Starting phenix.real_space_refine on Sun Aug 24 16:52:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fr6_29396/08_2025/8fr6_29396.map" } resolution = 2.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 129 5.16 5 C 13248 2.51 5 N 3426 2.21 5 O 4434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21237 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "I" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.97, per 1000 atoms: 0.23 Number of scatterers: 21237 At special positions: 0 Unit cell: (154.38, 146.08, 126.16, 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 129 16.00 O 4434 8.00 N 3426 7.00 C 13248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN e 4 " - " MAN e 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA k 3 " - " MAN k 4 " " BMA p 3 " - " MAN p 4 " " BMA s 3 " - " MAN s 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 6 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 6 " " BMA k 3 " - " MAN k 5 " " BMA p 3 " - " MAN p 5 " " BMA s 3 " - " MAN s 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 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 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 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 X 2 " - " BMA X 3 " " 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " 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 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " 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 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " 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-ASN " NAG 0 1 " - " ASN I 160 " " NAG 1 1 " - " ASN I 392 " " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 137 " " NAG I 603 " - " ASN I 339 " " NAG I 604 " - " ASN I 355 " " NAG M 1 " - " ASN C 133 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 197 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 276 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 160 " " NAG Z 1 " - " ASN C 392 " " NAG a 1 " - " ASN G 133 " " NAG b 1 " - " ASN G 156 " " NAG c 1 " - " ASN G 197 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 262 " " NAG f 1 " - " ASN G 276 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " " NAG j 1 " - " ASN G 363 " " NAG k 1 " - " ASN G 386 " " NAG l 1 " - " ASN G 448 " " NAG m 1 " - " ASN G 160 " " NAG n 1 " - " ASN G 392 " " NAG o 1 " - " ASN I 133 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 234 " " NAG s 1 " - " ASN I 262 " " NAG t 1 " - " ASN I 276 " " NAG u 1 " - " ASN I 295 " " NAG v 1 " - " ASN I 301 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 363 " " NAG y 1 " - " ASN I 386 " " NAG z 1 " - " ASN I 448 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 763.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 21.4% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 4.101A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.102A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.737A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.852A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.102A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.736A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.851A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 101 through 115 Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.737A pdb=" N ARG I 151 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 354 removed outlier: 3.897A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 4.255A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.851A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.251A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.252A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.562A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.189A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.483A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.264A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.904A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS G 201 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 177 removed outlier: 4.563A pdb=" N GLU G 190 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.190A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.190A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.484A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 121 through 122 removed outlier: 4.325A pdb=" N CYS I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 169 through 177 removed outlier: 4.562A pdb=" N GLU I 190 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.364A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.190A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 11.190A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.483A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU D 10 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.239A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.239A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.393A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.310A pdb=" N GLU J 10 " --> pdb=" O ILE J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.238A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.394A pdb=" N GLY K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 14 removed outlier: 4.394A pdb=" N GLY K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2178 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: 5.77 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6386 1.34 - 1.47: 5725 1.47 - 1.59: 9354 1.59 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 21639 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" N ARG C 500 " pdb=" CA ARG C 500 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.44e-02 4.82e+03 4.69e+00 bond pdb=" N ARG I 500 " pdb=" CA ARG I 500 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.44e-02 4.82e+03 4.65e+00 ... (remaining 21634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 27657 1.42 - 2.83: 1204 2.83 - 4.25: 306 4.25 - 5.67: 134 5.67 - 7.08: 63 Bond angle restraints: 29364 Sorted by residual: angle pdb=" C ARG G 500 " pdb=" CA ARG G 500 " pdb=" CB ARG G 500 " ideal model delta sigma weight residual 110.72 103.64 7.08 1.77e+00 3.19e-01 1.60e+01 angle pdb=" C ARG I 500 " pdb=" CA ARG I 500 " pdb=" CB ARG I 500 " ideal model delta sigma weight residual 110.72 103.64 7.08 1.77e+00 3.19e-01 1.60e+01 angle pdb=" C ARG C 500 " pdb=" CA ARG C 500 " pdb=" CB ARG C 500 " ideal model delta sigma weight residual 110.72 103.66 7.06 1.77e+00 3.19e-01 1.59e+01 angle pdb=" N CYS I 501 " pdb=" CA CYS I 501 " pdb=" C CYS I 501 " ideal model delta sigma weight residual 110.48 115.13 -4.65 1.48e+00 4.57e-01 9.87e+00 angle pdb=" N CYS G 501 " pdb=" CA CYS G 501 " pdb=" C CYS G 501 " ideal model delta sigma weight residual 110.48 115.11 -4.63 1.48e+00 4.57e-01 9.79e+00 ... (remaining 29359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 13204 22.00 - 44.00: 1172 44.00 - 66.00: 255 66.00 - 87.99: 228 87.99 - 109.99: 138 Dihedral angle restraints: 14997 sinusoidal: 7950 harmonic: 7047 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.22 53.78 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS G 501 " pdb=" CB CYS G 501 " ideal model delta sinusoidal sigma weight residual 93.00 39.38 53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 14994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3136 0.059 - 0.119: 504 0.119 - 0.178: 98 0.178 - 0.237: 3 0.237 - 0.296: 33 Chirality restraints: 3774 Sorted by residual: chirality pdb=" C5 BMA y 3 " pdb=" C4 BMA y 3 " pdb=" C6 BMA y 3 " pdb=" O5 BMA y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C5 BMA k 3 " pdb=" C4 BMA k 3 " pdb=" C6 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3771 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 43 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO L 44 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 43 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO K 44 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO K 44 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 44 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 43 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO E 44 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " -0.021 5.00e-02 4.00e+02 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 446 2.68 - 3.24: 20228 3.24 - 3.79: 32574 3.79 - 4.35: 45562 4.35 - 4.90: 73237 Nonbonded interactions: 172047 Sorted by model distance: nonbonded pdb=" O GLN D 1 " pdb=" NE2 GLN D 1 " model vdw 2.125 3.120 nonbonded pdb=" O GLN H 1 " pdb=" NE2 GLN H 1 " model vdw 2.126 3.120 nonbonded pdb=" O GLN J 1 " pdb=" NE2 GLN J 1 " model vdw 2.126 3.120 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR I 139 " pdb=" OD1 ASP I 141 " model vdw 2.221 3.040 ... (remaining 172042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'T' selection = chain 'a' selection = chain 'c' selection = chain 'h' selection = chain 'o' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'b' selection = chain 'k' selection = chain 'p' selection = chain 'y' } ncs_group { reference = chain 'Q' selection = chain 'e' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.120 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.830 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.047 21840 Z= 0.245 Angle : 0.831 10.600 29925 Z= 0.343 Chirality : 0.054 0.296 3774 Planarity : 0.004 0.042 3504 Dihedral : 22.072 109.992 10335 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.98 % Allowed : 20.51 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 2406 helix: 0.96 (0.27), residues: 468 sheet: 0.35 (0.19), residues: 732 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 504 TYR 0.011 0.001 TYR E 49 PHE 0.007 0.001 PHE C 53 TRP 0.018 0.001 TRP C 35 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00500 (21639) covalent geometry : angle 0.79221 (29364) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.04256 ( 84) hydrogen bonds : bond 0.19226 ( 771) hydrogen bonds : angle 8.29329 ( 2178) link_ALPHA1-2 : bond 0.00305 ( 3) link_ALPHA1-2 : angle 1.88420 ( 9) link_ALPHA1-3 : bond 0.00242 ( 9) link_ALPHA1-3 : angle 1.92905 ( 27) link_ALPHA1-6 : bond 0.00525 ( 9) link_ALPHA1-6 : angle 1.53590 ( 27) link_BETA1-4 : bond 0.00658 ( 75) link_BETA1-4 : angle 2.50601 ( 225) link_NAG-ASN : bond 0.00179 ( 63) link_NAG-ASN : angle 1.67912 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.8324 (tp30) cc_final: 0.8113 (tp30) REVERT: G 356 ASN cc_start: 0.8789 (p0) cc_final: 0.8568 (p0) REVERT: I 356 ASN cc_start: 0.8720 (p0) cc_final: 0.8495 (p0) REVERT: D 64 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.7491 (mtm-85) REVERT: H 64 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7567 (mtm-85) REVERT: J 32 TYR cc_start: 0.7785 (m-80) cc_final: 0.7252 (m-80) outliers start: 21 outliers final: 18 residues processed: 301 average time/residue: 0.6479 time to fit residues: 221.4613 Evaluate side-chains 252 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN A 656 ASN A 658 GLN B 652 GLN B 656 ASN F 652 GLN F 656 ASN F 658 GLN I 411 ASN D 1 GLN D 96 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 96 GLN L 30 ASN J 1 GLN K 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064577 restraints weight = 40555.716| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.61 r_work: 0.2726 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21840 Z= 0.182 Angle : 0.732 9.183 29925 Z= 0.340 Chirality : 0.047 0.269 3774 Planarity : 0.004 0.049 3504 Dihedral : 15.543 77.391 5879 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.43 % Allowed : 21.07 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2406 helix: 1.27 (0.26), residues: 456 sheet: 0.26 (0.18), residues: 759 loop : 0.17 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 500 TYR 0.029 0.002 TYR H 27 PHE 0.012 0.001 PHE C 53 TRP 0.009 0.001 TRP I 96 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00413 (21639) covalent geometry : angle 0.68066 (29364) SS BOND : bond 0.00709 ( 42) SS BOND : angle 1.34721 ( 84) hydrogen bonds : bond 0.04283 ( 771) hydrogen bonds : angle 5.66958 ( 2178) link_ALPHA1-2 : bond 0.00670 ( 3) link_ALPHA1-2 : angle 1.88634 ( 9) link_ALPHA1-3 : bond 0.01092 ( 9) link_ALPHA1-3 : angle 2.18724 ( 27) link_ALPHA1-6 : bond 0.00543 ( 9) link_ALPHA1-6 : angle 1.73863 ( 27) link_BETA1-4 : bond 0.00765 ( 75) link_BETA1-4 : angle 2.48436 ( 225) link_NAG-ASN : bond 0.00391 ( 63) link_NAG-ASN : angle 1.86804 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 356 ASN cc_start: 0.8908 (p0) cc_final: 0.8596 (p0) REVERT: G 356 ASN cc_start: 0.8883 (p0) cc_final: 0.8615 (p0) REVERT: I 356 ASN cc_start: 0.8862 (p0) cc_final: 0.8554 (p0) REVERT: D 31 ASP cc_start: 0.8440 (t0) cc_final: 0.8015 (t0) REVERT: D 96 GLN cc_start: 0.7355 (mt0) cc_final: 0.6928 (mt0) REVERT: E 32 TYR cc_start: 0.6541 (m-80) cc_final: 0.6089 (m-80) REVERT: E 75 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.4944 (mp) REVERT: H 31 ASP cc_start: 0.8453 (t0) cc_final: 0.8117 (t0) REVERT: H 64 ARG cc_start: 0.6393 (ttp-170) cc_final: 0.5967 (mtm-85) REVERT: H 96 GLN cc_start: 0.7408 (mt0) cc_final: 0.7104 (mt0) REVERT: L 48 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6664 (mm) REVERT: L 75 ILE cc_start: 0.5207 (OUTLIER) cc_final: 0.4798 (mp) REVERT: J 31 ASP cc_start: 0.8568 (t0) cc_final: 0.7869 (t0) REVERT: J 96 GLN cc_start: 0.7378 (tt0) cc_final: 0.6930 (tp40) REVERT: K 36 TYR cc_start: 0.6824 (m-80) cc_final: 0.6466 (m-80) REVERT: K 48 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6939 (mm) REVERT: K 75 ILE cc_start: 0.5442 (OUTLIER) cc_final: 0.5053 (mp) outliers start: 52 outliers final: 16 residues processed: 285 average time/residue: 0.5989 time to fit residues: 195.6258 Evaluate side-chains 266 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN C 94 ASN G 94 ASN I 94 ASN I 411 ASN D 30 ASN D 43 HIS E 30 ASN J 30 ASN J 43 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065548 restraints weight = 40586.242| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.63 r_work: 0.2755 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21840 Z= 0.132 Angle : 0.666 9.581 29925 Z= 0.307 Chirality : 0.046 0.249 3774 Planarity : 0.004 0.045 3504 Dihedral : 11.344 67.731 5851 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.25 % Allowed : 22.71 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2406 helix: 1.47 (0.26), residues: 456 sheet: 0.17 (0.18), residues: 762 loop : 0.25 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 500 TYR 0.027 0.002 TYR L 49 PHE 0.014 0.001 PHE H 63 TRP 0.009 0.001 TRP A 631 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00291 (21639) covalent geometry : angle 0.61793 (29364) SS BOND : bond 0.00282 ( 42) SS BOND : angle 0.81773 ( 84) hydrogen bonds : bond 0.03611 ( 771) hydrogen bonds : angle 5.20385 ( 2178) link_ALPHA1-2 : bond 0.00632 ( 3) link_ALPHA1-2 : angle 1.74769 ( 9) link_ALPHA1-3 : bond 0.01138 ( 9) link_ALPHA1-3 : angle 1.49732 ( 27) link_ALPHA1-6 : bond 0.00620 ( 9) link_ALPHA1-6 : angle 1.68114 ( 27) link_BETA1-4 : bond 0.00701 ( 75) link_BETA1-4 : angle 2.30139 ( 225) link_NAG-ASN : bond 0.00235 ( 63) link_NAG-ASN : angle 1.84814 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8872 (p0) cc_final: 0.8556 (p0) REVERT: C 416 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8127 (pp) REVERT: G 114 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: G 356 ASN cc_start: 0.8824 (p0) cc_final: 0.8555 (p0) REVERT: I 100 MET cc_start: 0.8843 (ptm) cc_final: 0.8618 (ptp) REVERT: I 356 ASN cc_start: 0.8832 (p0) cc_final: 0.8573 (p0) REVERT: D 28 LYS cc_start: 0.8411 (pmtt) cc_final: 0.8064 (ptmm) REVERT: D 31 ASP cc_start: 0.8599 (t0) cc_final: 0.8289 (p0) REVERT: D 32 TYR cc_start: 0.7807 (m-80) cc_final: 0.7429 (m-10) REVERT: D 64 ARG cc_start: 0.6662 (ttm170) cc_final: 0.6429 (mtm-85) REVERT: D 96 GLN cc_start: 0.7569 (mt0) cc_final: 0.7364 (tp40) REVERT: E 32 TYR cc_start: 0.6613 (m-80) cc_final: 0.6188 (m-80) REVERT: E 58 VAL cc_start: 0.5821 (OUTLIER) cc_final: 0.5549 (p) REVERT: E 75 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4840 (mp) REVERT: H 39 GLN cc_start: 0.8329 (tp40) cc_final: 0.8107 (tp-100) REVERT: H 64 ARG cc_start: 0.6337 (ttp-170) cc_final: 0.5927 (mtm-85) REVERT: H 96 GLN cc_start: 0.7647 (mt0) cc_final: 0.7408 (mt0) REVERT: L 48 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6820 (mm) REVERT: L 75 ILE cc_start: 0.4768 (OUTLIER) cc_final: 0.4475 (mp) REVERT: J 94 ARG cc_start: 0.8408 (ptt180) cc_final: 0.8043 (ptt180) REVERT: J 96 GLN cc_start: 0.7539 (tt0) cc_final: 0.7276 (tt0) REVERT: K 48 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6854 (mm) REVERT: K 75 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.4956 (mp) outliers start: 48 outliers final: 20 residues processed: 289 average time/residue: 0.5144 time to fit residues: 170.6950 Evaluate side-chains 271 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.0870 chunk 99 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 215 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN C 103 GLN I 103 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 43 HIS L 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.063213 restraints weight = 40483.547| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.63 r_work: 0.2693 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21840 Z= 0.230 Angle : 0.710 9.972 29925 Z= 0.330 Chirality : 0.047 0.261 3774 Planarity : 0.004 0.047 3504 Dihedral : 9.212 58.737 5850 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.23 % Allowed : 21.91 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2406 helix: 1.36 (0.26), residues: 459 sheet: 0.16 (0.18), residues: 759 loop : 0.15 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 617 TYR 0.030 0.002 TYR H 27 PHE 0.013 0.001 PHE C 383 TRP 0.016 0.001 TRP G 35 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00536 (21639) covalent geometry : angle 0.65994 (29364) SS BOND : bond 0.00290 ( 42) SS BOND : angle 0.89552 ( 84) hydrogen bonds : bond 0.04207 ( 771) hydrogen bonds : angle 5.19606 ( 2178) link_ALPHA1-2 : bond 0.00460 ( 3) link_ALPHA1-2 : angle 1.77773 ( 9) link_ALPHA1-3 : bond 0.01115 ( 9) link_ALPHA1-3 : angle 1.71963 ( 27) link_ALPHA1-6 : bond 0.00741 ( 9) link_ALPHA1-6 : angle 1.62780 ( 27) link_BETA1-4 : bond 0.00653 ( 75) link_BETA1-4 : angle 2.32467 ( 225) link_NAG-ASN : bond 0.00525 ( 63) link_NAG-ASN : angle 2.10828 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8891 (p0) cc_final: 0.8551 (p0) REVERT: F 655 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7662 (ttpp) REVERT: G 114 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: G 356 ASN cc_start: 0.8853 (p0) cc_final: 0.8570 (p0) REVERT: G 504 ARG cc_start: 0.7194 (mmm-85) cc_final: 0.6643 (mmt90) REVERT: I 356 ASN cc_start: 0.8853 (p0) cc_final: 0.8540 (p0) REVERT: D 39 GLN cc_start: 0.7445 (tp-100) cc_final: 0.7212 (tp40) REVERT: D 59 TYR cc_start: 0.7277 (m-80) cc_final: 0.7060 (m-80) REVERT: D 96 GLN cc_start: 0.7760 (mt0) cc_final: 0.7366 (tt0) REVERT: E 30 ASN cc_start: 0.6334 (t0) cc_final: 0.5826 (t0) REVERT: E 32 TYR cc_start: 0.6772 (m-80) cc_final: 0.6011 (m-80) REVERT: E 58 VAL cc_start: 0.5782 (OUTLIER) cc_final: 0.5557 (p) REVERT: H 3 GLN cc_start: 0.7840 (pp30) cc_final: 0.7640 (pp30) REVERT: H 28 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9013 (pmtt) REVERT: H 31 ASP cc_start: 0.8766 (t0) cc_final: 0.8210 (t0) REVERT: H 32 TYR cc_start: 0.7993 (m-10) cc_final: 0.7489 (m-10) REVERT: H 39 GLN cc_start: 0.8316 (tp40) cc_final: 0.8080 (tp40) REVERT: H 64 ARG cc_start: 0.6417 (ttp-170) cc_final: 0.5921 (mtm-85) REVERT: H 95 LEU cc_start: 0.8453 (tp) cc_final: 0.8097 (tm) REVERT: L 32 TYR cc_start: 0.6790 (m-80) cc_final: 0.6070 (m-80) REVERT: L 48 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6950 (mm) REVERT: L 75 ILE cc_start: 0.4608 (OUTLIER) cc_final: 0.4319 (mp) REVERT: J 28 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9045 (pmtt) REVERT: J 31 ASP cc_start: 0.8804 (t0) cc_final: 0.8256 (t0) REVERT: J 32 TYR cc_start: 0.7933 (m-80) cc_final: 0.7628 (m-10) REVERT: J 96 GLN cc_start: 0.7675 (tt0) cc_final: 0.7412 (mt0) REVERT: K 30 ASN cc_start: 0.6519 (t0) cc_final: 0.6166 (t0) REVERT: K 48 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6807 (mm) REVERT: K 50 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8468 (tptp) outliers start: 69 outliers final: 33 residues processed: 291 average time/residue: 0.5690 time to fit residues: 189.4517 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 184 optimal weight: 0.1980 chunk 190 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 0.0040 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.119010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065712 restraints weight = 40333.718| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.62 r_work: 0.2753 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21840 Z= 0.117 Angle : 0.632 9.587 29925 Z= 0.296 Chirality : 0.044 0.251 3774 Planarity : 0.004 0.049 3504 Dihedral : 8.282 56.089 5850 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.29 % Allowed : 23.17 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2406 helix: 1.52 (0.26), residues: 459 sheet: 0.21 (0.18), residues: 747 loop : 0.22 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 61 TYR 0.055 0.002 TYR L 49 PHE 0.014 0.001 PHE C 53 TRP 0.008 0.001 TRP I 96 HIS 0.002 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00251 (21639) covalent geometry : angle 0.58831 (29364) SS BOND : bond 0.00219 ( 42) SS BOND : angle 0.72158 ( 84) hydrogen bonds : bond 0.03212 ( 771) hydrogen bonds : angle 4.96192 ( 2178) link_ALPHA1-2 : bond 0.00561 ( 3) link_ALPHA1-2 : angle 1.81011 ( 9) link_ALPHA1-3 : bond 0.01190 ( 9) link_ALPHA1-3 : angle 1.58955 ( 27) link_ALPHA1-6 : bond 0.00874 ( 9) link_ALPHA1-6 : angle 1.72282 ( 27) link_BETA1-4 : bond 0.00632 ( 75) link_BETA1-4 : angle 1.97352 ( 225) link_NAG-ASN : bond 0.00211 ( 63) link_NAG-ASN : angle 1.93230 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8510 (pt0) cc_final: 0.8269 (pm20) REVERT: C 72 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7467 (m-70) REVERT: C 356 ASN cc_start: 0.8854 (p0) cc_final: 0.8542 (p0) REVERT: C 416 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8092 (pp) REVERT: C 504 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6567 (mmt90) REVERT: F 571 TRP cc_start: 0.7453 (m-10) cc_final: 0.7242 (m-10) REVERT: F 655 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7604 (ttpp) REVERT: G 114 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: G 356 ASN cc_start: 0.8795 (p0) cc_final: 0.8515 (p0) REVERT: G 504 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6544 (mmt90) REVERT: I 356 ASN cc_start: 0.8798 (p0) cc_final: 0.8508 (p0) REVERT: I 504 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6559 (mmt90) REVERT: D 28 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8991 (pmtt) REVERT: D 31 ASP cc_start: 0.8890 (t0) cc_final: 0.8178 (t0) REVERT: D 32 TYR cc_start: 0.7943 (m-10) cc_final: 0.6945 (m-10) REVERT: D 39 GLN cc_start: 0.7461 (tp-100) cc_final: 0.7238 (tp40) REVERT: D 59 TYR cc_start: 0.7292 (m-80) cc_final: 0.7058 (m-80) REVERT: D 96 GLN cc_start: 0.7805 (mt0) cc_final: 0.7372 (tt0) REVERT: E 30 ASN cc_start: 0.6301 (t0) cc_final: 0.5750 (t0) REVERT: E 32 TYR cc_start: 0.6844 (m-80) cc_final: 0.5927 (m-80) REVERT: E 48 ILE cc_start: 0.7875 (mm) cc_final: 0.7619 (mm) REVERT: E 83 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7068 (mm) REVERT: H 28 LYS cc_start: 0.9215 (ptmm) cc_final: 0.8945 (pmtt) REVERT: H 31 ASP cc_start: 0.8764 (t0) cc_final: 0.8175 (t0) REVERT: H 32 TYR cc_start: 0.8047 (m-80) cc_final: 0.7461 (m-10) REVERT: H 64 ARG cc_start: 0.6356 (ttp-170) cc_final: 0.5959 (mtm-85) REVERT: H 94 ARG cc_start: 0.8462 (ptt180) cc_final: 0.8005 (ptt180) REVERT: H 96 GLN cc_start: 0.7665 (mt0) cc_final: 0.7364 (mt0) REVERT: L 32 TYR cc_start: 0.6905 (m-80) cc_final: 0.5998 (m-80) REVERT: L 48 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7829 (mm) REVERT: L 50 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8603 (tmmt) REVERT: L 75 ILE cc_start: 0.4566 (OUTLIER) cc_final: 0.4339 (mp) REVERT: L 83 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7027 (mm) REVERT: L 93 HIS cc_start: 0.8554 (m90) cc_final: 0.8180 (m-70) REVERT: J 28 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9011 (pmtt) REVERT: J 31 ASP cc_start: 0.8780 (t0) cc_final: 0.8358 (t0) REVERT: J 32 TYR cc_start: 0.7887 (m-80) cc_final: 0.7563 (m-10) REVERT: J 94 ARG cc_start: 0.8321 (ptt180) cc_final: 0.8036 (ptt180) REVERT: J 95 LEU cc_start: 0.8461 (tp) cc_final: 0.8116 (tm) REVERT: J 96 GLN cc_start: 0.7794 (tt0) cc_final: 0.7276 (tp-100) REVERT: K 30 ASN cc_start: 0.6625 (t0) cc_final: 0.6239 (t0) REVERT: K 48 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6797 (mm) REVERT: K 50 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8460 (tptp) REVERT: K 83 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6879 (mm) outliers start: 49 outliers final: 19 residues processed: 290 average time/residue: 0.6097 time to fit residues: 202.7152 Evaluate side-chains 276 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064934 restraints weight = 40491.806| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.60 r_work: 0.2735 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21840 Z= 0.139 Angle : 0.633 9.742 29925 Z= 0.294 Chirality : 0.044 0.258 3774 Planarity : 0.003 0.048 3504 Dihedral : 7.760 56.381 5850 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 23.41 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2406 helix: 1.55 (0.26), residues: 459 sheet: 0.17 (0.18), residues: 756 loop : 0.31 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 61 TYR 0.031 0.002 TYR E 49 PHE 0.013 0.001 PHE C 53 TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00315 (21639) covalent geometry : angle 0.59093 (29364) SS BOND : bond 0.00225 ( 42) SS BOND : angle 0.69681 ( 84) hydrogen bonds : bond 0.03357 ( 771) hydrogen bonds : angle 4.87061 ( 2178) link_ALPHA1-2 : bond 0.00492 ( 3) link_ALPHA1-2 : angle 1.78723 ( 9) link_ALPHA1-3 : bond 0.01155 ( 9) link_ALPHA1-3 : angle 1.61778 ( 27) link_ALPHA1-6 : bond 0.00951 ( 9) link_ALPHA1-6 : angle 1.66301 ( 27) link_BETA1-4 : bond 0.00635 ( 75) link_BETA1-4 : angle 1.93594 ( 225) link_NAG-ASN : bond 0.00288 ( 63) link_NAG-ASN : angle 1.87312 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8841 (p0) cc_final: 0.8536 (p0) REVERT: C 416 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8207 (pp) REVERT: C 504 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6592 (mmt90) REVERT: F 571 TRP cc_start: 0.7478 (m-10) cc_final: 0.7264 (m-10) REVERT: F 621 GLU cc_start: 0.8669 (pt0) cc_final: 0.8355 (pm20) REVERT: G 114 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: G 356 ASN cc_start: 0.8791 (p0) cc_final: 0.8503 (p0) REVERT: G 504 ARG cc_start: 0.7130 (mmm-85) cc_final: 0.6616 (mmt90) REVERT: I 356 ASN cc_start: 0.8786 (p0) cc_final: 0.8498 (p0) REVERT: I 504 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6673 (mmt90) REVERT: D 28 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9006 (pmtt) REVERT: D 31 ASP cc_start: 0.8892 (t0) cc_final: 0.8285 (t0) REVERT: D 32 TYR cc_start: 0.8006 (m-80) cc_final: 0.6841 (m-10) REVERT: D 59 TYR cc_start: 0.7300 (m-80) cc_final: 0.7088 (m-80) REVERT: D 96 GLN cc_start: 0.7825 (mt0) cc_final: 0.7360 (mt0) REVERT: E 30 ASN cc_start: 0.6672 (t0) cc_final: 0.6135 (t0) REVERT: E 32 TYR cc_start: 0.6777 (m-80) cc_final: 0.5895 (m-80) REVERT: E 83 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7094 (mm) REVERT: H 23 LYS cc_start: 0.8923 (tppp) cc_final: 0.8666 (tppt) REVERT: H 28 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8987 (pmtt) REVERT: H 31 ASP cc_start: 0.8774 (t0) cc_final: 0.8183 (t0) REVERT: H 64 ARG cc_start: 0.6379 (ttp-170) cc_final: 0.5991 (mtm-85) REVERT: H 95 LEU cc_start: 0.8511 (tp) cc_final: 0.8150 (tm) REVERT: H 96 GLN cc_start: 0.7733 (mt0) cc_final: 0.7282 (mt0) REVERT: L 32 TYR cc_start: 0.6763 (m-80) cc_final: 0.5803 (m-80) REVERT: L 48 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7577 (mm) REVERT: L 50 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8531 (tptp) REVERT: L 83 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6966 (mm) REVERT: L 93 HIS cc_start: 0.8511 (m90) cc_final: 0.8158 (m-70) REVERT: J 28 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8929 (pmtt) REVERT: J 31 ASP cc_start: 0.8811 (t0) cc_final: 0.8172 (t0) REVERT: J 32 TYR cc_start: 0.8030 (m-80) cc_final: 0.7632 (m-10) REVERT: J 94 ARG cc_start: 0.8330 (ptt180) cc_final: 0.8085 (ptt180) REVERT: J 96 GLN cc_start: 0.7871 (tt0) cc_final: 0.7626 (mt0) REVERT: K 30 ASN cc_start: 0.6778 (t0) cc_final: 0.6391 (t0) REVERT: K 50 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8496 (tptp) REVERT: K 83 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6871 (mm) outliers start: 60 outliers final: 26 residues processed: 287 average time/residue: 0.6011 time to fit residues: 197.1361 Evaluate side-chains 271 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 232 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 165 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.117155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063135 restraints weight = 40439.249| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.64 r_work: 0.2693 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21840 Z= 0.222 Angle : 0.685 9.959 29925 Z= 0.320 Chirality : 0.046 0.262 3774 Planarity : 0.004 0.050 3504 Dihedral : 7.646 58.358 5850 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.14 % Allowed : 22.85 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2406 helix: 1.51 (0.26), residues: 456 sheet: 0.17 (0.18), residues: 747 loop : 0.24 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.029 0.002 TYR K 49 PHE 0.013 0.001 PHE J 63 TRP 0.013 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00521 (21639) covalent geometry : angle 0.64216 (29364) SS BOND : bond 0.00324 ( 42) SS BOND : angle 0.90381 ( 84) hydrogen bonds : bond 0.03945 ( 771) hydrogen bonds : angle 5.02407 ( 2178) link_ALPHA1-2 : bond 0.00367 ( 3) link_ALPHA1-2 : angle 1.82560 ( 9) link_ALPHA1-3 : bond 0.01051 ( 9) link_ALPHA1-3 : angle 1.62563 ( 27) link_ALPHA1-6 : bond 0.00954 ( 9) link_ALPHA1-6 : angle 1.60679 ( 27) link_BETA1-4 : bond 0.00635 ( 75) link_BETA1-4 : angle 1.96555 ( 225) link_NAG-ASN : bond 0.00489 ( 63) link_NAG-ASN : angle 2.07963 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8456 (pt0) cc_final: 0.8036 (pm20) REVERT: C 356 ASN cc_start: 0.8870 (p0) cc_final: 0.8545 (p0) REVERT: F 571 TRP cc_start: 0.7543 (m-10) cc_final: 0.7326 (m-10) REVERT: F 655 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7521 (tmmm) REVERT: G 114 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: G 308 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8167 (mpt-90) REVERT: G 356 ASN cc_start: 0.8814 (p0) cc_final: 0.8503 (p0) REVERT: I 356 ASN cc_start: 0.8829 (p0) cc_final: 0.8485 (p0) REVERT: D 28 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9018 (pmtt) REVERT: D 31 ASP cc_start: 0.8885 (t0) cc_final: 0.8239 (t0) REVERT: D 32 TYR cc_start: 0.8002 (m-80) cc_final: 0.6982 (m-10) REVERT: D 59 TYR cc_start: 0.7303 (m-80) cc_final: 0.7041 (m-80) REVERT: D 96 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: E 30 ASN cc_start: 0.6734 (t0) cc_final: 0.6260 (t0) REVERT: E 32 TYR cc_start: 0.6829 (m-80) cc_final: 0.5881 (m-80) REVERT: E 83 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7075 (mm) REVERT: H 32 TYR cc_start: 0.7978 (m-10) cc_final: 0.7596 (m-10) REVERT: H 64 ARG cc_start: 0.6346 (ttp-170) cc_final: 0.5959 (mtm-85) REVERT: H 96 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: L 32 TYR cc_start: 0.6664 (m-80) cc_final: 0.5744 (m-80) REVERT: L 50 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8439 (tptp) REVERT: L 83 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6977 (mm) REVERT: J 28 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8912 (pmtt) REVERT: J 95 LEU cc_start: 0.8468 (tp) cc_final: 0.8125 (tm) REVERT: K 30 ASN cc_start: 0.6847 (t0) cc_final: 0.6438 (t0) REVERT: K 50 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8485 (tptp) REVERT: K 83 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6979 (mm) outliers start: 67 outliers final: 35 residues processed: 286 average time/residue: 0.6209 time to fit residues: 202.8838 Evaluate side-chains 274 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 411 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.118087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064623 restraints weight = 40405.253| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.60 r_work: 0.2729 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21840 Z= 0.143 Angle : 0.653 9.703 29925 Z= 0.306 Chirality : 0.044 0.254 3774 Planarity : 0.004 0.085 3504 Dihedral : 7.317 56.498 5850 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.00 % Allowed : 23.64 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2406 helix: 1.52 (0.26), residues: 459 sheet: 0.20 (0.18), residues: 738 loop : 0.26 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG I 504 TYR 0.037 0.002 TYR K 49 PHE 0.013 0.001 PHE K 89 TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00324 (21639) covalent geometry : angle 0.61341 (29364) SS BOND : bond 0.00246 ( 42) SS BOND : angle 0.81467 ( 84) hydrogen bonds : bond 0.03410 ( 771) hydrogen bonds : angle 4.90827 ( 2178) link_ALPHA1-2 : bond 0.00437 ( 3) link_ALPHA1-2 : angle 1.83461 ( 9) link_ALPHA1-3 : bond 0.01101 ( 9) link_ALPHA1-3 : angle 1.58224 ( 27) link_ALPHA1-6 : bond 0.01014 ( 9) link_ALPHA1-6 : angle 1.65817 ( 27) link_BETA1-4 : bond 0.00614 ( 75) link_BETA1-4 : angle 1.83394 ( 225) link_NAG-ASN : bond 0.00276 ( 63) link_NAG-ASN : angle 1.94262 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8514 (pt0) cc_final: 0.8118 (pm20) REVERT: C 268 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: C 356 ASN cc_start: 0.8855 (p0) cc_final: 0.8542 (p0) REVERT: C 416 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8211 (pp) REVERT: F 571 TRP cc_start: 0.7490 (m-10) cc_final: 0.7270 (m-10) REVERT: F 621 GLU cc_start: 0.8631 (pt0) cc_final: 0.8356 (pm20) REVERT: F 655 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7618 (ttpp) REVERT: G 114 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: G 356 ASN cc_start: 0.8787 (p0) cc_final: 0.8496 (p0) REVERT: G 504 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6716 (mmt90) REVERT: I 356 ASN cc_start: 0.8794 (p0) cc_final: 0.8491 (p0) REVERT: I 504 ARG cc_start: 0.7072 (mmm160) cc_final: 0.6616 (mmt-90) REVERT: D 28 LYS cc_start: 0.9300 (ptmm) cc_final: 0.9006 (pmtt) REVERT: D 31 ASP cc_start: 0.8860 (t0) cc_final: 0.8127 (t0) REVERT: D 32 TYR cc_start: 0.8036 (m-80) cc_final: 0.6903 (m-10) REVERT: D 95 LEU cc_start: 0.8569 (tp) cc_final: 0.8243 (tm) REVERT: D 96 GLN cc_start: 0.7835 (mt0) cc_final: 0.7352 (tt0) REVERT: E 30 ASN cc_start: 0.6806 (t0) cc_final: 0.6310 (t0) REVERT: E 32 TYR cc_start: 0.6806 (m-80) cc_final: 0.5724 (m-80) REVERT: E 83 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7095 (mm) REVERT: H 31 ASP cc_start: 0.8658 (t0) cc_final: 0.8405 (p0) REVERT: H 64 ARG cc_start: 0.6374 (ttp-170) cc_final: 0.5979 (mtm-85) REVERT: H 95 LEU cc_start: 0.8439 (tp) cc_final: 0.8082 (tm) REVERT: H 96 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7368 (tp40) REVERT: L 32 TYR cc_start: 0.6718 (m-80) cc_final: 0.5712 (m-80) REVERT: L 50 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8553 (tptp) REVERT: L 83 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6998 (mm) REVERT: L 93 HIS cc_start: 0.8472 (m90) cc_final: 0.8094 (m-70) REVERT: J 28 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8935 (pmtt) REVERT: J 31 ASP cc_start: 0.8777 (t0) cc_final: 0.8300 (t0) REVERT: J 32 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: J 95 LEU cc_start: 0.8484 (tp) cc_final: 0.8152 (tm) REVERT: K 30 ASN cc_start: 0.6896 (t0) cc_final: 0.6515 (t0) REVERT: K 50 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8414 (tptp) REVERT: K 83 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6963 (mm) outliers start: 64 outliers final: 34 residues processed: 293 average time/residue: 0.6184 time to fit residues: 206.4541 Evaluate side-chains 282 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 102 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 183 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 411 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.117905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064546 restraints weight = 40348.715| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.60 r_work: 0.2725 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21840 Z= 0.153 Angle : 0.660 9.769 29925 Z= 0.310 Chirality : 0.044 0.259 3774 Planarity : 0.004 0.089 3504 Dihedral : 7.168 56.339 5850 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.20 % Allowed : 24.49 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.18), residues: 2406 helix: 1.55 (0.26), residues: 459 sheet: 0.23 (0.18), residues: 741 loop : 0.27 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 504 TYR 0.018 0.001 TYR H 32 PHE 0.015 0.001 PHE K 89 TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00350 (21639) covalent geometry : angle 0.62267 (29364) SS BOND : bond 0.00242 ( 42) SS BOND : angle 0.78396 ( 84) hydrogen bonds : bond 0.03434 ( 771) hydrogen bonds : angle 4.89838 ( 2178) link_ALPHA1-2 : bond 0.00416 ( 3) link_ALPHA1-2 : angle 1.80757 ( 9) link_ALPHA1-3 : bond 0.01075 ( 9) link_ALPHA1-3 : angle 1.55333 ( 27) link_ALPHA1-6 : bond 0.01027 ( 9) link_ALPHA1-6 : angle 1.62145 ( 27) link_BETA1-4 : bond 0.00621 ( 75) link_BETA1-4 : angle 1.82431 ( 225) link_NAG-ASN : bond 0.00313 ( 63) link_NAG-ASN : angle 1.91600 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8852 (p0) cc_final: 0.8543 (p0) REVERT: C 416 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8205 (pp) REVERT: F 571 TRP cc_start: 0.7509 (m-10) cc_final: 0.7286 (m-10) REVERT: F 621 GLU cc_start: 0.8648 (pt0) cc_final: 0.8344 (pm20) REVERT: F 655 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7628 (ttpp) REVERT: G 114 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: G 356 ASN cc_start: 0.8780 (p0) cc_final: 0.8470 (p0) REVERT: G 504 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6728 (mmt90) REVERT: I 232 LYS cc_start: 0.8883 (tppt) cc_final: 0.8538 (mmtp) REVERT: I 356 ASN cc_start: 0.8780 (p0) cc_final: 0.8475 (p0) REVERT: I 504 ARG cc_start: 0.7114 (mmm160) cc_final: 0.6694 (mmt90) REVERT: D 23 LYS cc_start: 0.8835 (tppp) cc_final: 0.8551 (tppt) REVERT: D 28 LYS cc_start: 0.9307 (ptmm) cc_final: 0.9005 (pmtt) REVERT: D 31 ASP cc_start: 0.8855 (t0) cc_final: 0.8130 (t0) REVERT: D 32 TYR cc_start: 0.8032 (m-80) cc_final: 0.6805 (m-10) REVERT: D 96 GLN cc_start: 0.7830 (mt0) cc_final: 0.7352 (mt0) REVERT: E 30 ASN cc_start: 0.6833 (t0) cc_final: 0.6325 (t0) REVERT: E 32 TYR cc_start: 0.6708 (m-80) cc_final: 0.5777 (m-80) REVERT: E 83 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7105 (mm) REVERT: H 23 LYS cc_start: 0.8896 (tppp) cc_final: 0.8626 (tppt) REVERT: H 64 ARG cc_start: 0.6375 (ttp-170) cc_final: 0.5986 (mtm-85) REVERT: H 95 LEU cc_start: 0.8446 (tp) cc_final: 0.8085 (tm) REVERT: H 96 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: L 30 ASN cc_start: 0.6239 (t0) cc_final: 0.5778 (t0) REVERT: L 32 TYR cc_start: 0.6650 (m-80) cc_final: 0.5576 (m-80) REVERT: L 50 LYS cc_start: 0.8893 (mmtm) cc_final: 0.8492 (tptp) REVERT: L 83 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7022 (mm) REVERT: L 93 HIS cc_start: 0.8473 (m90) cc_final: 0.8082 (m-70) REVERT: J 31 ASP cc_start: 0.8788 (t0) cc_final: 0.8520 (t0) REVERT: J 32 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: J 95 LEU cc_start: 0.8453 (tp) cc_final: 0.7983 (tm) REVERT: K 30 ASN cc_start: 0.6876 (t0) cc_final: 0.6460 (t0) REVERT: K 49 TYR cc_start: 0.8021 (p90) cc_final: 0.7771 (p90) REVERT: K 50 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8404 (tptp) REVERT: K 83 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6974 (mm) outliers start: 47 outliers final: 35 residues processed: 271 average time/residue: 0.6096 time to fit residues: 189.0422 Evaluate side-chains 278 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.118479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.065487 restraints weight = 40511.405| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.59 r_work: 0.2749 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21840 Z= 0.129 Angle : 0.644 9.663 29925 Z= 0.303 Chirality : 0.044 0.256 3774 Planarity : 0.004 0.079 3504 Dihedral : 6.897 55.253 5850 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.92 % Allowed : 24.77 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2406 helix: 1.60 (0.26), residues: 459 sheet: 0.28 (0.19), residues: 738 loop : 0.28 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 504 TYR 0.036 0.001 TYR E 49 PHE 0.015 0.001 PHE K 89 TRP 0.011 0.001 TRP E 35 HIS 0.002 0.000 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00293 (21639) covalent geometry : angle 0.60863 (29364) SS BOND : bond 0.00209 ( 42) SS BOND : angle 0.72934 ( 84) hydrogen bonds : bond 0.03164 ( 771) hydrogen bonds : angle 4.81184 ( 2178) link_ALPHA1-2 : bond 0.00457 ( 3) link_ALPHA1-2 : angle 1.77482 ( 9) link_ALPHA1-3 : bond 0.01074 ( 9) link_ALPHA1-3 : angle 1.48690 ( 27) link_ALPHA1-6 : bond 0.01069 ( 9) link_ALPHA1-6 : angle 1.60483 ( 27) link_BETA1-4 : bond 0.00618 ( 75) link_BETA1-4 : angle 1.75568 ( 225) link_NAG-ASN : bond 0.00222 ( 63) link_NAG-ASN : angle 1.81168 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8487 (pt0) cc_final: 0.8228 (pm20) REVERT: B 652 GLN cc_start: 0.8247 (tp40) cc_final: 0.8003 (tp40) REVERT: C 356 ASN cc_start: 0.8840 (p0) cc_final: 0.8543 (p0) REVERT: C 416 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (pp) REVERT: C 504 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6636 (mmt-90) REVERT: F 571 TRP cc_start: 0.7464 (m-10) cc_final: 0.7249 (m-10) REVERT: F 621 GLU cc_start: 0.8638 (pt0) cc_final: 0.8337 (pm20) REVERT: F 655 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7595 (ttpp) REVERT: G 114 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: G 356 ASN cc_start: 0.8754 (p0) cc_final: 0.8459 (p0) REVERT: I 232 LYS cc_start: 0.8851 (tppt) cc_final: 0.8517 (mmtp) REVERT: I 356 ASN cc_start: 0.8759 (p0) cc_final: 0.8464 (p0) REVERT: I 504 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6812 (mmt90) REVERT: D 23 LYS cc_start: 0.8840 (tppp) cc_final: 0.8562 (tppt) REVERT: D 28 LYS cc_start: 0.9310 (ptmm) cc_final: 0.8999 (pmtt) REVERT: D 31 ASP cc_start: 0.8846 (t0) cc_final: 0.8079 (t0) REVERT: D 32 TYR cc_start: 0.8015 (m-80) cc_final: 0.6783 (m-10) REVERT: D 59 TYR cc_start: 0.7127 (m-80) cc_final: 0.6750 (m-80) REVERT: D 95 LEU cc_start: 0.8456 (tp) cc_final: 0.8191 (tm) REVERT: D 96 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: E 30 ASN cc_start: 0.6974 (t0) cc_final: 0.6471 (t0) REVERT: E 32 TYR cc_start: 0.6591 (m-80) cc_final: 0.5677 (m-80) REVERT: E 83 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7091 (mm) REVERT: H 23 LYS cc_start: 0.8888 (tppp) cc_final: 0.8640 (tppt) REVERT: H 64 ARG cc_start: 0.6280 (ttp-170) cc_final: 0.5892 (mtm-85) REVERT: H 96 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: L 30 ASN cc_start: 0.6224 (t0) cc_final: 0.5722 (t0) REVERT: L 32 TYR cc_start: 0.6570 (m-80) cc_final: 0.5481 (m-80) REVERT: L 50 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8494 (tptp) REVERT: L 83 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7043 (mm) REVERT: L 93 HIS cc_start: 0.8444 (m90) cc_final: 0.8024 (m-70) REVERT: J 31 ASP cc_start: 0.8757 (t0) cc_final: 0.8198 (t0) REVERT: J 32 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: J 96 GLN cc_start: 0.7837 (mt0) cc_final: 0.7127 (tp40) REVERT: K 30 ASN cc_start: 0.7001 (t0) cc_final: 0.6525 (t0) REVERT: K 32 TYR cc_start: 0.6401 (m-80) cc_final: 0.6158 (m-80) REVERT: K 49 TYR cc_start: 0.7908 (p90) cc_final: 0.7659 (p90) REVERT: K 50 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8355 (tptp) REVERT: K 83 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7091 (mm) outliers start: 41 outliers final: 27 residues processed: 279 average time/residue: 0.6260 time to fit residues: 199.9625 Evaluate side-chains 277 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 231 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 348 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065268 restraints weight = 40443.117| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.59 r_work: 0.2743 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21840 Z= 0.134 Angle : 0.651 9.729 29925 Z= 0.307 Chirality : 0.043 0.257 3774 Planarity : 0.004 0.085 3504 Dihedral : 6.804 55.436 5850 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.92 % Allowed : 25.00 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2406 helix: 1.61 (0.26), residues: 459 sheet: 0.27 (0.19), residues: 744 loop : 0.30 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 504 TYR 0.019 0.001 TYR H 32 PHE 0.022 0.001 PHE J 100A TRP 0.012 0.001 TRP E 35 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00304 (21639) covalent geometry : angle 0.61762 (29364) SS BOND : bond 0.00210 ( 42) SS BOND : angle 0.73174 ( 84) hydrogen bonds : bond 0.03204 ( 771) hydrogen bonds : angle 4.77826 ( 2178) link_ALPHA1-2 : bond 0.00441 ( 3) link_ALPHA1-2 : angle 1.75050 ( 9) link_ALPHA1-3 : bond 0.01036 ( 9) link_ALPHA1-3 : angle 1.46867 ( 27) link_ALPHA1-6 : bond 0.01055 ( 9) link_ALPHA1-6 : angle 1.51974 ( 27) link_BETA1-4 : bond 0.00618 ( 75) link_BETA1-4 : angle 1.75515 ( 225) link_NAG-ASN : bond 0.00262 ( 63) link_NAG-ASN : angle 1.80075 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9346.19 seconds wall clock time: 159 minutes 57.59 seconds (9597.59 seconds total)