B 39 ASN B 76 ASN B 109 ASN B 167 ASN B 187 HIS B 203 HIS B 277 GLN B 340 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN B 407 GLN B 414 ASN B 437 GLN B 492 ASN B 587 GLN B 600 ASN C 39 ASN C 76 ASN C 109 ASN C 167 ASN C 187 HIS C 203 HIS C 277 GLN C 337 ASN C 340 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 407 GLN C 414 ASN C 587 GLN C 600 ASN D 39 ASN D 76 ASN D 109 ASN D 167 ASN D 187 HIS D 203 HIS D 337 ASN D 340 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN D 407 GLN D 414 ASN D 437 GLN D 476 ASN D 478 GLN D 556 GLN D 587 GLN D 600 ASN E 36 ASN E 39 ASN E 76 ASN E 109 ASN E 137 ASN E 187 HIS E 340 ASN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN E 407 GLN E 414 ASN E 478 GLN E 492 ASN E 556 GLN E 587 GLN F 39 ASN F 76 ASN F 109 ASN F 167 ASN F 187 HIS F 203 HIS F 277 GLN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN F 407 GLN F 414 ASN F 492 ASN F 556 GLN F 600 ASN G 39 ASN G 89 ASN G 109 ASN G 187 HIS G 203 HIS G 277 GLN G 300 ASN G 340 ASN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN G 407 GLN G 414 ASN G 478 GLN G 492 ASN G 587 GLN G 600 ASN H 39 ASN H 76 ASN H 109 ASN H 167 ASN H 187 HIS H 203 HIS H 300 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN H 407 GLN H 414 ASN H 476 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 556 GLN H 587 GLN H 600 ASN I 39 ASN I 76 ASN I 109 ASN I 187 HIS I 277 GLN I 340 ASN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN I 407 GLN I 414 ASN I 437 GLN I 478 GLN I 556 GLN I 587 GLN I 600 ASN J 39 ASN J 76 ASN J 109 ASN J 167 ASN J 187 HIS J 203 HIS J 277 GLN ** J 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 387 ASN J 414 ASN J 478 GLN J 587 GLN J 600 ASN K 36 ASN K 39 ASN K 76 ASN K 109 ASN K 167 ASN K 187 HIS K 203 HIS K 277 GLN K 337 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN K 407 GLN K 414 ASN K 437 GLN K 492 ASN K 587 GLN K 600 ASN L 36 ASN L 39 ASN L 109 ASN L 167 ASN L 187 HIS L 203 HIS L 277 GLN L 337 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 387 ASN L 407 GLN L 414 ASN L 437 GLN L 476 ASN L 478 GLN L 587 GLN M 39 ASN M 76 ASN M 109 ASN M 167 ASN M 187 HIS M 203 HIS M 277 GLN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 387 ASN M 407 GLN M 414 ASN M 437 GLN M 478 GLN M 556 GLN M 587 GLN N 39 ASN N 76 ASN N 109 ASN N 167 ASN N 187 HIS N 203 HIS N 277 GLN N 340 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 387 ASN N 407 GLN N 414 ASN N 437 GLN N 478 GLN N 492 ASN N 587 GLN N 600 ASN O 36 ASN O 39 ASN O 109 ASN O 167 ASN O 187 HIS O 203 HIS O 277 GLN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 387 ASN O 407 GLN O 414 ASN O 437 GLN O 476 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN O 600 ASN P 39 ASN P 76 ASN P 109 ASN P 167 ASN P 187 HIS P 203 HIS P 277 GLN P 300 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 387 ASN P 407 GLN P 409 HIS ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 587 GLN Total number of N/Q/H flips: 230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 73232 Z= 0.260 Angle : 0.652 8.277 99360 Z= 0.339 Chirality : 0.045 0.169 11376 Planarity : 0.006 0.053 12848 Dihedral : 7.089 58.417 10728 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.91 % Allowed : 9.27 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % 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: -1.70 (0.08), residues: 8976 helix: -0.60 (0.10), residues: 2128 sheet: -0.48 (0.11), residues: 2048 loop : -1.67 (0.08), residues: 4800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 275 HIS 0.010 0.002 HIS M 409 PHE 0.023 0.002 PHE M 393 TYR 0.014 0.002 TYR J 365 ARG 0.010 0.001 ARG M 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 961 time to evaluate : 6.476 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 594 ILE cc_start: 0.9354 (mp) cc_final: 0.9148 (mm) REVERT: B 14 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 42 MET cc_start: 0.7010 (mmm) cc_final: 0.6804 (mmm) REVERT: B 46 MET cc_start: 0.8469 (mmt) cc_final: 0.8184 (mmm) REVERT: B 334 THR cc_start: 0.8198 (m) cc_final: 0.7772 (p) REVERT: C 471 ILE cc_start: 0.8320 (pt) cc_final: 0.8100 (pt) REVERT: C 478 GLN cc_start: 0.8106 (tt0) cc_final: 0.7789 (tt0) REVERT: D 156 LYS cc_start: 0.7922 (tptp) cc_final: 0.7460 (tptp) REVERT: D 160 ASP cc_start: 0.7513 (m-30) cc_final: 0.7299 (m-30) REVERT: D 334 THR cc_start: 0.8133 (m) cc_final: 0.7666 (p) REVERT: E 433 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7123 (tm-30) REVERT: F 14 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8272 (t) REVERT: F 42 MET cc_start: 0.6862 (mmm) cc_final: 0.6646 (mmm) REVERT: F 46 MET cc_start: 0.8318 (mmt) cc_final: 0.8050 (mmm) REVERT: F 305 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9185 (mp) REVERT: F 476 ASN cc_start: 0.7942 (t0) cc_final: 0.7666 (t0) REVERT: F 492 ASN cc_start: 0.7953 (m-40) cc_final: 0.7520 (m110) REVERT: F 584 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8623 (mm) REVERT: F 600 ASN cc_start: 0.8357 (m110) cc_final: 0.8010 (m-40) REVERT: G 334 THR cc_start: 0.7843 (m) cc_final: 0.7417 (p) REVERT: G 433 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6999 (tm-30) REVERT: G 478 GLN cc_start: 0.7722 (tt0) cc_final: 0.7518 (tt0) REVERT: G 585 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6819 (mmt) REVERT: I 301 MET cc_start: 0.9155 (mmt) cc_final: 0.8881 (mmm) REVERT: I 562 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7554 (tppp) REVERT: I 591 ASN cc_start: 0.7922 (m110) cc_final: 0.7657 (p0) REVERT: J 14 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (t) REVERT: J 42 MET cc_start: 0.7217 (mmm) cc_final: 0.6969 (mmm) REVERT: J 46 MET cc_start: 0.8532 (mmt) cc_final: 0.8165 (mmm) REVERT: J 305 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9133 (mp) REVERT: J 334 THR cc_start: 0.8015 (m) cc_final: 0.7617 (p) REVERT: J 597 ASN cc_start: 0.8363 (p0) cc_final: 0.8149 (p0) REVERT: J 600 ASN cc_start: 0.8460 (m110) cc_final: 0.7919 (m-40) REVERT: K 234 LYS cc_start: 0.7356 (mmmt) cc_final: 0.7130 (tptt) REVERT: K 334 THR cc_start: 0.8165 (m) cc_final: 0.7784 (p) REVERT: K 433 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7111 (tm-30) REVERT: K 594 ILE cc_start: 0.9322 (mp) cc_final: 0.8507 (mm) REVERT: K 595 VAL cc_start: 0.8609 (t) cc_final: 0.8404 (t) REVERT: K 614 ARG cc_start: 0.7966 (tmm-80) cc_final: 0.7700 (tmm-80) REVERT: L 234 LYS cc_start: 0.7222 (mmmt) cc_final: 0.7020 (tptt) REVERT: L 334 THR cc_start: 0.8202 (m) cc_final: 0.7737 (p) REVERT: L 594 ILE cc_start: 0.9279 (mp) cc_final: 0.8404 (mm) REVERT: N 102 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6382 (tp) REVERT: N 334 THR cc_start: 0.8309 (m) cc_final: 0.7934 (p) REVERT: N 393 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6708 (p90) REVERT: N 410 GLU cc_start: 0.8256 (mp0) cc_final: 0.8027 (mm-30) REVERT: N 434 ASP cc_start: 0.7944 (p0) cc_final: 0.7739 (p0) REVERT: N 474 MET cc_start: 0.7911 (mmm) cc_final: 0.7445 (mmp) REVERT: N 562 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7262 (tppp) REVERT: O 46 MET cc_start: 0.8454 (mmm) cc_final: 0.7995 (mmt) REVERT: O 172 MET cc_start: 0.8144 (tpt) cc_final: 0.7888 (mmm) REVERT: O 234 LYS cc_start: 0.7106 (mmmt) cc_final: 0.6883 (tptt) REVERT: O 393 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6915 (p90) REVERT: O 433 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7356 (tm-30) REVERT: O 585 MET cc_start: 0.7332 (tpp) cc_final: 0.7098 (mmt) REVERT: O 594 ILE cc_start: 0.9296 (mp) cc_final: 0.8562 (mm) REVERT: P 125 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8061 (tppt) REVERT: P 156 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7674 (mtmm) outliers start: 229 outliers final: 74 residues processed: 1131 average time/residue: 1.3222 time to fit residues: 2021.5692 Evaluate side-chains 883 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 797 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 596 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 393 PHE Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 585 MET Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 393 PHE Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 562 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 352 CYS Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 352 CYS Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 586 SER Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 393 PHE Chi-restraints excluded: chain N residue 562 LYS Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 241 SER Chi-restraints excluded: chain O residue 334 THR Chi-restraints excluded: chain O residue 393 PHE Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 393 PHE Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 689 optimal weight: 3.9990 chunk 563 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 829 optimal weight: 3.9990 chunk 896 optimal weight: 6.9990 chunk 738 optimal weight: 9.9990 chunk 822 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 665 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 409 HIS A 492 ASN A 600 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 414 ASN B 478 GLN B 600 ASN C 99 ASN C 337 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 478 GLN C 492 ASN D 39 ASN D 74 GLN D 99 ASN D 337 ASN D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN D 600 ASN E 203 HIS E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS F 340 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 GLN F 414 ASN F 478 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 99 ASN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 600 ASN H 74 GLN H 337 ASN H 340 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS H 414 ASN H 437 GLN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 203 HIS ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN I 492 ASN I 600 ASN ** J 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 GLN J 407 GLN J 414 ASN J 437 GLN ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 556 GLN K 99 ASN K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 476 ASN L 492 ASN L 600 ASN M 340 ASN M 358 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS M 492 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 ASN O 600 ASN P 74 GLN P 340 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS P 414 ASN ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 73232 Z= 0.351 Angle : 0.680 9.245 99360 Z= 0.351 Chirality : 0.047 0.167 11376 Planarity : 0.006 0.058 12848 Dihedral : 6.956 58.788 10726 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.17 % Allowed : 11.47 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % 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: -1.14 (0.08), residues: 8976 helix: 0.50 (0.11), residues: 2176 sheet: -0.56 (0.10), residues: 2176 loop : -1.47 (0.08), residues: 4624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 447 HIS 0.011 0.002 HIS L 409 PHE 0.023 0.002 PHE N 296 TYR 0.013 0.002 TYR I 61 ARG 0.009 0.001 ARG J 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 870 time to evaluate : 6.441 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ILE cc_start: 0.9279 (mp) cc_final: 0.9032 (mp) REVERT: A 614 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7930 (tmm-80) REVERT: B 46 MET cc_start: 0.8462 (mmt) cc_final: 0.8246 (mmm) REVERT: B 334 THR cc_start: 0.8430 (m) cc_final: 0.7992 (p) REVERT: B 344 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: C 156 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7698 (mtmp) REVERT: D 171 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7573 (mmm160) REVERT: D 334 THR cc_start: 0.8358 (m) cc_final: 0.8039 (p) REVERT: D 433 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 433 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 539 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7946 (pttm) REVERT: E 551 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (mp) REVERT: F 46 MET cc_start: 0.8451 (mmt) cc_final: 0.8191 (mmm) REVERT: F 305 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9158 (mp) REVERT: F 358 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7457 (p0) REVERT: F 600 ASN cc_start: 0.8155 (m110) cc_final: 0.7809 (m-40) REVERT: G 14 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8620 (t) REVERT: G 334 THR cc_start: 0.8347 (m) cc_final: 0.7917 (p) REVERT: G 433 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6981 (tm-30) REVERT: G 478 GLN cc_start: 0.7896 (tt0) cc_final: 0.7675 (tt0) REVERT: G 539 LYS cc_start: 0.8237 (pttm) cc_final: 0.8021 (pttt) REVERT: I 156 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7778 (ttmt) REVERT: I 383 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8343 (tp) REVERT: I 551 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8060 (mt) REVERT: J 46 MET cc_start: 0.8619 (mmt) cc_final: 0.8285 (mmm) REVERT: J 105 PHE cc_start: 0.6877 (m-80) cc_final: 0.6611 (m-80) REVERT: J 305 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9153 (mp) REVERT: J 334 THR cc_start: 0.8376 (m) cc_final: 0.7968 (p) REVERT: J 600 ASN cc_start: 0.8274 (m110) cc_final: 0.7810 (m-40) REVERT: K 84 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7648 (mt) REVERT: K 334 THR cc_start: 0.8472 (m) cc_final: 0.8053 (p) REVERT: K 393 PHE cc_start: 0.6781 (m-80) cc_final: 0.6555 (m-10) REVERT: K 433 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7219 (tm-30) REVERT: K 594 ILE cc_start: 0.9268 (mp) cc_final: 0.8774 (mm) REVERT: L 304 ASP cc_start: 0.7454 (p0) cc_final: 0.6977 (p0) REVERT: L 334 THR cc_start: 0.8409 (m) cc_final: 0.8121 (p) REVERT: L 393 PHE cc_start: 0.7026 (m-80) cc_final: 0.6806 (m-10) REVERT: L 410 GLU cc_start: 0.8172 (mp0) cc_final: 0.7842 (mm-30) REVERT: L 539 LYS cc_start: 0.8485 (pttt) cc_final: 0.8224 (ptpt) REVERT: M 66 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: M 393 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: N 334 THR cc_start: 0.8438 (m) cc_final: 0.7969 (p) REVERT: N 393 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: N 410 GLU cc_start: 0.8256 (mp0) cc_final: 0.8032 (mm-30) REVERT: N 474 MET cc_start: 0.8008 (mmm) cc_final: 0.7542 (mmp) REVERT: O 46 MET cc_start: 0.8589 (mmm) cc_final: 0.8175 (mmt) REVERT: O 84 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7594 (mt) REVERT: O 393 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6999 (p90) REVERT: O 433 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7246 (tm-30) REVERT: O 575 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: P 66 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: P 156 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7754 (mtmt) REVERT: P 301 MET cc_start: 0.9170 (mmm) cc_final: 0.8959 (tpp) REVERT: P 410 GLU cc_start: 0.8046 (mp0) cc_final: 0.7846 (mm-30) REVERT: P 585 MET cc_start: 0.7123 (mmt) cc_final: 0.6590 (mmt) outliers start: 249 outliers final: 110 residues processed: 1047 average time/residue: 1.3315 time to fit residues: 1891.6229 Evaluate side-chains 905 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 778 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 393 PHE Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 352 CYS Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 156 LYS Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 210 GLN Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 551 ILE Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 596 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 403 HIS Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 352 CYS Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 393 PHE Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 584 LEU Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 241 SER Chi-restraints excluded: chain O residue 334 THR Chi-restraints excluded: chain O residue 393 PHE Chi-restraints excluded: chain O residue 403 HIS Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 586 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 0.7980 chunk 623 optimal weight: 6.9990 chunk 430 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 395 optimal weight: 6.9990 chunk 557 optimal weight: 4.9990 chunk 832 optimal weight: 8.9990 chunk 881 optimal weight: 0.5980 chunk 435 optimal weight: 10.0000 chunk 789 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 600 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN B 600 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN D 337 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN F 358 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS F 492 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN ** G 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS J 137 ASN ** J 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 600 ASN ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 GLN L 337 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 476 ASN L 492 ASN L 600 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS M 476 ASN M 492 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS O 414 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 ASN P 137 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 73232 Z= 0.262 Angle : 0.623 9.552 99360 Z= 0.319 Chirality : 0.044 0.168 11376 Planarity : 0.005 0.041 12848 Dihedral : 6.618 57.071 10722 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.60 % Allowed : 11.62 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 8976 helix: 1.17 (0.12), residues: 2080 sheet: -0.39 (0.11), residues: 2176 loop : -1.19 (0.09), residues: 4720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.010 0.002 HIS A 409 PHE 0.018 0.002 PHE E 116 TYR 0.013 0.002 TYR H 140 ARG 0.009 0.001 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 851 time to evaluate : 6.358 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: symmetry clash REVERT: A 614 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7950 (tmm-80) REVERT: B 334 THR cc_start: 0.8450 (m) cc_final: 0.8023 (p) REVERT: B 353 GLU cc_start: 0.7612 (pp20) cc_final: 0.7350 (pm20) REVERT: B 411 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: B 492 ASN cc_start: 0.8002 (m-40) cc_final: 0.7636 (m110) REVERT: C 14 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8670 (t) REVERT: C 46 MET cc_start: 0.8453 (mmt) cc_final: 0.8225 (mmt) REVERT: C 84 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7584 (mt) REVERT: C 156 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7670 (mtmp) REVERT: D 171 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7464 (mtp180) REVERT: D 334 THR cc_start: 0.8347 (m) cc_final: 0.8029 (p) REVERT: D 433 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7322 (tm-30) REVERT: E 42 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6826 (mmm) REVERT: E 433 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 539 LYS cc_start: 0.8259 (ptpt) cc_final: 0.7966 (pttm) REVERT: F 46 MET cc_start: 0.8415 (mmt) cc_final: 0.8181 (mmm) REVERT: F 305 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9149 (mp) REVERT: F 358 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7444 (p0) REVERT: F 600 ASN cc_start: 0.8039 (m110) cc_final: 0.7662 (m-40) REVERT: G 14 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8691 (t) REVERT: G 334 THR cc_start: 0.8415 (m) cc_final: 0.7990 (p) REVERT: G 344 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: G 433 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7023 (tm-30) REVERT: G 478 GLN cc_start: 0.7935 (tt0) cc_final: 0.7726 (tt0) REVERT: H 66 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: J 46 MET cc_start: 0.8603 (mmt) cc_final: 0.8302 (mmm) REVERT: J 305 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9163 (mp) REVERT: J 334 THR cc_start: 0.8317 (m) cc_final: 0.7901 (p) REVERT: J 410 GLU cc_start: 0.8267 (mp0) cc_final: 0.8003 (mm-30) REVERT: J 411 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7281 (tm-30) REVERT: J 492 ASN cc_start: 0.8333 (t160) cc_final: 0.8091 (t160) REVERT: J 594 ILE cc_start: 0.9277 (mp) cc_final: 0.8771 (mm) REVERT: J 597 ASN cc_start: 0.7862 (p0) cc_final: 0.7621 (p0) REVERT: J 600 ASN cc_start: 0.8193 (m110) cc_final: 0.7678 (m-40) REVERT: K 84 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7600 (mt) REVERT: K 334 THR cc_start: 0.8433 (m) cc_final: 0.8017 (p) REVERT: L 304 ASP cc_start: 0.7449 (p0) cc_final: 0.6981 (p0) REVERT: L 334 THR cc_start: 0.8384 (m) cc_final: 0.8093 (p) REVERT: L 393 PHE cc_start: 0.7073 (m-80) cc_final: 0.6810 (m-10) REVERT: L 493 LEU cc_start: 0.8217 (tp) cc_final: 0.7992 (tp) REVERT: L 539 LYS cc_start: 0.8467 (pttt) cc_final: 0.8201 (ptpt) REVERT: L 614 ARG cc_start: 0.7901 (tmm-80) cc_final: 0.7565 (tmm-80) REVERT: M 393 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: N 334 THR cc_start: 0.8379 (m) cc_final: 0.7931 (p) REVERT: N 393 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: N 410 GLU cc_start: 0.8339 (mp0) cc_final: 0.8028 (mm-30) REVERT: N 474 MET cc_start: 0.8073 (mmm) cc_final: 0.7629 (mmp) REVERT: O 14 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8683 (t) REVERT: O 46 MET cc_start: 0.8631 (mmm) cc_final: 0.8193 (mmt) REVERT: O 84 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (mt) REVERT: O 433 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7159 (tm-30) REVERT: O 575 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7398 (mtp85) REVERT: P 66 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: P 156 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7663 (mtmt) REVERT: P 410 GLU cc_start: 0.8108 (mp0) cc_final: 0.7879 (mm-30) REVERT: P 585 MET cc_start: 0.7179 (mmt) cc_final: 0.6657 (mmt) outliers start: 283 outliers final: 136 residues processed: 1053 average time/residue: 1.2745 time to fit residues: 1836.4190 Evaluate side-chains 924 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 771 time to evaluate : 6.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 393 PHE Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 352 CYS Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 210 GLN Chi-restraints excluded: chain I residue 352 CYS Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 557 VAL Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 586 SER Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 352 CYS Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain M residue 586 SER Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 352 CYS Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 393 PHE Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 210 GLN Chi-restraints excluded: chain O residue 241 SER Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 734 optimal weight: 5.9990 chunk 500 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 656 optimal weight: 0.0270 chunk 363 optimal weight: 4.9990 chunk 752 optimal weight: 2.9990 chunk 609 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 450 optimal weight: 0.0470 chunk 791 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 414 ASN B 137 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 600 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 600 ASN D 137 ASN D 277 GLN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN F 137 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS F 437 GLN F 492 ASN G 76 ASN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN H 137 ASN H 277 GLN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN H 476 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN ** J 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 GLN J 409 HIS ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 600 ASN L 137 ASN ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 492 ASN L 600 ASN M 277 GLN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS M 492 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 556 GLN N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS O 476 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 ASN P 277 GLN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS P 414 ASN P 437 GLN ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 73232 Z= 0.179 Angle : 0.582 10.290 99360 Z= 0.294 Chirality : 0.042 0.173 11376 Planarity : 0.004 0.038 12848 Dihedral : 6.188 55.145 10720 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.04 % Allowed : 12.87 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8976 helix: 1.63 (0.12), residues: 2016 sheet: -0.31 (0.11), residues: 2176 loop : -1.13 (0.09), residues: 4784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.010 0.001 HIS L 409 PHE 0.015 0.001 PHE B 393 TYR 0.013 0.001 TYR L 140 ARG 0.011 0.001 ARG H 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 846 time to evaluate : 6.870 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: A 130 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (m) REVERT: A 209 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7775 (tm) REVERT: A 614 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7875 (tmm-80) REVERT: B 334 THR cc_start: 0.8370 (m) cc_final: 0.7983 (p) REVERT: B 411 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: C 66 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: C 393 PHE cc_start: 0.6532 (m-80) cc_final: 0.6291 (m-10) REVERT: C 433 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6879 (tm-30) REVERT: D 334 THR cc_start: 0.8266 (m) cc_final: 0.7960 (p) REVERT: D 433 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 156 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7652 (ttmt) REVERT: E 433 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7564 (tm-30) REVERT: E 539 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7886 (pttm) REVERT: F 46 MET cc_start: 0.8356 (mmt) cc_final: 0.8090 (mmm) REVERT: F 305 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9186 (mp) REVERT: F 344 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: F 353 GLU cc_start: 0.7629 (pp20) cc_final: 0.7399 (pm20) REVERT: F 600 ASN cc_start: 0.7936 (m110) cc_final: 0.7572 (m-40) REVERT: G 126 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7992 (p0) REVERT: G 334 THR cc_start: 0.8343 (m) cc_final: 0.7917 (p) REVERT: G 344 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: G 353 GLU cc_start: 0.7578 (pp20) cc_final: 0.7159 (pm20) REVERT: G 433 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6871 (tm-30) REVERT: G 478 GLN cc_start: 0.7848 (tt0) cc_final: 0.7613 (tt0) REVERT: H 66 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: I 209 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7609 (tm) REVERT: J 46 MET cc_start: 0.8566 (mmt) cc_final: 0.8266 (mmm) REVERT: J 305 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9163 (mp) REVERT: J 334 THR cc_start: 0.8249 (m) cc_final: 0.7875 (p) REVERT: J 344 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: J 410 GLU cc_start: 0.8259 (mp0) cc_final: 0.8016 (mm-30) REVERT: J 411 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: J 492 ASN cc_start: 0.8275 (t160) cc_final: 0.8022 (t0) REVERT: J 600 ASN cc_start: 0.8147 (m110) cc_final: 0.7926 (m-40) REVERT: K 334 THR cc_start: 0.8373 (m) cc_final: 0.7964 (p) REVERT: L 66 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: L 202 ASP cc_start: 0.8426 (m-30) cc_final: 0.8199 (m-30) REVERT: L 304 ASP cc_start: 0.7338 (p0) cc_final: 0.6902 (p0) REVERT: L 334 THR cc_start: 0.8263 (m) cc_final: 0.7942 (p) REVERT: L 393 PHE cc_start: 0.7099 (m-80) cc_final: 0.6816 (m-10) REVERT: L 614 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7576 (tmm-80) REVERT: M 209 LEU cc_start: 0.7792 (tp) cc_final: 0.7547 (tp) REVERT: M 393 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: N 305 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9134 (mp) REVERT: N 334 THR cc_start: 0.8340 (m) cc_final: 0.7929 (p) REVERT: N 358 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7410 (p0) REVERT: N 393 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: N 410 GLU cc_start: 0.8331 (mp0) cc_final: 0.8079 (mm-30) REVERT: N 474 MET cc_start: 0.8131 (mmm) cc_final: 0.7611 (mmp) REVERT: O 46 MET cc_start: 0.8645 (mmm) cc_final: 0.8198 (mmt) REVERT: O 433 GLU cc_start: 0.7638 (tm-30) cc_final: 0.6821 (tm-30) REVERT: O 434 ASP cc_start: 0.8129 (p0) cc_final: 0.7903 (p0) REVERT: O 435 VAL cc_start: 0.8729 (p) cc_final: 0.8521 (m) REVERT: O 575 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: P 156 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7644 (mtmm) REVERT: P 410 GLU cc_start: 0.8042 (mp0) cc_final: 0.7788 (mm-30) REVERT: P 585 MET cc_start: 0.7136 (mmt) cc_final: 0.6616 (mmt) REVERT: P 594 ILE cc_start: 0.9157 (mm) cc_final: 0.8948 (mp) outliers start: 239 outliers final: 127 residues processed: 1010 average time/residue: 1.2564 time to fit residues: 1738.9333 Evaluate side-chains 920 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 773 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 210 GLN Chi-restraints excluded: chain I residue 352 CYS Chi-restraints excluded: chain I residue 567 THR Chi-restraints excluded: chain I residue 596 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain J residue 411 GLU Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain J residue 596 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 358 ASN Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 352 CYS Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 567 THR Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 305 LEU Chi-restraints excluded: chain N residue 352 CYS Chi-restraints excluded: chain N residue 358 ASN Chi-restraints excluded: chain N residue 393 PHE Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain O residue 102 LEU 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 471 ILE Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain O residue 596 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 296 optimal weight: 1.9990 chunk 793 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 517 optimal weight: 0.6980 chunk 217 optimal weight: 20.0000 chunk 882 optimal weight: 0.8980 chunk 732 optimal weight: 2.9990 chunk 408 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 463 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN B 600 ASN C 39 ASN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 414 ASN C 600 ASN D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 ASN E 39 ASN E 99 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 GLN F 409 HIS F 492 ASN G 39 ASN G 74 GLN G 277 GLN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 39 ASN I 99 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 366 GLN J 409 HIS ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 277 GLN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 600 ASN ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 GLN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 476 ASN L 492 ASN L 600 ASN M 39 ASN M 99 ASN M 358 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS N 39 ASN N 99 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 437 GLN ** N 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN O 39 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 GLN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS O 414 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS P 414 ASN ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 73232 Z= 0.218 Angle : 0.604 13.425 99360 Z= 0.304 Chirality : 0.043 0.177 11376 Planarity : 0.004 0.044 12848 Dihedral : 6.093 56.151 10720 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.17 % Allowed : 13.39 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 8976 helix: 1.79 (0.11), residues: 2016 sheet: -0.25 (0.11), residues: 2176 loop : -1.05 (0.09), residues: 4784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.010 0.001 HIS M 409 PHE 0.019 0.002 PHE C 359 TYR 0.012 0.001 TYR L 140 ARG 0.009 0.001 ARG G 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 822 time to evaluate : 6.995 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: symmetry clash REVERT: A 614 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7874 (tmm-80) REVERT: B 334 THR cc_start: 0.8357 (m) cc_final: 0.7949 (p) REVERT: B 344 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: B 353 GLU cc_start: 0.7583 (pp20) cc_final: 0.7311 (pm20) REVERT: B 411 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: B 492 ASN cc_start: 0.8010 (m-40) cc_final: 0.7634 (m110) REVERT: B 594 ILE cc_start: 0.9265 (mp) cc_final: 0.8424 (mm) REVERT: B 597 ASN cc_start: 0.7972 (p0) cc_final: 0.7373 (p0) REVERT: C 126 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7946 (p0) REVERT: D 42 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6704 (mmm) REVERT: D 171 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7559 (mmm160) REVERT: D 334 THR cc_start: 0.8286 (m) cc_final: 0.7975 (p) REVERT: D 433 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7371 (tm-30) REVERT: E 156 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7697 (ttmt) REVERT: E 539 LYS cc_start: 0.8308 (ptpt) cc_final: 0.7980 (pttm) REVERT: F 46 MET cc_start: 0.8375 (mmt) cc_final: 0.8093 (mmm) REVERT: F 305 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9188 (mp) REVERT: F 393 PHE cc_start: 0.6702 (m-80) cc_final: 0.6403 (m-10) REVERT: F 597 ASN cc_start: 0.7570 (t0) cc_final: 0.7331 (t0) REVERT: F 600 ASN cc_start: 0.7853 (m110) cc_final: 0.7648 (m-40) REVERT: G 126 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7996 (p0) REVERT: G 334 THR cc_start: 0.8408 (m) cc_final: 0.7993 (p) REVERT: G 344 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: G 433 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6867 (tm-30) REVERT: G 478 GLN cc_start: 0.7858 (tt0) cc_final: 0.7619 (tt0) REVERT: H 66 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: I 209 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7654 (tm) REVERT: I 411 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7539 (tm-30) REVERT: J 46 MET cc_start: 0.8563 (mmt) cc_final: 0.8285 (mmm) REVERT: J 305 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9193 (mp) REVERT: J 334 THR cc_start: 0.8283 (m) cc_final: 0.7903 (p) REVERT: J 344 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: J 410 GLU cc_start: 0.8328 (mp0) cc_final: 0.8013 (mm-30) REVERT: J 600 ASN cc_start: 0.8068 (m110) cc_final: 0.7851 (m-40) REVERT: K 84 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7521 (mt) REVERT: K 334 THR cc_start: 0.8419 (m) cc_final: 0.8006 (p) REVERT: L 66 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: L 202 ASP cc_start: 0.8446 (m-30) cc_final: 0.8212 (m-30) REVERT: L 301 MET cc_start: 0.9142 (mmm) cc_final: 0.8866 (tpp) REVERT: L 304 ASP cc_start: 0.7302 (p0) cc_final: 0.6883 (p0) REVERT: L 334 THR cc_start: 0.8285 (m) cc_final: 0.7964 (p) REVERT: L 393 PHE cc_start: 0.7148 (m-80) cc_final: 0.6799 (m-10) REVERT: L 614 ARG cc_start: 0.7930 (tmm-80) cc_final: 0.7592 (tmm-80) REVERT: M 209 LEU cc_start: 0.7807 (tp) cc_final: 0.7534 (tp) REVERT: M 304 ASP cc_start: 0.7495 (p0) cc_final: 0.7106 (p0) REVERT: M 393 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: N 164 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6288 (mpp-170) REVERT: N 334 THR cc_start: 0.8354 (m) cc_final: 0.7941 (p) REVERT: N 353 GLU cc_start: 0.7882 (pp20) cc_final: 0.7476 (pm20) REVERT: N 410 GLU cc_start: 0.8313 (mp0) cc_final: 0.8068 (mm-30) REVERT: N 474 MET cc_start: 0.8153 (mmm) cc_final: 0.7698 (mmp) REVERT: O 46 MET cc_start: 0.8658 (mmm) cc_final: 0.8167 (mmt) REVERT: O 84 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7479 (mt) REVERT: O 433 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6851 (tm-30) REVERT: O 435 VAL cc_start: 0.8744 (p) cc_final: 0.8525 (m) REVERT: O 575 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7439 (mtp85) REVERT: P 66 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: P 156 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7723 (mtmm) REVERT: P 585 MET cc_start: 0.7096 (mmt) cc_final: 0.6595 (mmt) outliers start: 249 outliers final: 154 residues processed: 989 average time/residue: 1.2947 time to fit residues: 1752.3288 Evaluate side-chains 954 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 781 time to evaluate : 6.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 546 GLN Chi-restraints excluded: chain I residue 567 THR Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 596 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 344 GLN Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 596 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain K residue 596 THR Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 567 THR Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 352 CYS Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain N residue 615 LEU Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU 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 241 SER Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Chi-restraints excluded: chain P residue 625 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 850 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 502 optimal weight: 6.9990 chunk 644 optimal weight: 4.9990 chunk 499 optimal weight: 4.9990 chunk 742 optimal weight: 2.9990 chunk 492 optimal weight: 2.9990 chunk 879 optimal weight: 0.5980 chunk 550 optimal weight: 5.9990 chunk 535 optimal weight: 5.9990 chunk 405 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 99 ASN A 277 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 414 ASN A 492 ASN B 39 ASN B 99 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 414 ASN C 600 ASN D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 492 ASN D 600 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN E 492 ASN F 39 ASN F 99 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS ** F 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 ASN G 358 ASN ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN H 39 ASN H 99 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS H 414 ASN H 476 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 39 ASN J 99 ASN ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 99 ASN L 277 GLN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 492 ASN L 600 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS N 277 GLN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 358 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS ** O 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 ASN P 39 ASN P 99 ASN P 277 GLN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 73232 Z= 0.276 Angle : 0.638 13.421 99360 Z= 0.323 Chirality : 0.045 0.189 11376 Planarity : 0.005 0.056 12848 Dihedral : 6.147 57.513 10720 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.35 % Allowed : 13.63 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 8976 helix: 1.84 (0.12), residues: 1984 sheet: -0.21 (0.11), residues: 2176 loop : -0.98 (0.09), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 34 HIS 0.012 0.002 HIS L 409 PHE 0.020 0.002 PHE K 393 TYR 0.030 0.001 TYR D 413 ARG 0.012 0.001 ARG E 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 790 time to evaluate : 6.423 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7874 (tmm-80) REVERT: B 42 MET cc_start: 0.7553 (mmm) cc_final: 0.7210 (mmm) REVERT: B 334 THR cc_start: 0.8400 (m) cc_final: 0.7962 (p) REVERT: B 344 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: B 492 ASN cc_start: 0.8109 (m-40) cc_final: 0.7738 (m110) REVERT: C 84 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7548 (mt) REVERT: C 126 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7969 (p0) REVERT: D 171 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7553 (mmm160) REVERT: D 247 LYS cc_start: 0.8261 (tppt) cc_final: 0.8061 (tppt) REVERT: D 334 THR cc_start: 0.8343 (m) cc_final: 0.8035 (p) REVERT: D 614 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7795 (ttp80) REVERT: E 334 THR cc_start: 0.8438 (m) cc_final: 0.7865 (p) REVERT: E 433 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7744 (tm-30) REVERT: E 539 LYS cc_start: 0.8369 (ptpt) cc_final: 0.8040 (pttm) REVERT: F 46 MET cc_start: 0.8441 (mmt) cc_final: 0.8163 (mmm) REVERT: F 305 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9175 (mp) REVERT: F 353 GLU cc_start: 0.7819 (pp20) cc_final: 0.7458 (pm20) REVERT: F 393 PHE cc_start: 0.6769 (m-80) cc_final: 0.6510 (m-10) REVERT: F 600 ASN cc_start: 0.7772 (m110) cc_final: 0.7496 (m-40) REVERT: G 84 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7567 (mt) REVERT: G 126 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7991 (p0) REVERT: G 344 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: G 353 GLU cc_start: 0.7725 (pp20) cc_final: 0.7251 (pm20) REVERT: G 433 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6904 (tm-30) REVERT: G 478 GLN cc_start: 0.7985 (tt0) cc_final: 0.7759 (tt0) REVERT: H 66 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: H 493 LEU cc_start: 0.8058 (tp) cc_final: 0.7742 (tp) REVERT: H 614 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7568 (tmm-80) REVERT: I 209 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7714 (tm) REVERT: I 411 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7419 (tm-30) REVERT: J 46 MET cc_start: 0.8557 (mmt) cc_final: 0.8302 (mmm) REVERT: J 305 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9182 (mp) REVERT: J 334 THR cc_start: 0.8364 (m) cc_final: 0.7964 (p) REVERT: J 410 GLU cc_start: 0.8258 (mp0) cc_final: 0.7985 (mm-30) REVERT: J 600 ASN cc_start: 0.8040 (m110) cc_final: 0.7729 (m-40) REVERT: K 84 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7559 (mt) REVERT: K 334 THR cc_start: 0.8439 (m) cc_final: 0.8027 (p) REVERT: K 358 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7148 (p0) REVERT: L 66 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: L 301 MET cc_start: 0.9146 (mmm) cc_final: 0.8890 (tpp) REVERT: L 304 ASP cc_start: 0.7243 (p0) cc_final: 0.6883 (p0) REVERT: L 334 THR cc_start: 0.8329 (m) cc_final: 0.8043 (p) REVERT: L 393 PHE cc_start: 0.7154 (m-80) cc_final: 0.6918 (m-10) REVERT: L 539 LYS cc_start: 0.8557 (pttt) cc_final: 0.8231 (ptpt) REVERT: M 304 ASP cc_start: 0.7531 (p0) cc_final: 0.7223 (p0) REVERT: M 393 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: N 164 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6468 (mpp-170) REVERT: N 334 THR cc_start: 0.8411 (m) cc_final: 0.7979 (p) REVERT: N 358 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7398 (p0) REVERT: N 393 PHE cc_start: 0.6669 (m-80) cc_final: 0.6432 (m-10) REVERT: N 409 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7570 (t-170) REVERT: N 410 GLU cc_start: 0.8369 (mp0) cc_final: 0.8028 (mm-30) REVERT: N 474 MET cc_start: 0.8181 (mmm) cc_final: 0.7750 (mmp) REVERT: O 46 MET cc_start: 0.8645 (mmm) cc_final: 0.8261 (mmm) REVERT: O 84 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7527 (mt) REVERT: O 433 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7172 (tm-30) REVERT: O 575 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: P 66 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: P 156 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7710 (mtmm) REVERT: P 410 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: P 585 MET cc_start: 0.7075 (mmt) cc_final: 0.6580 (mmt) outliers start: 263 outliers final: 168 residues processed: 976 average time/residue: 1.3182 time to fit residues: 1768.1004 Evaluate side-chains 950 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 761 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 352 CYS Chi-restraints excluded: chain I residue 546 GLN Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 567 THR Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 596 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain J residue 584 LEU Chi-restraints excluded: chain J residue 596 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 358 ASN Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain K residue 596 THR Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 584 LEU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 352 CYS Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 567 THR Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 352 CYS Chi-restraints excluded: chain N residue 358 ASN Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 409 HIS Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain N residue 615 LEU Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU 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 241 SER Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain O residue 600 ASN Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 chunk 524 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 558 optimal weight: 2.9990 chunk 598 optimal weight: 0.9980 chunk 434 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 690 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 99 ASN A 277 GLN A 358 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 414 ASN B 39 ASN B 99 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 414 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN D 600 ASN E 137 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN E 492 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 HIS G 414 ASN H 39 ASN H 99 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS H 414 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 409 HIS ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 99 ASN L 277 GLN L 358 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 492 ASN L 600 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 437 GLN ** N 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 GLN O 358 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS ** O 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 476 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 600 ASN P 39 ASN P 99 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS P 414 ASN ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 73232 Z= 0.234 Angle : 0.627 12.324 99360 Z= 0.314 Chirality : 0.044 0.187 11376 Planarity : 0.004 0.059 12848 Dihedral : 6.032 57.029 10720 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.08 % Allowed : 14.28 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 8976 helix: 1.92 (0.12), residues: 1984 sheet: -0.18 (0.11), residues: 2176 loop : -0.94 (0.09), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.012 0.001 HIS N 409 PHE 0.019 0.002 PHE C 393 TYR 0.026 0.001 TYR D 413 ARG 0.012 0.001 ARG E 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 781 time to evaluate : 6.520 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7641 (tm) REVERT: A 614 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7886 (tmm-80) REVERT: B 334 THR cc_start: 0.8380 (m) cc_final: 0.7958 (p) REVERT: B 344 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: B 353 GLU cc_start: 0.7611 (pp20) cc_final: 0.7354 (pm20) REVERT: B 492 ASN cc_start: 0.8119 (m-40) cc_final: 0.7772 (m110) REVERT: C 84 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7526 (mt) REVERT: C 126 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7957 (p0) REVERT: D 171 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7510 (mmm160) REVERT: D 334 THR cc_start: 0.8351 (m) cc_final: 0.8045 (p) REVERT: D 614 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7819 (ttp80) REVERT: E 156 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: E 209 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7709 (tm) REVERT: E 433 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 539 LYS cc_start: 0.8355 (ptpt) cc_final: 0.8028 (pttm) REVERT: F 46 MET cc_start: 0.8393 (mmt) cc_final: 0.8143 (mmm) REVERT: F 305 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9174 (mp) REVERT: F 600 ASN cc_start: 0.7751 (m110) cc_final: 0.7526 (m-40) REVERT: G 126 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7952 (p0) REVERT: G 433 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6910 (tm-30) REVERT: G 478 GLN cc_start: 0.7936 (tt0) cc_final: 0.7711 (tt0) REVERT: H 66 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: H 493 LEU cc_start: 0.8078 (tp) cc_final: 0.7737 (tp) REVERT: H 614 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7602 (tmm-80) REVERT: I 209 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7714 (tm) REVERT: I 411 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7375 (tm-30) REVERT: J 46 MET cc_start: 0.8589 (mmt) cc_final: 0.8377 (mmm) REVERT: J 305 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9179 (mp) REVERT: J 334 THR cc_start: 0.8377 (m) cc_final: 0.7990 (p) REVERT: J 410 GLU cc_start: 0.8319 (mp0) cc_final: 0.7962 (mm-30) REVERT: J 600 ASN cc_start: 0.7954 (m110) cc_final: 0.7591 (m-40) REVERT: K 66 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: K 84 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7538 (mt) REVERT: K 334 THR cc_start: 0.8408 (m) cc_final: 0.7991 (p) REVERT: L 66 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: L 304 ASP cc_start: 0.7216 (p0) cc_final: 0.6876 (p0) REVERT: L 334 THR cc_start: 0.8291 (m) cc_final: 0.7961 (p) REVERT: L 393 PHE cc_start: 0.7226 (m-80) cc_final: 0.7009 (m-10) REVERT: L 539 LYS cc_start: 0.8539 (pttt) cc_final: 0.8218 (ptpt) REVERT: L 614 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7811 (tmm-80) REVERT: M 209 LEU cc_start: 0.7820 (tp) cc_final: 0.7544 (tp) REVERT: M 304 ASP cc_start: 0.7554 (p0) cc_final: 0.7245 (p0) REVERT: M 393 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: N 164 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6397 (mpp-170) REVERT: N 334 THR cc_start: 0.8395 (m) cc_final: 0.7974 (p) REVERT: N 358 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7385 (p0) REVERT: N 410 GLU cc_start: 0.8256 (mp0) cc_final: 0.8033 (mm-30) REVERT: N 474 MET cc_start: 0.8135 (mmm) cc_final: 0.7722 (mmp) REVERT: O 46 MET cc_start: 0.8674 (mmm) cc_final: 0.8161 (mmt) REVERT: O 84 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7511 (mt) REVERT: O 433 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6998 (tm-30) REVERT: O 575 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7459 (mtp85) REVERT: P 66 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: P 156 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7678 (mtmm) REVERT: P 410 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (mm-30) outliers start: 242 outliers final: 153 residues processed: 945 average time/residue: 1.2892 time to fit residues: 1667.8719 Evaluate side-chains 927 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 753 time to evaluate : 6.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 210 GLN Chi-restraints excluded: chain I residue 546 GLN Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain K residue 596 THR Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 584 LEU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 358 ASN Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain N residue 615 LEU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU 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 241 SER Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain O residue 600 ASN Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 171 ARG Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 1.9990 chunk 842 optimal weight: 40.0000 chunk 768 optimal weight: 1.9990 chunk 819 optimal weight: 2.9990 chunk 841 optimal weight: 2.9990 chunk 493 optimal weight: 4.9990 chunk 356 optimal weight: 0.9980 chunk 643 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 740 optimal weight: 10.0000 chunk 774 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 99 ASN A 277 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN B 39 ASN B 99 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 414 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN D 600 ASN E 167 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN E 492 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS ** F 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN H 39 ASN H 99 ASN H 277 GLN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 492 ASN H 600 ASN I 167 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 409 HIS ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 99 ASN L 358 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 478 GLN L 492 ASN L 600 ASN M 277 GLN M 358 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 414 ASN ** N 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 GLN O 358 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS ** O 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 476 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN P 99 ASN P 277 GLN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 600 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 73232 Z= 0.299 Angle : 0.662 11.983 99360 Z= 0.334 Chirality : 0.045 0.189 11376 Planarity : 0.005 0.063 12848 Dihedral : 6.132 58.397 10720 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.02 % Allowed : 14.51 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 8976 helix: 1.86 (0.12), residues: 1984 sheet: -0.17 (0.11), residues: 2176 loop : -0.96 (0.09), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 34 HIS 0.010 0.002 HIS M 409 PHE 0.024 0.002 PHE P 393 TYR 0.026 0.002 TYR D 413 ARG 0.013 0.001 ARG E 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 796 time to evaluate : 6.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7594 (tm) REVERT: A 614 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7903 (tmm-80) REVERT: B 42 MET cc_start: 0.7464 (mmm) cc_final: 0.7148 (mmm) REVERT: B 334 THR cc_start: 0.8470 (m) cc_final: 0.8055 (p) REVERT: B 344 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: B 492 ASN cc_start: 0.8107 (m-40) cc_final: 0.7754 (m110) REVERT: C 84 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7533 (mt) REVERT: C 126 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 171 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7529 (mmm160) REVERT: D 334 THR cc_start: 0.8357 (m) cc_final: 0.8044 (p) REVERT: D 614 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7812 (ttp80) REVERT: E 209 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7746 (tm) REVERT: E 334 THR cc_start: 0.8434 (m) cc_final: 0.7864 (p) REVERT: E 433 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7675 (tm-30) REVERT: E 539 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8128 (pttm) REVERT: F 46 MET cc_start: 0.8408 (mmt) cc_final: 0.8152 (mmm) REVERT: F 305 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9183 (mp) REVERT: F 353 GLU cc_start: 0.7845 (pp20) cc_final: 0.7424 (pm20) REVERT: F 476 ASN cc_start: 0.7920 (t0) cc_final: 0.7618 (t0) REVERT: F 600 ASN cc_start: 0.7780 (m110) cc_final: 0.7534 (m-40) REVERT: G 84 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7600 (mt) REVERT: G 126 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8048 (p0) REVERT: G 433 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6923 (tm-30) REVERT: G 478 GLN cc_start: 0.8012 (tt0) cc_final: 0.7784 (tt0) REVERT: H 66 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: H 614 ARG cc_start: 0.7888 (tmm-80) cc_final: 0.7632 (tmm-80) REVERT: I 209 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7659 (tm) REVERT: I 411 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7533 (tm-30) REVERT: J 46 MET cc_start: 0.8563 (mmt) cc_final: 0.8322 (mmm) REVERT: J 305 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9166 (mp) REVERT: J 334 THR cc_start: 0.8434 (m) cc_final: 0.8044 (p) REVERT: J 410 GLU cc_start: 0.8336 (mp0) cc_final: 0.7963 (mm-30) REVERT: J 600 ASN cc_start: 0.7943 (m110) cc_final: 0.7567 (m-40) REVERT: K 66 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: K 84 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7567 (mt) REVERT: K 334 THR cc_start: 0.8512 (m) cc_final: 0.8108 (p) REVERT: L 66 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: L 304 ASP cc_start: 0.7258 (p0) cc_final: 0.6802 (p0) REVERT: L 334 THR cc_start: 0.8361 (m) cc_final: 0.8071 (p) REVERT: L 539 LYS cc_start: 0.8587 (pttt) cc_final: 0.8277 (ptpt) REVERT: L 614 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7757 (tmm-80) REVERT: M 304 ASP cc_start: 0.7536 (p0) cc_final: 0.7309 (p0) REVERT: M 393 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: N 164 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6482 (mpp-170) REVERT: N 334 THR cc_start: 0.8440 (m) cc_final: 0.8019 (p) REVERT: N 353 GLU cc_start: 0.8015 (pp20) cc_final: 0.7548 (pm20) REVERT: N 358 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7398 (p0) REVERT: N 409 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (t-170) REVERT: N 410 GLU cc_start: 0.8277 (mp0) cc_final: 0.8046 (mm-30) REVERT: N 474 MET cc_start: 0.8149 (mmm) cc_final: 0.7764 (mmp) REVERT: O 46 MET cc_start: 0.8677 (mmm) cc_final: 0.8302 (mmm) REVERT: O 84 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7561 (mt) REVERT: O 433 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7036 (tm-30) REVERT: O 575 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: P 66 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: P 156 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7702 (mtmm) REVERT: P 410 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7937 (mm-30) outliers start: 237 outliers final: 164 residues processed: 959 average time/residue: 1.2600 time to fit residues: 1661.6284 Evaluate side-chains 957 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 771 time to evaluate : 6.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 592 THR Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 546 GLN Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 557 VAL Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 584 LEU Chi-restraints excluded: chain K residue 596 THR Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 584 LEU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 567 THR Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 358 ASN Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 409 HIS Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain N residue 615 LEU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU 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 241 SER Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain O residue 596 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 171 ARG Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Chi-restraints excluded: chain P residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 4.9990 chunk 537 optimal weight: 2.9990 chunk 866 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 chunk 602 optimal weight: 4.9990 chunk 908 optimal weight: 10.0000 chunk 836 optimal weight: 3.9990 chunk 723 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 558 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 358 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 414 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN D 600 ASN E 277 GLN ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 414 ASN E 492 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS ** F 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 HIS G 414 ASN H 39 ASN H 99 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 492 ASN H 600 ASN I 277 GLN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 414 ASN ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN K 478 GLN L 39 ASN L 99 ASN L 358 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS L 414 ASN L 492 ASN L 600 ASN M 277 GLN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS M 414 ASN M 476 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 478 GLN N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 358 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS O 414 ASN O 478 GLN P 39 ASN P 99 ASN ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 478 GLN P 600 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 73232 Z= 0.398 Angle : 0.722 13.405 99360 Z= 0.367 Chirality : 0.049 0.191 11376 Planarity : 0.005 0.066 12848 Dihedral : 6.393 59.848 10720 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.89 % Allowed : 14.96 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 8976 helix: 1.69 (0.12), residues: 1984 sheet: -0.18 (0.11), residues: 2176 loop : -1.00 (0.08), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 34 HIS 0.051 0.002 HIS N 409 PHE 0.024 0.002 PHE H 393 TYR 0.026 0.002 TYR D 413 ARG 0.014 0.001 ARG E 614 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17952 Ramachandran restraints generated. 8976 Oldfield, 0 Emsley, 8976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 770 time to evaluate : 6.545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7891 (tmm-80) REVERT: B 334 THR cc_start: 0.8523 (m) cc_final: 0.8115 (p) REVERT: B 344 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: B 492 ASN cc_start: 0.8098 (m-40) cc_final: 0.7722 (m110) REVERT: C 84 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7570 (mt) REVERT: C 126 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8076 (p0) REVERT: C 209 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7729 (mm) REVERT: D 171 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7545 (mmm160) REVERT: D 334 THR cc_start: 0.8476 (m) cc_final: 0.8186 (p) REVERT: D 614 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7757 (ttp80) REVERT: E 209 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7634 (tm) REVERT: E 334 THR cc_start: 0.8460 (m) cc_final: 0.7860 (p) REVERT: E 433 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7687 (tm-30) REVERT: E 539 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8223 (pttm) REVERT: F 46 MET cc_start: 0.8465 (mmt) cc_final: 0.8203 (mmm) REVERT: F 305 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9175 (mp) REVERT: F 353 GLU cc_start: 0.7887 (pp20) cc_final: 0.7649 (pp20) REVERT: F 476 ASN cc_start: 0.8023 (t0) cc_final: 0.7705 (t0) REVERT: F 600 ASN cc_start: 0.7738 (m110) cc_final: 0.7489 (m-40) REVERT: G 84 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7606 (mt) REVERT: G 126 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8083 (p0) REVERT: G 433 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6958 (tm-30) REVERT: G 478 GLN cc_start: 0.8043 (tt0) cc_final: 0.7801 (tt0) REVERT: H 125 LYS cc_start: 0.8139 (tppt) cc_final: 0.7895 (ttpp) REVERT: H 614 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7670 (tmm-80) REVERT: I 209 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7590 (tm) REVERT: I 334 THR cc_start: 0.8424 (m) cc_final: 0.7842 (p) REVERT: J 46 MET cc_start: 0.8575 (mmt) cc_final: 0.8340 (mmm) REVERT: J 305 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9123 (mp) REVERT: J 334 THR cc_start: 0.8523 (m) cc_final: 0.8148 (p) REVERT: J 410 GLU cc_start: 0.8232 (mp0) cc_final: 0.8032 (mm-30) REVERT: J 600 ASN cc_start: 0.7885 (m110) cc_final: 0.7513 (m-40) REVERT: K 66 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: K 84 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7569 (mt) REVERT: K 334 THR cc_start: 0.8589 (m) cc_final: 0.8223 (p) REVERT: L 66 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: L 304 ASP cc_start: 0.7187 (p0) cc_final: 0.6871 (p0) REVERT: L 334 THR cc_start: 0.8493 (m) cc_final: 0.8207 (p) REVERT: L 539 LYS cc_start: 0.8659 (pttt) cc_final: 0.8344 (ptpt) REVERT: L 614 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7767 (tmm-80) REVERT: M 304 ASP cc_start: 0.7680 (p0) cc_final: 0.7421 (p0) REVERT: M 393 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: N 164 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6580 (mpp-170) REVERT: N 334 THR cc_start: 0.8548 (m) cc_final: 0.8145 (p) REVERT: N 353 GLU cc_start: 0.8012 (pp20) cc_final: 0.7654 (pp20) REVERT: N 474 MET cc_start: 0.8078 (mmm) cc_final: 0.7766 (mmp) REVERT: O 46 MET cc_start: 0.8672 (mmm) cc_final: 0.8364 (mmm) REVERT: O 84 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7576 (mt) REVERT: O 433 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6929 (tm-30) REVERT: O 575 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7473 (mtp85) REVERT: P 66 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: P 410 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: P 539 LYS cc_start: 0.8642 (pttt) cc_final: 0.8357 (ptpt) outliers start: 227 outliers final: 158 residues processed: 935 average time/residue: 1.2857 time to fit residues: 1643.2998 Evaluate side-chains 930 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 753 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 592 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 567 THR Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 210 GLN Chi-restraints excluded: chain H residue 241 SER Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 435 VAL Chi-restraints excluded: chain H residue 567 THR Chi-restraints excluded: chain H residue 570 SER Chi-restraints excluded: chain H residue 580 THR Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 171 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 546 GLN Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 210 GLN Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 570 SER Chi-restraints excluded: chain J residue 580 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 338 SER Chi-restraints excluded: chain K residue 557 VAL Chi-restraints excluded: chain K residue 567 THR Chi-restraints excluded: chain K residue 570 SER Chi-restraints excluded: chain K residue 596 THR Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 210 GLN Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 434 ASP Chi-restraints excluded: chain L residue 567 THR Chi-restraints excluded: chain L residue 570 SER Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 210 GLN Chi-restraints excluded: chain M residue 393 PHE Chi-restraints excluded: chain M residue 435 VAL Chi-restraints excluded: chain M residue 557 VAL Chi-restraints excluded: chain M residue 570 SER Chi-restraints excluded: chain M residue 584 LEU Chi-restraints excluded: chain M residue 605 ILE Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 368 CYS Chi-restraints excluded: chain N residue 409 HIS Chi-restraints excluded: chain N residue 567 THR Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 586 SER Chi-restraints excluded: chain N residue 615 LEU Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 102 LEU 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 241 SER Chi-restraints excluded: chain O residue 505 SER Chi-restraints excluded: chain O residue 567 THR Chi-restraints excluded: chain O residue 570 SER Chi-restraints excluded: chain O residue 575 ARG Chi-restraints excluded: chain O residue 596 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 171 ARG Chi-restraints excluded: chain P residue 378 LEU Chi-restraints excluded: chain P residue 410 GLU Chi-restraints excluded: chain P residue 434 ASP Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 567 THR Chi-restraints excluded: chain P residue 570 SER Chi-restraints excluded: chain P residue 580 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 30.0000 chunk 574 optimal weight: 0.7980 chunk 770 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 667 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 724 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 744 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 99 ASN A 277 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 99 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 99 ASN D 358 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN D 600 ASN E 277 GLN E 366 GLN E 409 HIS E 414 ASN E 492 ASN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN ** F 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN H 39 ASN H 99 ASN H 337 ASN ** H 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 HIS H 414 ASN H 476 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 492 ASN H 600 ASN ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS I 414 ASN J 366 GLN J 414 ASN ** J 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN L 39 ASN L 99 ASN L 358 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 HIS ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 492 ASN L 600 ASN M 277 GLN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 HIS M 414 ASN ** N 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 409 HIS N 414 ASN N 478 GLN N 600 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 358 ASN ** O 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 409 HIS ** O 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 476 ASN ** O 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 409 HIS ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.172808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116483 restraints weight = 83936.050| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.39 r_work: 0.3125 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 73232 Z= 0.212 Angle : 0.642 13.196 99360 Z= 0.318 Chirality : 0.043 0.189 11376 Planarity : 0.004 0.063 12848 Dihedral : 5.992 56.778 10720 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.33 % Allowed : 15.67 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.09), residues: 8976 helix: 1.97 (0.12), residues: 1984 sheet: -0.13 (0.11), residues: 2176 loop : -0.88 (0.09), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 613 HIS 0.010 0.001 HIS M 409 PHE 0.023 0.002 PHE P 393 TYR 0.025 0.001 TYR D 413 ARG 0.014 0.001 ARG E 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28180.92 seconds wall clock time: 489 minutes 53.51 seconds (29393.51 seconds total)