Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 18:10:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/04_2023/7w6m_32329.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/04_2023/7w6m_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_32329/04_2023/7w6m_32329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/04_2023/7w6m_32329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/04_2023/7w6m_32329.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6m_32329/04_2023/7w6m_32329.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 15.42, per 1000 atoms: 0.50 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: 16.31 Conformation dependent library (CDL) restraints added in 4.4 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: 2.35 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: 15.38 Time building geometry restraints manager: 17.04 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 - 16.89: 15303 16.89 - 33.79: 1356 33.79 - 50.68: 239 50.68 - 67.57: 55 67.57 - 84.46: 42 Dihedral angle restraints: 16995 sinusoidal: 6351 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 16992 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.240 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 82.690 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.260 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.780 ------------------------------------------------------------------------------- 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 : 13.619 84.464 10074 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 % 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 *********************** 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 : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3241 time to fit residues: 124.8820 Evaluate side-chains 144 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3001 ------------------------------------------------------------------------------- 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 ** C 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8115 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 31386 Z= 0.252 Angle : 0.663 9.396 42765 Z= 0.323 Chirality : 0.049 0.482 5547 Planarity : 0.003 0.025 5205 Dihedral : 4.026 16.927 3951 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.19 % 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: -0.77 (0.14), residues: 3666 helix: 0.39 (0.18), residues: 807 sheet: 0.26 (0.16), residues: 966 loop : -1.33 (0.14), residues: 1893 *********************** 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 201 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 198 average time/residue: 0.3418 time to fit residues: 120.1318 Evaluate side-chains 137 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4513 ------------------------------------------------------------------------------- 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: 0.9980 chunk 103 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS A1061 GLN A1117 GLN B1061 GLN B1095 ASN ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31386 Z= 0.205 Angle : 0.631 9.393 42765 Z= 0.303 Chirality : 0.048 0.479 5547 Planarity : 0.003 0.033 5205 Dihedral : 3.990 20.185 3951 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.00 % 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: -0.83 (0.14), residues: 3666 helix: 0.36 (0.18), residues: 813 sheet: 0.22 (0.17), residues: 927 loop : -1.36 (0.14), residues: 1926 *********************** 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 197 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3768 time to fit residues: 128.9556 Evaluate side-chains 143 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3564 ------------------------------------------------------------------------------- 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: 8.9990 chunk 250 optimal weight: 30.0000 chunk 172 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 chunk 158 optimal weight: 0.0030 chunk 223 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 chunk 353 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1095 ASN C1117 GLN ** C1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 31386 Z= 0.145 Angle : 0.614 9.684 42765 Z= 0.286 Chirality : 0.049 0.499 5547 Planarity : 0.003 0.033 5205 Dihedral : 3.850 20.269 3951 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: -0.66 (0.14), residues: 3666 helix: 0.52 (0.18), residues: 813 sheet: 0.42 (0.17), residues: 921 loop : -1.32 (0.14), residues: 1932 *********************** 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 205 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.735 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3549 time to fit residues: 130.2734 Evaluate side-chains 142 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4181 ------------------------------------------------------------------------------- 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: 0.7980 chunk 200 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 263 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A1061 GLN B 97 GLN B1061 GLN C 97 GLN ** C 903 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: 0.8071 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 31386 Z= 0.145 Angle : 0.605 9.673 42765 Z= 0.282 Chirality : 0.048 0.490 5547 Planarity : 0.003 0.034 5205 Dihedral : 3.851 22.161 3951 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.06 % 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: -0.64 (0.14), residues: 3666 helix: 0.62 (0.18), residues: 807 sheet: 0.36 (0.16), residues: 942 loop : -1.32 (0.14), residues: 1917 *********************** 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 204 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 3.018 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.3693 time to fit residues: 134.1653 Evaluate side-chains 145 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 3.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4995 ------------------------------------------------------------------------------- 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: 10.0000 chunk 318 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN B1061 GLN ** C 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 31386 Z= 0.158 Angle : 0.610 9.645 42765 Z= 0.287 Chirality : 0.048 0.491 5547 Planarity : 0.003 0.034 5205 Dihedral : 3.884 21.150 3951 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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: 0.68 (0.18), residues: 807 sheet: 0.45 (0.17), residues: 924 loop : -1.37 (0.14), residues: 1935 *********************** 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 204 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 3.405 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3391 time to fit residues: 124.1334 Evaluate side-chains 144 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5629 ------------------------------------------------------------------------------- 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: 30.0000 chunk 201 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 200 optimal weight: 0.0570 chunk 298 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 162 optimal weight: 8.9990 overall best weight: 1.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN B1061 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 31386 Z= 0.160 Angle : 0.617 9.656 42765 Z= 0.289 Chirality : 0.049 0.493 5547 Planarity : 0.003 0.034 5205 Dihedral : 3.882 20.535 3951 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.00 % 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: -0.61 (0.14), residues: 3666 helix: 0.75 (0.18), residues: 807 sheet: 0.47 (0.16), residues: 963 loop : -1.42 (0.14), residues: 1896 *********************** 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 202 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3529 time to fit residues: 126.5309 Evaluate side-chains 143 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4275 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 277 optimal weight: 0.0060 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A1061 GLN B 277 GLN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C1061 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 31386 Z= 0.253 Angle : 0.684 9.619 42765 Z= 0.330 Chirality : 0.050 0.488 5547 Planarity : 0.004 0.036 5205 Dihedral : 4.279 21.443 3951 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.00 % 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: -0.83 (0.14), residues: 3666 helix: 0.59 (0.19), residues: 807 sheet: 0.23 (0.17), residues: 924 loop : -1.48 (0.14), residues: 1935 *********************** 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 186 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.557 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3834 time to fit residues: 124.7622 Evaluate side-chains 130 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6244 ------------------------------------------------------------------------------- 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: 4.9990 chunk 337 optimal weight: 0.0670 chunk 308 optimal weight: 0.3980 chunk 328 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** 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 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: 0.8124 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 : 0.002 0.046 31386 Z= 0.158 Angle : 0.648 10.098 42765 Z= 0.303 Chirality : 0.050 0.511 5547 Planarity : 0.003 0.035 5205 Dihedral : 4.134 25.763 3951 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: -0.71 (0.14), residues: 3666 helix: 0.71 (0.19), residues: 804 sheet: 0.39 (0.17), residues: 930 loop : -1.46 (0.13), residues: 1932 *********************** 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 199 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.275 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3596 time to fit residues: 125.6712 Evaluate side-chains 137 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3366 ------------------------------------------------------------------------------- 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: 6.9990 chunk 347 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 335 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 224 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN B 277 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 31386 Z= 0.153 Angle : 0.644 10.022 42765 Z= 0.299 Chirality : 0.049 0.508 5547 Planarity : 0.003 0.036 5205 Dihedral : 4.054 25.940 3951 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: 0.79 (0.18), residues: 801 sheet: 0.48 (0.17), residues: 930 loop : -1.44 (0.13), residues: 1935 ********************** 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 196 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3547 time to fit residues: 124.3576 Evaluate side-chains 143 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4693 ------------------------------------------------------------------------------- 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: 2.9990 chunk 309 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 GLN A1095 ASN B 114 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050589 restraints weight = 187574.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051960 restraints weight = 135182.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052915 restraints weight = 108907.081| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 31386 Z= 0.271 Angle : 0.692 9.591 42765 Z= 0.335 Chirality : 0.050 0.491 5547 Planarity : 0.004 0.035 5205 Dihedral : 4.381 24.962 3951 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.00 % 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: -0.91 (0.14), residues: 3666 helix: 0.55 (0.19), residues: 810 sheet: 0.21 (0.17), residues: 930 loop : -1.57 (0.13), residues: 1926 =============================================================================== Job complete usr+sys time: 4104.74 seconds wall clock time: 78 minutes 52.50 seconds (4732.50 seconds total)