Starting phenix.real_space_refine on Thu Mar 21 17:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/03_2024/7w6m_32329.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 123 5.16 5 C 19362 2.51 5 N 4776 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30756 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "B" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "C" Number of atoms: 9400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9400 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 45, 'TRANS': 1178} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.15, per 1000 atoms: 0.49 Number of scatterers: 30756 At special positions: 0 Unit cell: (147, 151.2, 183.4, 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 123 16.00 O 6495 8.00 N 4776 7.00 C 19362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA n 3 " - " MAN n 5 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 5 " " BMA s 3 " - " MAN s 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 4 " " NAG K 1 " - " FUC K 5 " " NAG R 1 " - " FUC R 3 " " NAG S 1 " - " FUC S 4 " " NAG U 1 " - " FUC U 4 " " NAG Z 1 " - " FUC Z 5 " " NAG g 1 " - " FUC g 3 " " NAG h 1 " - " FUC h 4 " " NAG j 1 " - " FUC j 4 " " NAG o 1 " - " FUC o 5 " " NAG v 1 " - " FUC v 3 " NAG-ASN " NAG A1401 " - " ASN A 118 " " NAG A1402 " - " ASN A 425 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 351 " " NAG A1405 " - " ASN A1249 " " NAG A1406 " - " ASN A1009 " " NAG B1401 " - " ASN B 118 " " NAG B1402 " - " ASN B 425 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 351 " " NAG B1405 " - " ASN B1249 " " NAG B1406 " - " ASN B1009 " " NAG C1401 " - " ASN C 118 " " NAG C1402 " - " ASN C 425 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 351 " " NAG C1405 " - " ASN C1249 " " NAG C1406 " - " ASN C1009 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 264 " " NAG F 1 " - " ASN A 300 " " NAG G 1 " - " ASN A 324 " " NAG H 1 " - " ASN A 344 " " NAG I 1 " - " ASN A 381 " " NAG J 1 " - " ASN A 514 " " NAG K 1 " - " ASN A 556 " " NAG L 1 " - " ASN A 688 " " NAG M 1 " - " ASN A 726 " " NAG N 1 " - " ASN A 781 " " NAG O 1 " - " ASN A 787 " " NAG P 1 " - " ASN A 873 " " NAG Q 1 " - " ASN A1232 " " NAG R 1 " - " ASN A 743 " " NAG S 1 " - " ASN B 216 " " NAG T 1 " - " ASN B 264 " " NAG U 1 " - " ASN B 300 " " NAG V 1 " - " ASN B 324 " " NAG W 1 " - " ASN B 344 " " NAG X 1 " - " ASN B 381 " " NAG Y 1 " - " ASN B 514 " " NAG Z 1 " - " ASN B 556 " " NAG a 1 " - " ASN B 688 " " NAG b 1 " - " ASN B 726 " " NAG c 1 " - " ASN B 781 " " NAG d 1 " - " ASN B 787 " " NAG e 1 " - " ASN B 873 " " NAG f 1 " - " ASN B1232 " " NAG g 1 " - " ASN B 743 " " NAG h 1 " - " ASN C 216 " " NAG i 1 " - " ASN C 264 " " NAG j 1 " - " ASN C 300 " " NAG k 1 " - " ASN C 324 " " NAG l 1 " - " ASN C 344 " " NAG m 1 " - " ASN C 381 " " NAG n 1 " - " ASN C 514 " " NAG o 1 " - " ASN C 556 " " NAG p 1 " - " ASN C 688 " " NAG q 1 " - " ASN C 726 " " NAG r 1 " - " ASN C 781 " " NAG s 1 " - " ASN C 787 " " NAG t 1 " - " ASN C 873 " " NAG u 1 " - " ASN C1232 " " NAG v 1 " - " ASN C 743 " Time building additional restraints: 16.63 Conformation dependent library (CDL) restraints added in 6.0 seconds 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 50 sheets defined 24.5% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.798A pdb=" N THR A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.260A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.508A pdb=" N PHE A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 466 through 475 removed outlier: 3.604A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.733A pdb=" N LYS A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 852 removed outlier: 3.659A pdb=" N LEU A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 917 through 923 removed outlier: 3.715A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 removed outlier: 3.622A pdb=" N ALA A 932 " --> pdb=" O ASP A 928 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.519A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1014 Processing helix chain 'A' and resid 1016 through 1020 removed outlier: 3.631A pdb=" N ALA A1020 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.770A pdb=" N ASN A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1058 removed outlier: 4.101A pdb=" N THR A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1058' Processing helix chain 'A' and resid 1066 through 1072 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.939A pdb=" N GLU A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1123 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.833A pdb=" N THR B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.502A pdb=" N GLY B 292 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 4.254A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.513A pdb=" N PHE B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.902A pdb=" N ASP B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP B 434 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.740A pdb=" N LYS B 820 " --> pdb=" O ASN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 852 removed outlier: 3.750A pdb=" N LEU B 852 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 862 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 removed outlier: 3.615A pdb=" N ALA B 932 " --> pdb=" O ASP B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 959 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.527A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1014 Processing helix chain 'B' and resid 1016 through 1020 removed outlier: 3.636A pdb=" N ALA B1020 " --> pdb=" O VAL B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1047 removed outlier: 3.760A pdb=" N ASN B1043 " --> pdb=" O GLN B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1058 removed outlier: 4.098A pdb=" N THR B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B1057 " --> pdb=" O THR B1053 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B1058 " --> pdb=" O VAL B1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1049 through 1058' Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1075 through 1122 removed outlier: 3.948A pdb=" N GLU B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1198 removed outlier: 4.382A pdb=" N HIS B1197 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1242 Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.800A pdb=" N THR C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.673A pdb=" N GLY C 292 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 removed outlier: 4.234A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.502A pdb=" N PHE C 360 " --> pdb=" O HIS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.907A pdb=" N ASP C 433 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP C 434 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.723A pdb=" N LYS C 820 " --> pdb=" O ASN C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 852 removed outlier: 3.732A pdb=" N LEU C 852 " --> pdb=" O VAL C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 917 through 923 removed outlier: 3.723A pdb=" N SER C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 937 removed outlier: 3.621A pdb=" N ALA C 932 " --> pdb=" O ASP C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 959 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.508A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1014 Processing helix chain 'C' and resid 1016 through 1020 removed outlier: 3.624A pdb=" N ALA C1020 " --> pdb=" O VAL C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1047 removed outlier: 3.755A pdb=" N ASN C1043 " --> pdb=" O GLN C1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1058 removed outlier: 4.111A pdb=" N THR C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C1054 " --> pdb=" O THR C1050 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C1055 " --> pdb=" O GLN C1051 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C1057 " --> pdb=" O THR C1053 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS C1058 " --> pdb=" O VAL C1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1049 through 1058' Processing helix chain 'C' and resid 1066 through 1072 Processing helix chain 'C' and resid 1075 through 1122 removed outlier: 3.957A pdb=" N GLU C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1198 removed outlier: 4.385A pdb=" N HIS C1197 " --> pdb=" O LEU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 Processing helix chain 'C' and resid 1247 through 1254 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 removed outlier: 4.869A pdb=" N LEU A 107 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 322 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 441 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 320 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 443 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 318 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.337A pdb=" N ASN A 445 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 281 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 443 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 283 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 441 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 285 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP A 439 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 452 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.494A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 388 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 6.987A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 716 " --> pdb=" O HIS A 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.165A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 532 through 536 removed outlier: 6.737A pdb=" N TYR A 619 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 590 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 621 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 588 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 623 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A 625 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A 584 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 532 through 536 removed outlier: 7.308A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 removed outlier: 4.244A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 782 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1166 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 797 removed outlier: 4.135A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1220 through 1223 Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 184 removed outlier: 3.757A pdb=" N TYR B 181 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 175 " --> pdb=" O TYR B 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 154 removed outlier: 4.872A pdb=" N LEU B 107 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 322 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 441 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 320 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER B 443 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA B 318 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 3.516A pdb=" N SER B 275 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN B 445 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 281 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 443 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 283 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 441 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 285 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP B 439 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 462 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 452 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG B 460 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.502A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 388 " --> pdb=" O CYS B 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 483 through 488 removed outlier: 6.993A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 716 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.157A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 532 through 536 removed outlier: 6.739A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 532 through 536 removed outlier: 7.306A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 619 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 599 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 781 through 786 removed outlier: 3.684A pdb=" N ILE B 782 " --> pdb=" O VAL B1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B1166 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 797 removed outlier: 4.131A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD4, first strand: chain 'B' and resid 880 through 883 removed outlier: 6.491A pdb=" N SER B 881 " --> pdb=" O LYS B 893 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 893 " --> pdb=" O SER B 881 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 883 " --> pdb=" O VAL B 891 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1220 through 1223 Processing sheet with id=AD6, first strand: chain 'B' and resid 1187 through 1191 Processing sheet with id=AD7, first strand: chain 'C' and resid 46 through 51 Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.601A pdb=" N TYR C 181 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 148 through 154 removed outlier: 4.880A pdb=" N LEU C 107 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN C 322 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 441 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 320 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER C 443 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA C 318 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 270 through 286 removed outlier: 3.534A pdb=" N SER C 275 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 449 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 462 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 452 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 295 through 298 removed outlier: 4.501A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 388 " --> pdb=" O CYS C 373 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 483 through 488 removed outlier: 6.802A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 716 " --> pdb=" O HIS C 737 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.167A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 532 through 536 removed outlier: 6.738A pdb=" N TYR C 619 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 590 " --> pdb=" O TYR C 619 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 621 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 588 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR C 623 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 625 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER C 584 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 532 through 536 removed outlier: 7.304A pdb=" N LEU C 603 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 617 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 601 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 619 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 599 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AE9, first strand: chain 'C' and resid 781 through 786 removed outlier: 3.673A pdb=" N ILE C 782 " --> pdb=" O VAL C1166 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1166 " --> pdb=" O ILE C 782 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 789 through 797 removed outlier: 4.127A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF3, first strand: chain 'C' and resid 880 through 883 removed outlier: 6.496A pdb=" N SER C 881 " --> pdb=" O LYS C 893 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 893 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 883 " --> pdb=" O VAL C 891 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1220 through 1223 Processing sheet with id=AF5, first strand: chain 'C' and resid 1187 through 1191 1167 hydrogen bonds defined for protein. 3180 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: 13.92 Time building geometry restraints manager: 17.44 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: 9399 1.34 - 1.46: 7875 1.46 - 1.58: 13959 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 31386 Sorted by residual: bond pdb=" C1 NAG C1403 " pdb=" O5 NAG C1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG B1403 " pdb=" O5 NAG B1403 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 31381 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 703 106.37 - 113.29: 18284 113.29 - 120.20: 10157 120.20 - 127.12: 13391 127.12 - 134.03: 230 Bond angle restraints: 42765 Sorted by residual: angle pdb=" N VAL A 674 " pdb=" CA VAL A 674 " pdb=" C VAL A 674 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N GLN A 993 " pdb=" CA GLN A 993 " pdb=" CB GLN A 993 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N GLN B 993 " pdb=" CA GLN B 993 " pdb=" CB GLN B 993 " ideal model delta sigma weight residual 114.17 109.85 4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N GLN C 993 " pdb=" CA GLN C 993 " pdb=" CB GLN C 993 " ideal model delta sigma weight residual 114.17 109.89 4.28 1.14e+00 7.69e-01 1.41e+01 angle pdb=" C GLY A1135 " pdb=" N ASP A1136 " pdb=" CA ASP A1136 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.42e+00 ... (remaining 42760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 18953 24.52 - 49.04: 1131 49.04 - 73.56: 307 73.56 - 98.08: 351 98.08 - 122.60: 321 Dihedral angle restraints: 21063 sinusoidal: 10419 harmonic: 10644 Sorted by residual: dihedral pdb=" CB CYS B 464 " pdb=" SG CYS B 464 " pdb=" SG CYS B 473 " pdb=" CB CYS B 473 " ideal model delta sinusoidal sigma weight residual 93.00 164.46 -71.46 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C 464 " pdb=" SG CYS C 464 " pdb=" SG CYS C 473 " pdb=" CB CYS C 473 " ideal model delta sinusoidal sigma weight residual 93.00 163.83 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 464 " pdb=" SG CYS A 464 " pdb=" SG CYS A 473 " pdb=" CB CYS A 473 " ideal model delta sinusoidal sigma weight residual 93.00 162.49 -69.49 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 21060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 5435 0.143 - 0.286: 97 0.286 - 0.429: 12 0.429 - 0.572: 0 0.572 - 0.715: 3 Chirality restraints: 5547 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN C 726 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 5544 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 902 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.55e+00 pdb=" CG PHE C 902 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 902 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 902 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 902 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 902 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 902 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 902 " 0.010 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 902 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 902 " 0.010 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE B 902 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 902 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 902 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 902 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 639 2.67 - 3.22: 29797 3.22 - 3.78: 47305 3.78 - 4.34: 60996 4.34 - 4.90: 96196 Nonbonded interactions: 234933 Sorted by model distance: nonbonded pdb=" OG1 THR A 167 " pdb=" OG1 THR A 174 " model vdw 2.107 2.440 nonbonded pdb=" OG1 THR C 167 " pdb=" OG1 THR C 174 " model vdw 2.118 2.440 nonbonded pdb=" OG1 THR B 167 " pdb=" OG1 THR B 174 " model vdw 2.157 2.440 nonbonded pdb=" O ASP B 899 " pdb=" ND2 ASN B 903 " model vdw 2.167 2.520 nonbonded pdb=" O ASP C 899 " pdb=" ND2 ASN C 903 " model vdw 2.169 2.520 ... (remaining 234928 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' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'S' selection = chain 'U' selection = chain 'h' selection = chain 'j' } ncs_group { reference = (chain 'E' and resid 1 through 4) selection = (chain 'J' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) selection = (chain 'M' and resid 1 through 4) selection = (chain 'N' and resid 1 through 4) selection = (chain 'O' and resid 1 through 4) selection = (chain 'Q' and resid 1 through 4) selection = (chain 'T' and resid 1 through 4) selection = (chain 'Y' and resid 1 through 4) selection = (chain 'Z' and resid 1 through 4) selection = (chain 'a' and resid 1 through 4) selection = (chain 'b' and resid 1 through 4) selection = (chain 'c' and resid 1 through 4) selection = (chain 'd' and resid 1 through 4) selection = (chain 'f' and resid 1 through 4) selection = (chain 'i' and resid 1 through 4) selection = (chain 'n' and resid 1 through 4) selection = (chain 'o' and resid 1 through 4) selection = (chain 'p' and resid 1 through 4) selection = (chain 'q' and resid 1 through 4) selection = (chain 'r' and resid 1 through 4) selection = (chain 's' and resid 1 through 4) selection = (chain 'u' and resid 1 through 4) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'X' selection = chain 'm' } 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 group one per residue 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: 0.770 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: 0.060 Extract box with map and model: 4.400 Check model and map are aligned: 0.460 Set scattering table: 0.250 Process input model: 86.600 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.005 0.073 31386 Z= 0.304 Angle : 0.834 7.895 42765 Z= 0.358 Chirality : 0.059 0.715 5547 Planarity : 0.003 0.031 5205 Dihedral : 25.500 122.597 14142 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3666 helix: 0.56 (0.19), residues: 783 sheet: 0.46 (0.17), residues: 924 loop : -1.30 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 168 HIS 0.004 0.000 HIS B 737 PHE 0.028 0.001 PHE C 902 TYR 0.012 0.001 TYR B 291 ARG 0.004 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.7865 (m-80) cc_final: 0.7658 (m-80) REVERT: A 215 LEU cc_start: 0.9043 (mm) cc_final: 0.8769 (mm) REVERT: A 644 MET cc_start: 0.7555 (ppp) cc_final: 0.6889 (ppp) REVERT: A 1040 GLU cc_start: 0.9336 (tp30) cc_final: 0.9015 (tp30) REVERT: A 1074 LEU cc_start: 0.7872 (tt) cc_final: 0.7621 (tt) REVERT: A 1117 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8944 (tp-100) REVERT: B 204 MET cc_start: 0.8714 (ppp) cc_final: 0.8431 (tmm) REVERT: B 563 TYR cc_start: 0.8965 (m-80) cc_final: 0.8713 (m-80) REVERT: B 644 MET cc_start: 0.7507 (ppp) cc_final: 0.7223 (ppp) REVERT: B 939 MET cc_start: 0.8665 (mmp) cc_final: 0.7927 (mmp) REVERT: B 1040 GLU cc_start: 0.9337 (tp30) cc_final: 0.9088 (tp30) REVERT: B 1074 LEU cc_start: 0.8464 (tt) cc_final: 0.8262 (tt) REVERT: B 1117 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8953 (tp40) REVERT: C 176 PHE cc_start: 0.9038 (m-80) cc_final: 0.8717 (m-80) REVERT: C 180 ILE cc_start: 0.9230 (tp) cc_final: 0.8992 (tp) REVERT: C 181 TYR cc_start: 0.7966 (m-80) cc_final: 0.7757 (m-80) REVERT: C 563 TYR cc_start: 0.8778 (m-80) cc_final: 0.8503 (m-80) REVERT: C 644 MET cc_start: 0.7150 (ppp) cc_final: 0.6886 (ppp) REVERT: C 938 VAL cc_start: 0.9635 (t) cc_final: 0.9425 (t) REVERT: C 939 MET cc_start: 0.8872 (mmp) cc_final: 0.8125 (mmm) REVERT: C 1040 GLU cc_start: 0.9354 (tp30) cc_final: 0.9085 (tp30) REVERT: C 1117 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8775 (tp40) REVERT: C 1220 PHE cc_start: 0.9085 (m-80) cc_final: 0.8854 (m-80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3235 time to fit residues: 124.5311 Evaluate side-chains 154 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 286 optimal weight: 0.0980 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 GLN A1061 GLN A1149 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 GLN B1061 GLN ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN C1023 GLN C1061 GLN ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1149 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 31386 Z= 0.256 Angle : 0.761 10.260 42765 Z= 0.345 Chirality : 0.052 0.438 5547 Planarity : 0.003 0.026 5205 Dihedral : 23.448 107.554 8019 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3666 helix: 0.38 (0.18), residues: 807 sheet: 0.28 (0.16), residues: 966 loop : -1.33 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 168 HIS 0.006 0.001 HIS B1155 PHE 0.034 0.001 PHE C 902 TYR 0.017 0.001 TYR C 413 ARG 0.004 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 3.367 Fit side-chains revert: symmetry clash REVERT: A 176 PHE cc_start: 0.9010 (m-80) cc_final: 0.8705 (m-80) REVERT: A 180 ILE cc_start: 0.9283 (tp) cc_final: 0.9070 (tp) REVERT: A 181 TYR cc_start: 0.8041 (m-80) cc_final: 0.7818 (m-80) REVERT: A 644 MET cc_start: 0.7759 (ppp) cc_final: 0.7097 (ppp) REVERT: A 939 MET cc_start: 0.8896 (mmp) cc_final: 0.8380 (mmm) REVERT: A 1040 GLU cc_start: 0.9366 (tp30) cc_final: 0.8903 (tm-30) REVERT: A 1074 LEU cc_start: 0.8145 (tt) cc_final: 0.7861 (tt) REVERT: A 1117 GLN cc_start: 0.9260 (tp-100) cc_final: 0.9007 (tp-100) REVERT: B 563 TYR cc_start: 0.8964 (m-80) cc_final: 0.8745 (m-80) REVERT: B 644 MET cc_start: 0.7535 (ppp) cc_final: 0.7083 (ppp) REVERT: B 939 MET cc_start: 0.8632 (mmp) cc_final: 0.8089 (mmm) REVERT: B 1040 GLU cc_start: 0.9378 (tp30) cc_final: 0.9108 (tp30) REVERT: B 1074 LEU cc_start: 0.8516 (tt) cc_final: 0.8259 (tt) REVERT: B 1117 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8859 (tp40) REVERT: C 176 PHE cc_start: 0.9075 (m-80) cc_final: 0.8777 (m-80) REVERT: C 180 ILE cc_start: 0.9237 (tp) cc_final: 0.9024 (tp) REVERT: C 181 TYR cc_start: 0.8058 (m-80) cc_final: 0.7783 (m-80) REVERT: C 291 TYR cc_start: 0.7610 (m-80) cc_final: 0.7163 (m-80) REVERT: C 563 TYR cc_start: 0.8898 (m-80) cc_final: 0.8599 (m-80) REVERT: C 644 MET cc_start: 0.7640 (ppp) cc_final: 0.7148 (ppp) REVERT: C 939 MET cc_start: 0.8851 (mmp) cc_final: 0.8274 (mmm) REVERT: C 1040 GLU cc_start: 0.9445 (tp30) cc_final: 0.9162 (tp30) REVERT: C 1074 LEU cc_start: 0.8268 (tp) cc_final: 0.7884 (tt) REVERT: C 1117 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8177 (tp-100) REVERT: C 1121 GLU cc_start: 0.8146 (pt0) cc_final: 0.7263 (pt0) REVERT: C 1220 PHE cc_start: 0.9168 (m-80) cc_final: 0.8789 (m-80) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.3309 time to fit residues: 116.0518 Evaluate side-chains 154 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 332 optimal weight: 0.0070 chunk 359 optimal weight: 0.8980 chunk 296 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN A1095 ASN B1061 GLN B1095 ASN ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1095 ASN ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31386 Z= 0.163 Angle : 0.720 9.604 42765 Z= 0.314 Chirality : 0.052 0.433 5547 Planarity : 0.003 0.032 5205 Dihedral : 20.698 110.111 8019 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3666 helix: 0.46 (0.18), residues: 813 sheet: 0.36 (0.17), residues: 927 loop : -1.30 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 168 HIS 0.002 0.000 HIS A 737 PHE 0.039 0.001 PHE A 902 TYR 0.016 0.001 TYR A 105 ARG 0.012 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 644 MET cc_start: 0.7798 (ppp) cc_final: 0.7068 (ppp) REVERT: A 939 MET cc_start: 0.8738 (mmp) cc_final: 0.8277 (mmm) REVERT: A 1040 GLU cc_start: 0.9333 (tp30) cc_final: 0.9085 (tp30) REVERT: A 1074 LEU cc_start: 0.8067 (tt) cc_final: 0.7776 (tt) REVERT: A 1117 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8953 (tp40) REVERT: A 1220 PHE cc_start: 0.9036 (m-80) cc_final: 0.8653 (m-80) REVERT: B 291 TYR cc_start: 0.8093 (m-80) cc_final: 0.7491 (m-80) REVERT: B 563 TYR cc_start: 0.8924 (m-80) cc_final: 0.8714 (m-80) REVERT: B 644 MET cc_start: 0.7677 (ppp) cc_final: 0.7175 (ppp) REVERT: B 939 MET cc_start: 0.8493 (mmp) cc_final: 0.7984 (mmm) REVERT: B 1040 GLU cc_start: 0.9339 (tp30) cc_final: 0.9084 (tp30) REVERT: B 1074 LEU cc_start: 0.8448 (tt) cc_final: 0.8122 (tt) REVERT: B 1117 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8734 (tp-100) REVERT: C 176 PHE cc_start: 0.9066 (m-80) cc_final: 0.8776 (m-80) REVERT: C 181 TYR cc_start: 0.8113 (m-80) cc_final: 0.7830 (m-80) REVERT: C 291 TYR cc_start: 0.7479 (m-10) cc_final: 0.6897 (m-80) REVERT: C 563 TYR cc_start: 0.8806 (m-80) cc_final: 0.8523 (m-80) REVERT: C 644 MET cc_start: 0.7482 (ppp) cc_final: 0.6994 (ppp) REVERT: C 845 SER cc_start: 0.9469 (t) cc_final: 0.9208 (t) REVERT: C 939 MET cc_start: 0.8673 (mmp) cc_final: 0.8032 (mmm) REVERT: C 1040 GLU cc_start: 0.9416 (tp30) cc_final: 0.9157 (tp30) REVERT: C 1074 LEU cc_start: 0.8628 (tp) cc_final: 0.8144 (tt) REVERT: C 1117 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8805 (tp-100) REVERT: C 1220 PHE cc_start: 0.9092 (m-80) cc_final: 0.8675 (m-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3532 time to fit residues: 125.6781 Evaluate side-chains 151 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 334 optimal weight: 0.9990 chunk 353 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 316 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS A1061 GLN B1061 GLN C1061 GLN ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31386 Z= 0.205 Angle : 0.735 9.624 42765 Z= 0.325 Chirality : 0.053 0.424 5547 Planarity : 0.003 0.033 5205 Dihedral : 18.357 109.575 8019 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3666 helix: 0.53 (0.18), residues: 810 sheet: 0.32 (0.17), residues: 927 loop : -1.31 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 168 HIS 0.004 0.001 HIS A1155 PHE 0.041 0.001 PHE A 902 TYR 0.010 0.001 TYR C 413 ARG 0.010 0.000 ARG C 994 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 3.380 Fit side-chains REVERT: A 176 PHE cc_start: 0.8996 (m-80) cc_final: 0.8640 (m-80) REVERT: A 644 MET cc_start: 0.7901 (ppp) cc_final: 0.7070 (ppp) REVERT: A 939 MET cc_start: 0.8665 (mmp) cc_final: 0.8284 (mmm) REVERT: A 1074 LEU cc_start: 0.8217 (tt) cc_final: 0.7901 (tt) REVERT: A 1117 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8889 (tp-100) REVERT: A 1220 PHE cc_start: 0.9026 (m-80) cc_final: 0.8628 (m-80) REVERT: B 291 TYR cc_start: 0.8231 (m-80) cc_final: 0.7436 (m-80) REVERT: B 563 TYR cc_start: 0.8933 (m-80) cc_final: 0.8725 (m-80) REVERT: B 644 MET cc_start: 0.7897 (ppp) cc_final: 0.7301 (ppp) REVERT: B 1074 LEU cc_start: 0.8496 (tt) cc_final: 0.8174 (tt) REVERT: C 149 LEU cc_start: 0.9411 (tp) cc_final: 0.9184 (tp) REVERT: C 180 ILE cc_start: 0.9313 (tp) cc_final: 0.9096 (tp) REVERT: C 181 TYR cc_start: 0.8161 (m-80) cc_final: 0.7915 (m-80) REVERT: C 291 TYR cc_start: 0.7569 (m-10) cc_final: 0.7021 (m-80) REVERT: C 563 TYR cc_start: 0.8866 (m-80) cc_final: 0.8548 (m-80) REVERT: C 644 MET cc_start: 0.7613 (ppp) cc_final: 0.7010 (ppp) REVERT: C 782 ILE cc_start: 0.9120 (tt) cc_final: 0.8771 (mm) REVERT: C 939 MET cc_start: 0.8600 (mmp) cc_final: 0.8104 (mmm) REVERT: C 1040 GLU cc_start: 0.9449 (tp30) cc_final: 0.9223 (tp30) REVERT: C 1074 LEU cc_start: 0.8311 (tp) cc_final: 0.7889 (tt) REVERT: C 1117 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8662 (tp-100) REVERT: C 1220 PHE cc_start: 0.9165 (m-80) cc_final: 0.8732 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3431 time to fit residues: 118.5042 Evaluate side-chains 146 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 263 optimal weight: 0.0970 chunk 145 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 317 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1095 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 429 HIS B1061 GLN B1095 ASN B1117 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS C1061 GLN C1095 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31386 Z= 0.300 Angle : 0.789 9.707 42765 Z= 0.362 Chirality : 0.053 0.397 5547 Planarity : 0.004 0.058 5205 Dihedral : 16.829 112.858 8019 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3666 helix: 0.23 (0.18), residues: 807 sheet: 0.09 (0.16), residues: 894 loop : -1.47 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 168 HIS 0.011 0.002 HIS C1155 PHE 0.047 0.002 PHE C 902 TYR 0.014 0.002 TYR B 751 ARG 0.019 0.001 ARG B 994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.8969 (m-80) cc_final: 0.8575 (m-80) REVERT: A 180 ILE cc_start: 0.9304 (tp) cc_final: 0.9095 (tp) REVERT: A 181 TYR cc_start: 0.8268 (m-80) cc_final: 0.7993 (m-80) REVERT: A 291 TYR cc_start: 0.8025 (m-80) cc_final: 0.7473 (m-80) REVERT: A 644 MET cc_start: 0.8028 (ppp) cc_final: 0.7101 (ppp) REVERT: A 939 MET cc_start: 0.8462 (mmp) cc_final: 0.8038 (mmm) REVERT: A 1074 LEU cc_start: 0.8261 (tt) cc_final: 0.8026 (tt) REVERT: A 1117 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8835 (tp-100) REVERT: A 1220 PHE cc_start: 0.9168 (m-80) cc_final: 0.8759 (m-80) REVERT: B 563 TYR cc_start: 0.8974 (m-80) cc_final: 0.8651 (m-80) REVERT: B 644 MET cc_start: 0.8165 (ppp) cc_final: 0.7472 (ppp) REVERT: B 1117 GLN cc_start: 0.9049 (tp40) cc_final: 0.8791 (tp40) REVERT: C 180 ILE cc_start: 0.9264 (tp) cc_final: 0.9030 (tp) REVERT: C 181 TYR cc_start: 0.8370 (m-80) cc_final: 0.8141 (m-80) REVERT: C 291 TYR cc_start: 0.7625 (m-10) cc_final: 0.7413 (m-80) REVERT: C 563 TYR cc_start: 0.8879 (m-80) cc_final: 0.8523 (m-80) REVERT: C 644 MET cc_start: 0.7995 (ppp) cc_final: 0.7204 (ppp) REVERT: C 1074 LEU cc_start: 0.8379 (tp) cc_final: 0.8024 (tt) REVERT: C 1117 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8667 (tp-100) REVERT: C 1220 PHE cc_start: 0.9282 (m-80) cc_final: 0.8875 (m-80) outliers start: 2 outliers final: 2 residues processed: 175 average time/residue: 0.3359 time to fit residues: 105.3461 Evaluate side-chains 141 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 277 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31386 Z= 0.184 Angle : 0.739 9.641 42765 Z= 0.327 Chirality : 0.053 0.416 5547 Planarity : 0.003 0.036 5205 Dihedral : 15.916 115.726 8019 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3666 helix: 0.41 (0.18), residues: 807 sheet: 0.30 (0.17), residues: 894 loop : -1.47 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 168 HIS 0.002 0.001 HIS A 737 PHE 0.027 0.001 PHE B 902 TYR 0.014 0.001 TYR B 291 ARG 0.013 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.437 Fit side-chains REVERT: A 176 PHE cc_start: 0.8967 (m-80) cc_final: 0.8577 (m-80) REVERT: A 181 TYR cc_start: 0.8237 (m-80) cc_final: 0.7972 (m-80) REVERT: A 291 TYR cc_start: 0.7897 (m-80) cc_final: 0.7350 (m-80) REVERT: A 644 MET cc_start: 0.8014 (ppp) cc_final: 0.7049 (ppp) REVERT: A 939 MET cc_start: 0.8390 (mmp) cc_final: 0.7994 (mmm) REVERT: A 1074 LEU cc_start: 0.8186 (tt) cc_final: 0.7888 (tt) REVERT: A 1220 PHE cc_start: 0.9134 (m-80) cc_final: 0.8743 (m-80) REVERT: B 91 PHE cc_start: 0.7898 (m-80) cc_final: 0.7116 (m-10) REVERT: B 291 TYR cc_start: 0.8003 (m-80) cc_final: 0.7294 (m-80) REVERT: B 563 TYR cc_start: 0.8918 (m-80) cc_final: 0.8598 (m-80) REVERT: B 644 MET cc_start: 0.8173 (ppp) cc_final: 0.7433 (ppp) REVERT: B 1074 LEU cc_start: 0.8581 (tt) cc_final: 0.8349 (tt) REVERT: B 1117 GLN cc_start: 0.8968 (tp40) cc_final: 0.8619 (tp-100) REVERT: C 149 LEU cc_start: 0.9438 (tp) cc_final: 0.9238 (tp) REVERT: C 180 ILE cc_start: 0.9247 (tp) cc_final: 0.9033 (tp) REVERT: C 181 TYR cc_start: 0.8356 (m-80) cc_final: 0.8116 (m-80) REVERT: C 563 TYR cc_start: 0.8795 (m-80) cc_final: 0.8437 (m-80) REVERT: C 644 MET cc_start: 0.7991 (ppp) cc_final: 0.7160 (ppp) REVERT: C 782 ILE cc_start: 0.9181 (tt) cc_final: 0.8656 (mm) REVERT: C 1074 LEU cc_start: 0.8340 (tp) cc_final: 0.7961 (tt) REVERT: C 1117 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8521 (tp-100) REVERT: C 1220 PHE cc_start: 0.9217 (m-80) cc_final: 0.8793 (m-80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3430 time to fit residues: 113.4631 Evaluate side-chains 142 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 201 optimal weight: 0.7980 chunk 258 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 215 optimal weight: 0.0470 chunk 162 optimal weight: 20.0000 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1095 ASN A1117 GLN B 97 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1095 ASN C 97 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS C1061 GLN C1095 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31386 Z= 0.181 Angle : 0.734 9.683 42765 Z= 0.322 Chirality : 0.052 0.424 5547 Planarity : 0.003 0.036 5205 Dihedral : 15.131 115.222 8019 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3666 helix: 0.54 (0.18), residues: 807 sheet: 0.26 (0.16), residues: 921 loop : -1.46 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.003 0.001 HIS A1155 PHE 0.023 0.001 PHE A 902 TYR 0.018 0.001 TYR C 413 ARG 0.005 0.001 ARG C1235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.972 Fit side-chains REVERT: A 149 LEU cc_start: 0.9462 (tp) cc_final: 0.9248 (tp) REVERT: A 176 PHE cc_start: 0.9014 (m-80) cc_final: 0.8645 (m-80) REVERT: A 181 TYR cc_start: 0.8246 (m-80) cc_final: 0.8003 (m-80) REVERT: A 291 TYR cc_start: 0.7902 (m-80) cc_final: 0.7586 (m-80) REVERT: A 644 MET cc_start: 0.8078 (ppp) cc_final: 0.7069 (ppp) REVERT: A 819 CYS cc_start: 0.9119 (m) cc_final: 0.8731 (p) REVERT: A 1074 LEU cc_start: 0.8278 (tt) cc_final: 0.7992 (tt) REVERT: A 1220 PHE cc_start: 0.9108 (m-80) cc_final: 0.8692 (m-80) REVERT: B 291 TYR cc_start: 0.8055 (m-80) cc_final: 0.7437 (m-80) REVERT: B 563 TYR cc_start: 0.8908 (m-80) cc_final: 0.8589 (m-80) REVERT: B 644 MET cc_start: 0.8188 (ppp) cc_final: 0.7473 (ppp) REVERT: B 1074 LEU cc_start: 0.8578 (tt) cc_final: 0.8326 (tt) REVERT: B 1117 GLN cc_start: 0.8940 (tp40) cc_final: 0.8589 (tp-100) REVERT: C 149 LEU cc_start: 0.9410 (tp) cc_final: 0.9192 (tp) REVERT: C 180 ILE cc_start: 0.9314 (tp) cc_final: 0.9081 (tp) REVERT: C 181 TYR cc_start: 0.8365 (m-80) cc_final: 0.8144 (m-80) REVERT: C 563 TYR cc_start: 0.8785 (m-80) cc_final: 0.8427 (m-80) REVERT: C 644 MET cc_start: 0.8000 (ppp) cc_final: 0.7140 (ppp) REVERT: C 782 ILE cc_start: 0.9100 (tt) cc_final: 0.8547 (mm) REVERT: C 939 MET cc_start: 0.7459 (mpp) cc_final: 0.7075 (mpp) REVERT: C 1074 LEU cc_start: 0.8348 (tp) cc_final: 0.8004 (tt) REVERT: C 1117 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8491 (tp-100) REVERT: C 1209 MET cc_start: 0.8399 (mmm) cc_final: 0.8180 (mmp) REVERT: C 1220 PHE cc_start: 0.9210 (m-80) cc_final: 0.8771 (m-80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3326 time to fit residues: 104.9863 Evaluate side-chains 146 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 277 optimal weight: 50.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1095 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1095 ASN ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1095 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31386 Z= 0.260 Angle : 0.776 9.737 42765 Z= 0.352 Chirality : 0.053 0.401 5547 Planarity : 0.004 0.049 5205 Dihedral : 14.430 113.528 8019 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3666 helix: 0.50 (0.18), residues: 792 sheet: 0.03 (0.16), residues: 927 loop : -1.55 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 168 HIS 0.006 0.001 HIS A1155 PHE 0.026 0.002 PHE A 902 TYR 0.017 0.001 TYR B 291 ARG 0.008 0.001 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.462 Fit side-chains REVERT: A 149 LEU cc_start: 0.9532 (tp) cc_final: 0.9330 (tp) REVERT: A 176 PHE cc_start: 0.8966 (m-80) cc_final: 0.8682 (m-80) REVERT: A 180 ILE cc_start: 0.9287 (tp) cc_final: 0.9080 (tp) REVERT: A 181 TYR cc_start: 0.8329 (m-80) cc_final: 0.8062 (m-80) REVERT: A 291 TYR cc_start: 0.8088 (m-80) cc_final: 0.7552 (m-80) REVERT: A 644 MET cc_start: 0.8137 (ppp) cc_final: 0.7089 (ppp) REVERT: A 939 MET cc_start: 0.8584 (mmp) cc_final: 0.8045 (mmm) REVERT: A 1074 LEU cc_start: 0.8220 (tt) cc_final: 0.7952 (tt) REVERT: A 1117 GLN cc_start: 0.9206 (tp40) cc_final: 0.8832 (tp-100) REVERT: A 1220 PHE cc_start: 0.9230 (m-80) cc_final: 0.8826 (m-80) REVERT: B 291 TYR cc_start: 0.8325 (m-80) cc_final: 0.7906 (m-80) REVERT: B 563 TYR cc_start: 0.9010 (m-80) cc_final: 0.8668 (m-80) REVERT: B 644 MET cc_start: 0.8297 (ppp) cc_final: 0.7540 (ppp) REVERT: B 844 GLU cc_start: 0.8843 (pp20) cc_final: 0.8617 (pp20) REVERT: B 1074 LEU cc_start: 0.8681 (tt) cc_final: 0.8445 (tt) REVERT: C 149 LEU cc_start: 0.9472 (tp) cc_final: 0.9271 (tp) REVERT: C 180 ILE cc_start: 0.9275 (tp) cc_final: 0.9046 (tp) REVERT: C 181 TYR cc_start: 0.8440 (m-80) cc_final: 0.8218 (m-80) REVERT: C 291 TYR cc_start: 0.7487 (m-80) cc_final: 0.6984 (m-80) REVERT: C 563 TYR cc_start: 0.8894 (m-80) cc_final: 0.8527 (m-80) REVERT: C 644 MET cc_start: 0.8189 (ppp) cc_final: 0.7283 (ppp) REVERT: C 658 LYS cc_start: 0.9258 (ptpt) cc_final: 0.8933 (pttt) REVERT: C 939 MET cc_start: 0.7498 (mpp) cc_final: 0.7106 (mpp) REVERT: C 1074 LEU cc_start: 0.8497 (tp) cc_final: 0.8157 (tt) REVERT: C 1117 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8611 (tp-100) REVERT: C 1220 PHE cc_start: 0.9301 (m-80) cc_final: 0.8871 (m-80) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3612 time to fit residues: 111.0933 Evaluate side-chains 141 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 3.9990 chunk 337 optimal weight: 0.5980 chunk 308 optimal weight: 0.7980 chunk 328 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 327 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN B1095 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31386 Z= 0.191 Angle : 0.755 9.745 42765 Z= 0.332 Chirality : 0.052 0.413 5547 Planarity : 0.003 0.036 5205 Dihedral : 13.666 113.910 8019 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3666 helix: 0.62 (0.18), residues: 792 sheet: 0.19 (0.16), residues: 918 loop : -1.53 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 168 HIS 0.003 0.001 HIS B1197 PHE 0.019 0.001 PHE C 896 TYR 0.018 0.001 TYR C 413 ARG 0.005 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.363 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.9521 (tp) cc_final: 0.9313 (tp) REVERT: A 176 PHE cc_start: 0.9005 (m-80) cc_final: 0.8753 (m-80) REVERT: A 180 ILE cc_start: 0.9256 (tp) cc_final: 0.9035 (tp) REVERT: A 181 TYR cc_start: 0.8327 (m-80) cc_final: 0.8086 (m-80) REVERT: A 291 TYR cc_start: 0.7998 (m-80) cc_final: 0.7501 (m-80) REVERT: A 644 MET cc_start: 0.8122 (ppp) cc_final: 0.7065 (ppp) REVERT: A 819 CYS cc_start: 0.9137 (m) cc_final: 0.8809 (p) REVERT: A 939 MET cc_start: 0.8588 (mmp) cc_final: 0.8082 (mmm) REVERT: A 1074 LEU cc_start: 0.8148 (tt) cc_final: 0.7847 (tt) REVERT: A 1117 GLN cc_start: 0.9134 (tp40) cc_final: 0.8824 (tp-100) REVERT: A 1209 MET cc_start: 0.8847 (mmp) cc_final: 0.8643 (mmp) REVERT: A 1220 PHE cc_start: 0.9217 (m-80) cc_final: 0.8814 (m-80) REVERT: B 91 PHE cc_start: 0.7636 (m-80) cc_final: 0.6667 (m-80) REVERT: B 291 TYR cc_start: 0.8267 (m-80) cc_final: 0.7852 (m-80) REVERT: B 563 TYR cc_start: 0.8993 (m-80) cc_final: 0.8637 (m-80) REVERT: B 644 MET cc_start: 0.8287 (ppp) cc_final: 0.7520 (ppp) REVERT: B 819 CYS cc_start: 0.9244 (m) cc_final: 0.8466 (p) REVERT: B 844 GLU cc_start: 0.8890 (pp20) cc_final: 0.8679 (pp20) REVERT: B 1074 LEU cc_start: 0.8640 (tt) cc_final: 0.8380 (tt) REVERT: B 1102 LEU cc_start: 0.9690 (pt) cc_final: 0.9402 (mp) REVERT: C 180 ILE cc_start: 0.9309 (tp) cc_final: 0.9072 (tp) REVERT: C 181 TYR cc_start: 0.8508 (m-80) cc_final: 0.8291 (m-80) REVERT: C 291 TYR cc_start: 0.7859 (m-80) cc_final: 0.7589 (m-80) REVERT: C 563 TYR cc_start: 0.8821 (m-80) cc_final: 0.8467 (m-80) REVERT: C 644 MET cc_start: 0.8183 (ppp) cc_final: 0.7322 (ppp) REVERT: C 658 LYS cc_start: 0.9247 (ptpt) cc_final: 0.8686 (pttt) REVERT: C 782 ILE cc_start: 0.9057 (tt) cc_final: 0.8491 (mm) REVERT: C 939 MET cc_start: 0.7539 (mpp) cc_final: 0.7114 (mpp) REVERT: C 1074 LEU cc_start: 0.8483 (tp) cc_final: 0.8132 (tt) REVERT: C 1117 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8524 (tp-100) REVERT: C 1220 PHE cc_start: 0.9268 (m-80) cc_final: 0.8792 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3503 time to fit residues: 114.4539 Evaluate side-chains 150 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 1.9990 chunk 347 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 335 optimal weight: 0.9990 chunk 290 optimal weight: 0.2980 chunk 30 optimal weight: 30.0000 chunk 224 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 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 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN A1095 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1095 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31386 Z= 0.176 Angle : 0.741 9.687 42765 Z= 0.325 Chirality : 0.051 0.426 5547 Planarity : 0.003 0.034 5205 Dihedral : 12.553 112.606 8019 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3666 helix: 0.70 (0.18), residues: 792 sheet: 0.35 (0.17), residues: 888 loop : -1.50 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 168 HIS 0.004 0.001 HIS C 270 PHE 0.019 0.001 PHE C 896 TYR 0.018 0.001 TYR C 413 ARG 0.004 0.000 ARG B 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.019 Fit side-chains REVERT: A 176 PHE cc_start: 0.8998 (m-80) cc_final: 0.8768 (m-80) REVERT: A 181 TYR cc_start: 0.8315 (m-80) cc_final: 0.8058 (m-80) REVERT: A 291 TYR cc_start: 0.7950 (m-80) cc_final: 0.7524 (m-80) REVERT: A 644 MET cc_start: 0.8148 (ppp) cc_final: 0.7173 (ppp) REVERT: A 819 CYS cc_start: 0.9129 (m) cc_final: 0.8786 (p) REVERT: A 939 MET cc_start: 0.8501 (mmp) cc_final: 0.8040 (mmm) REVERT: A 1074 LEU cc_start: 0.8292 (tt) cc_final: 0.8007 (tt) REVERT: A 1117 GLN cc_start: 0.9227 (tp40) cc_final: 0.8863 (tp-100) REVERT: A 1209 MET cc_start: 0.8898 (mmp) cc_final: 0.8678 (mmp) REVERT: A 1220 PHE cc_start: 0.9181 (m-80) cc_final: 0.8741 (m-80) REVERT: B 91 PHE cc_start: 0.7635 (m-80) cc_final: 0.6712 (m-80) REVERT: B 174 THR cc_start: 0.8736 (p) cc_final: 0.8468 (p) REVERT: B 291 TYR cc_start: 0.8232 (m-80) cc_final: 0.7848 (m-80) REVERT: B 563 TYR cc_start: 0.8935 (m-80) cc_final: 0.8564 (m-80) REVERT: B 644 MET cc_start: 0.8242 (ppp) cc_final: 0.7432 (ppp) REVERT: B 658 LYS cc_start: 0.9212 (ptpt) cc_final: 0.8796 (pttt) REVERT: B 819 CYS cc_start: 0.9209 (m) cc_final: 0.8415 (p) REVERT: B 844 GLU cc_start: 0.8929 (pp20) cc_final: 0.8725 (pp20) REVERT: B 1074 LEU cc_start: 0.8577 (tt) cc_final: 0.8302 (tt) REVERT: B 1102 LEU cc_start: 0.9677 (pt) cc_final: 0.9368 (mp) REVERT: B 1117 GLN cc_start: 0.9022 (tp40) cc_final: 0.8778 (tp-100) REVERT: C 149 LEU cc_start: 0.9457 (tp) cc_final: 0.9245 (tp) REVERT: C 176 PHE cc_start: 0.9116 (m-80) cc_final: 0.8903 (m-80) REVERT: C 181 TYR cc_start: 0.8467 (m-80) cc_final: 0.8260 (m-80) REVERT: C 563 TYR cc_start: 0.8772 (m-80) cc_final: 0.8408 (m-80) REVERT: C 644 MET cc_start: 0.8148 (ppp) cc_final: 0.7298 (ppp) REVERT: C 658 LYS cc_start: 0.9231 (ptpt) cc_final: 0.8813 (pttt) REVERT: C 782 ILE cc_start: 0.9051 (tt) cc_final: 0.8560 (mm) REVERT: C 1074 LEU cc_start: 0.8614 (tp) cc_final: 0.8252 (tt) REVERT: C 1117 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8509 (tp40) REVERT: C 1220 PHE cc_start: 0.9239 (m-80) cc_final: 0.8716 (m-80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3354 time to fit residues: 114.2064 Evaluate side-chains 158 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 36 optimal weight: 0.0170 chunk 53 optimal weight: 20.0000 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C 270 HIS ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.073049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050810 restraints weight = 175036.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052391 restraints weight = 119911.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053508 restraints weight = 93409.517| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31386 Z= 0.176 Angle : 0.725 10.325 42765 Z= 0.321 Chirality : 0.050 0.425 5547 Planarity : 0.003 0.036 5205 Dihedral : 11.620 111.233 8019 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 3666 helix: 0.77 (0.19), residues: 786 sheet: 0.38 (0.17), residues: 900 loop : -1.47 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 168 HIS 0.006 0.001 HIS C 270 PHE 0.020 0.001 PHE C 896 TYR 0.018 0.001 TYR C 413 ARG 0.004 0.001 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.97 seconds wall clock time: 85 minutes 5.18 seconds (5105.18 seconds total)