Starting phenix.real_space_refine on Wed Jun 18 16:04:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fr6_29396/06_2025/8fr6_29396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fr6_29396/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fr6_29396/06_2025/8fr6_29396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fr6_29396/06_2025/8fr6_29396.map" model { file = "/net/cci-nas-00/data/ceres_data/8fr6_29396/06_2025/8fr6_29396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fr6_29396/06_2025/8fr6_29396.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.68, per 1000 atoms: 0.69 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: 7.98 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.50 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: 8.55 Time building geometry restraints manager: 9.09 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: 0.07 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: 4.540 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 57.080 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (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 TRP 0.018 0.001 TRP C 35 HIS 0.002 0.001 HIS C 249 PHE 0.007 0.001 PHE C 53 TYR 0.011 0.001 TYR E 49 ARG 0.006 0.000 ARG C 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 63) link_NAG-ASN : angle 1.67912 ( 189) 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_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) hydrogen bonds : bond 0.19226 ( 771) hydrogen bonds : angle 8.29329 ( 2178) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.04256 ( 84) covalent geometry : bond 0.00500 (21639) covalent geometry : angle 0.79221 (29364) *********************** 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 : 2.788 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: 1.2602 time to fit residues: 434.8496 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 : 2.195 ------------------------------------------------------------------------------- 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 202 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 C 94 ASN F 652 GLN F 656 ASN F 658 GLN G 94 ASN I 411 ASN ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 96 GLN L 30 ASN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3916 r_free = 0.3916 target = 0.117645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063386 restraints weight = 40344.674| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.63 r_work: 0.2698 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21840 Z= 0.239 Angle : 0.763 9.724 29925 Z= 0.354 Chirality : 0.049 0.238 3774 Planarity : 0.004 0.048 3504 Dihedral : 15.601 77.348 5879 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.00 % Allowed : 20.74 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2406 helix: 1.15 (0.26), residues: 456 sheet: 0.24 (0.18), residues: 741 loop : 0.07 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 96 HIS 0.005 0.001 HIS D 35 PHE 0.014 0.001 PHE C 383 TYR 0.027 0.002 TYR H 27 ARG 0.007 0.001 ARG C 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 63) link_NAG-ASN : angle 2.01094 ( 189) link_ALPHA1-6 : bond 0.00528 ( 9) link_ALPHA1-6 : angle 1.70878 ( 27) link_BETA1-4 : bond 0.00805 ( 75) link_BETA1-4 : angle 2.53965 ( 225) link_ALPHA1-2 : bond 0.00650 ( 3) link_ALPHA1-2 : angle 1.95821 ( 9) link_ALPHA1-3 : bond 0.00955 ( 9) link_ALPHA1-3 : angle 1.99109 ( 27) hydrogen bonds : bond 0.04709 ( 771) hydrogen bonds : angle 5.74812 ( 2178) SS BOND : bond 0.00587 ( 42) SS BOND : angle 1.16150 ( 84) covalent geometry : bond 0.00558 (21639) covalent geometry : angle 0.71216 (29364) *********************** 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 322 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 2.297 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 356 ASN cc_start: 0.8934 (p0) cc_final: 0.8615 (p0) REVERT: F 655 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7181 (ptpp) REVERT: G 114 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: G 356 ASN cc_start: 0.8892 (p0) cc_final: 0.8619 (p0) REVERT: I 356 ASN cc_start: 0.8885 (p0) cc_final: 0.8552 (p0) REVERT: D 31 ASP cc_start: 0.8420 (t0) cc_final: 0.7974 (t0) REVERT: D 94 ARG cc_start: 0.8396 (ptt180) cc_final: 0.8167 (ptt180) REVERT: D 96 GLN cc_start: 0.7345 (mt0) cc_final: 0.6919 (mt0) REVERT: E 32 TYR cc_start: 0.6467 (m-80) cc_final: 0.6082 (m-80) REVERT: E 75 ILE cc_start: 0.5330 (OUTLIER) cc_final: 0.5005 (mp) REVERT: H 31 ASP cc_start: 0.8442 (t0) cc_final: 0.8088 (t0) REVERT: H 32 TYR cc_start: 0.7923 (m-80) cc_final: 0.7514 (m-10) REVERT: H 94 ARG cc_start: 0.8360 (ptt180) cc_final: 0.7923 (ptt180) REVERT: H 96 GLN cc_start: 0.7386 (mt0) cc_final: 0.7054 (mt0) REVERT: L 36 TYR cc_start: 0.7049 (m-80) cc_final: 0.6565 (m-80) REVERT: L 48 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6648 (mm) REVERT: L 75 ILE cc_start: 0.5052 (OUTLIER) cc_final: 0.4678 (mp) REVERT: J 31 ASP cc_start: 0.8560 (t0) cc_final: 0.7849 (t0) REVERT: J 96 GLN cc_start: 0.7380 (tt0) cc_final: 0.6928 (tp-100) REVERT: K 36 TYR cc_start: 0.6787 (m-80) cc_final: 0.6410 (m-80) REVERT: K 48 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6932 (mm) REVERT: K 75 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.5036 (mp) outliers start: 64 outliers final: 26 residues processed: 288 average time/residue: 1.2144 time to fit residues: 405.9169 Evaluate side-chains 279 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 518 VAL Chi-restraints excluded: chain B residue 639 THR 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 416 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 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 309 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain D residue 27 TYR 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 69 THR 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 69 THR 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 3 optimal weight: 0.7980 chunk 160 optimal weight: 0.0370 chunk 214 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN F 656 ASN I 94 ASN D 30 ASN D 43 HIS E 30 ASN H 30 ASN H 43 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3927 r_free = 0.3927 target = 0.118101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064223 restraints weight = 40238.280| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.62 r_work: 0.2718 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21840 Z= 0.167 Angle : 0.689 9.651 29925 Z= 0.317 Chirality : 0.047 0.254 3774 Planarity : 0.004 0.044 3504 Dihedral : 11.363 67.229 5856 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.29 % Allowed : 22.10 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2406 helix: 1.38 (0.26), residues: 456 sheet: 0.13 (0.18), residues: 762 loop : 0.20 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 623 HIS 0.003 0.001 HIS C 249 PHE 0.014 0.001 PHE H 63 TYR 0.027 0.002 TYR D 27 ARG 0.005 0.000 ARG I 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 63) link_NAG-ASN : angle 2.01193 ( 189) link_ALPHA1-6 : bond 0.00619 ( 9) link_ALPHA1-6 : angle 1.66581 ( 27) link_BETA1-4 : bond 0.00689 ( 75) link_BETA1-4 : angle 2.34186 ( 225) link_ALPHA1-2 : bond 0.00547 ( 3) link_ALPHA1-2 : angle 1.78107 ( 9) link_ALPHA1-3 : bond 0.01127 ( 9) link_ALPHA1-3 : angle 1.52687 ( 27) hydrogen bonds : bond 0.03925 ( 771) hydrogen bonds : angle 5.27415 ( 2178) SS BOND : bond 0.00297 ( 42) SS BOND : angle 0.83894 ( 84) covalent geometry : bond 0.00380 (21639) covalent geometry : angle 0.63858 (29364) *********************** 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: 49 poor density : 259 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8893 (p0) cc_final: 0.8560 (p0) REVERT: C 416 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8265 (pp) REVERT: G 114 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: G 356 ASN cc_start: 0.8842 (p0) cc_final: 0.8546 (p0) REVERT: I 356 ASN cc_start: 0.8848 (p0) cc_final: 0.8540 (p0) REVERT: D 31 ASP cc_start: 0.8607 (t0) cc_final: 0.8204 (t0) REVERT: D 32 TYR cc_start: 0.7883 (m-80) cc_final: 0.7347 (m-10) REVERT: D 59 TYR cc_start: 0.7273 (m-80) cc_final: 0.7065 (m-80) REVERT: D 96 GLN cc_start: 0.7595 (mt0) cc_final: 0.7287 (mt0) REVERT: E 30 ASN cc_start: 0.6167 (t0) cc_final: 0.5748 (t0) REVERT: E 32 TYR cc_start: 0.6576 (m-80) cc_final: 0.5987 (m-80) REVERT: E 58 VAL cc_start: 0.5818 (OUTLIER) cc_final: 0.5562 (p) REVERT: E 75 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4832 (mp) REVERT: H 64 ARG cc_start: 0.6343 (ttp-170) cc_final: 0.5939 (mtm-85) REVERT: H 96 GLN cc_start: 0.7787 (mt0) cc_final: 0.7414 (mt0) REVERT: L 48 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6930 (mm) REVERT: L 75 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4448 (mp) REVERT: J 94 ARG cc_start: 0.8383 (ptt180) cc_final: 0.8017 (ptt180) REVERT: J 96 GLN cc_start: 0.7587 (tt0) cc_final: 0.7355 (mt0) REVERT: K 48 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6969 (mm) REVERT: K 75 ILE cc_start: 0.5190 (OUTLIER) cc_final: 0.4896 (mp) outliers start: 49 outliers final: 18 residues processed: 288 average time/residue: 1.2097 time to fit residues: 400.8514 Evaluate side-chains 271 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 513 VAL 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 C residue 426 MET 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 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU 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 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain K residue 48 ILE 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 45 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 195 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 30 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.118611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064946 restraints weight = 40777.631| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.64 r_work: 0.2735 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21840 Z= 0.136 Angle : 0.654 9.651 29925 Z= 0.304 Chirality : 0.045 0.253 3774 Planarity : 0.004 0.049 3504 Dihedral : 9.120 58.725 5850 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.43 % Allowed : 22.33 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2406 helix: 1.50 (0.26), residues: 456 sheet: 0.17 (0.18), residues: 753 loop : 0.18 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 PHE 0.013 0.001 PHE C 53 TYR 0.049 0.002 TYR L 49 ARG 0.010 0.000 ARG C 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 63) link_NAG-ASN : angle 1.89982 ( 189) link_ALPHA1-6 : bond 0.00766 ( 9) link_ALPHA1-6 : angle 1.68197 ( 27) link_BETA1-4 : bond 0.00642 ( 75) link_BETA1-4 : angle 2.20938 ( 225) link_ALPHA1-2 : bond 0.00563 ( 3) link_ALPHA1-2 : angle 1.77653 ( 9) link_ALPHA1-3 : bond 0.01169 ( 9) link_ALPHA1-3 : angle 1.66141 ( 27) hydrogen bonds : bond 0.03481 ( 771) hydrogen bonds : angle 5.04721 ( 2178) SS BOND : bond 0.00239 ( 42) SS BOND : angle 0.73197 ( 84) covalent geometry : bond 0.00301 (21639) covalent geometry : angle 0.60678 (29364) *********************** 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 310 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: C 356 ASN cc_start: 0.8872 (p0) cc_final: 0.8555 (p0) REVERT: C 416 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8164 (pp) REVERT: C 504 ARG cc_start: 0.7109 (mmm160) cc_final: 0.6555 (mmt90) REVERT: F 655 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7100 (ptpp) REVERT: G 356 ASN cc_start: 0.8822 (p0) cc_final: 0.8539 (p0) REVERT: G 504 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6683 (mmt90) REVERT: I 356 ASN cc_start: 0.8824 (p0) cc_final: 0.8546 (p0) REVERT: I 504 ARG cc_start: 0.7137 (mmm160) cc_final: 0.6607 (mmt90) REVERT: D 31 ASP cc_start: 0.8615 (t0) cc_final: 0.8351 (OUTLIER) REVERT: D 32 TYR cc_start: 0.7806 (m-80) cc_final: 0.7521 (m-10) REVERT: D 39 GLN cc_start: 0.7492 (tp-100) cc_final: 0.7288 (tp40) REVERT: D 96 GLN cc_start: 0.7732 (mt0) cc_final: 0.7392 (mt0) REVERT: E 30 ASN cc_start: 0.6335 (t0) cc_final: 0.5826 (t0) REVERT: E 32 TYR cc_start: 0.6713 (m-80) cc_final: 0.5920 (m-80) REVERT: E 58 VAL cc_start: 0.5814 (OUTLIER) cc_final: 0.5588 (p) REVERT: H 3 GLN cc_start: 0.7871 (pp30) cc_final: 0.7671 (pp30) REVERT: H 28 LYS cc_start: 0.9279 (ptmm) cc_final: 0.8988 (pmtt) REVERT: H 31 ASP cc_start: 0.8743 (t0) cc_final: 0.8145 (t0) REVERT: H 32 TYR cc_start: 0.7850 (m-80) cc_final: 0.7468 (m-10) REVERT: H 64 ARG cc_start: 0.6301 (ttp-170) cc_final: 0.5913 (mtm-85) REVERT: L 32 TYR cc_start: 0.6888 (m-80) cc_final: 0.5881 (m-80) REVERT: L 48 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7876 (mm) REVERT: L 49 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7556 (p90) REVERT: L 50 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8580 (tmmt) REVERT: L 75 ILE cc_start: 0.4593 (OUTLIER) cc_final: 0.4307 (mp) REVERT: L 93 HIS cc_start: 0.8514 (m90) cc_final: 0.8160 (m-70) REVERT: J 28 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9032 (pmtt) REVERT: J 31 ASP cc_start: 0.8792 (t0) cc_final: 0.8259 (t0) REVERT: J 32 TYR cc_start: 0.7899 (m-80) cc_final: 0.7561 (m-10) REVERT: J 94 ARG cc_start: 0.8449 (ptt180) cc_final: 0.8241 (ptt180) REVERT: J 96 GLN cc_start: 0.7681 (tt0) cc_final: 0.7472 (mt0) REVERT: K 30 ASN cc_start: 0.6541 (t0) cc_final: 0.6104 (t0) REVERT: K 48 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6872 (mm) outliers start: 52 outliers final: 29 residues processed: 288 average time/residue: 1.2455 time to fit residues: 411.3947 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 657 GLU 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 C residue 426 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 66 HIS 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 I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 42 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE 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 K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL 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 160 optimal weight: 0.0050 chunk 130 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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** J 30 ASN ** 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 = 0.3929 r_free = 0.3929 target = 0.118221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064644 restraints weight = 40522.714| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.64 r_work: 0.2727 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21840 Z= 0.154 Angle : 0.649 9.733 29925 Z= 0.303 Chirality : 0.045 0.257 3774 Planarity : 0.004 0.050 3504 Dihedral : 8.355 56.712 5850 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.14 % Allowed : 22.47 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2406 helix: 1.53 (0.26), residues: 456 sheet: 0.18 (0.18), residues: 753 loop : 0.19 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 PHE 0.022 0.001 PHE E 55 TYR 0.032 0.002 TYR L 49 ARG 0.009 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 63) link_NAG-ASN : angle 1.95317 ( 189) link_ALPHA1-6 : bond 0.00854 ( 9) link_ALPHA1-6 : angle 1.66920 ( 27) link_BETA1-4 : bond 0.00640 ( 75) link_BETA1-4 : angle 2.05409 ( 225) link_ALPHA1-2 : bond 0.00500 ( 3) link_ALPHA1-2 : angle 1.77660 ( 9) link_ALPHA1-3 : bond 0.01169 ( 9) link_ALPHA1-3 : angle 1.62149 ( 27) hydrogen bonds : bond 0.03517 ( 771) hydrogen bonds : angle 4.98761 ( 2178) SS BOND : bond 0.00249 ( 42) SS BOND : angle 0.74435 ( 84) covalent geometry : bond 0.00349 (21639) covalent geometry : angle 0.60365 (29364) *********************** 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 319 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8545 (pt0) cc_final: 0.8341 (pm20) REVERT: C 356 ASN cc_start: 0.8869 (p0) cc_final: 0.8544 (p0) REVERT: C 416 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 504 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6615 (mmt90) REVERT: F 655 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7117 (ptpp) REVERT: G 114 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: G 356 ASN cc_start: 0.8812 (p0) cc_final: 0.8528 (p0) REVERT: G 504 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6742 (mmt90) REVERT: I 356 ASN cc_start: 0.8820 (p0) cc_final: 0.8543 (p0) REVERT: I 504 ARG cc_start: 0.7145 (mmm160) cc_final: 0.6664 (mmt90) REVERT: D 23 LYS cc_start: 0.9004 (tppp) cc_final: 0.8730 (tppt) REVERT: D 28 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8951 (pmtt) REVERT: D 31 ASP cc_start: 0.8869 (t0) cc_final: 0.8071 (OUTLIER) REVERT: D 32 TYR cc_start: 0.8052 (m-80) cc_final: 0.7362 (m-10) REVERT: D 39 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7200 (tp40) REVERT: D 59 TYR cc_start: 0.7287 (m-80) cc_final: 0.7064 (m-80) REVERT: D 96 GLN cc_start: 0.7865 (mt0) cc_final: 0.7473 (mt0) REVERT: E 30 ASN cc_start: 0.6358 (t0) cc_final: 0.5791 (t0) REVERT: E 32 TYR cc_start: 0.6831 (m-80) cc_final: 0.5962 (m-80) REVERT: H 28 LYS cc_start: 0.9247 (ptmm) cc_final: 0.9024 (pmtt) REVERT: H 31 ASP cc_start: 0.8775 (t0) cc_final: 0.8189 (t0) REVERT: H 32 TYR cc_start: 0.8008 (m-80) cc_final: 0.7639 (m-10) REVERT: H 64 ARG cc_start: 0.6411 (ttp-170) cc_final: 0.6041 (mtm-85) REVERT: H 95 LEU cc_start: 0.8468 (tp) cc_final: 0.8098 (tm) REVERT: H 96 GLN cc_start: 0.7706 (mt0) cc_final: 0.7314 (mt0) REVERT: L 32 TYR cc_start: 0.6802 (m-80) cc_final: 0.5788 (m-80) REVERT: L 48 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7602 (mm) REVERT: L 50 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8616 (tptp) REVERT: L 75 ILE cc_start: 0.4599 (OUTLIER) cc_final: 0.4343 (mp) REVERT: L 83 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6997 (mm) REVERT: L 93 HIS cc_start: 0.8567 (m90) cc_final: 0.8175 (m-70) REVERT: J 28 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9039 (pmtt) REVERT: J 31 ASP cc_start: 0.8813 (t0) cc_final: 0.8424 (t0) REVERT: J 32 TYR cc_start: 0.7972 (m-80) cc_final: 0.7605 (m-10) REVERT: J 95 LEU cc_start: 0.8520 (tp) cc_final: 0.8187 (tm) REVERT: J 96 GLN cc_start: 0.7835 (tt0) cc_final: 0.7336 (tp-100) REVERT: K 30 ASN cc_start: 0.6767 (t0) cc_final: 0.6363 (t0) REVERT: K 50 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8475 (tptp) outliers start: 67 outliers final: 35 residues processed: 296 average time/residue: 1.2592 time to fit residues: 429.8155 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU 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 655 LYS 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 42 VAL Chi-restraints excluded: chain I residue 56 SER 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 I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 83 LEU 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 J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 90 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 228 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** J 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.118595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065379 restraints weight = 40357.706| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.55 r_work: 0.2745 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2185 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= 0.129 Angle : 0.628 9.665 29925 Z= 0.294 Chirality : 0.044 0.254 3774 Planarity : 0.003 0.049 3504 Dihedral : 7.779 56.095 5850 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.46 % Allowed : 22.47 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2406 helix: 1.57 (0.26), residues: 459 sheet: 0.23 (0.18), residues: 744 loop : 0.25 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.002 0.000 HIS C 249 PHE 0.019 0.001 PHE E 55 TYR 0.030 0.001 TYR J 27 ARG 0.005 0.000 ARG E 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 63) link_NAG-ASN : angle 1.88197 ( 189) link_ALPHA1-6 : bond 0.00956 ( 9) link_ALPHA1-6 : angle 1.68679 ( 27) link_BETA1-4 : bond 0.00629 ( 75) link_BETA1-4 : angle 1.91728 ( 225) link_ALPHA1-2 : bond 0.00517 ( 3) link_ALPHA1-2 : angle 1.79735 ( 9) link_ALPHA1-3 : bond 0.01170 ( 9) link_ALPHA1-3 : angle 1.60954 ( 27) hydrogen bonds : bond 0.03263 ( 771) hydrogen bonds : angle 4.86994 ( 2178) SS BOND : bond 0.00219 ( 42) SS BOND : angle 0.68150 ( 84) covalent geometry : bond 0.00286 (21639) covalent geometry : angle 0.58643 (29364) *********************** 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 328 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8557 (pt0) cc_final: 0.8166 (pm20) REVERT: C 356 ASN cc_start: 0.8847 (p0) cc_final: 0.8538 (p0) REVERT: C 416 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 504 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6713 (mmt90) REVERT: F 571 TRP cc_start: 0.7467 (m-10) cc_final: 0.7246 (m-10) REVERT: F 621 GLU cc_start: 0.8670 (pt0) cc_final: 0.8366 (pm20) REVERT: F 655 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7165 (ptpp) REVERT: G 114 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: G 356 ASN cc_start: 0.8794 (p0) cc_final: 0.8493 (p0) REVERT: G 504 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6807 (mmt90) REVERT: I 356 ASN cc_start: 0.8785 (p0) cc_final: 0.8492 (p0) REVERT: I 504 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6720 (mmt90) REVERT: D 28 LYS cc_start: 0.9160 (ptmm) cc_final: 0.8891 (pmtt) REVERT: D 31 ASP cc_start: 0.8846 (t0) cc_final: 0.7991 (OUTLIER) REVERT: D 32 TYR cc_start: 0.8105 (m-80) cc_final: 0.7368 (m-10) REVERT: D 59 TYR cc_start: 0.7305 (m-80) cc_final: 0.7055 (m-80) REVERT: D 96 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: E 30 ASN cc_start: 0.6690 (t0) cc_final: 0.6181 (t0) REVERT: E 32 TYR cc_start: 0.6827 (m-80) cc_final: 0.6000 (m-80) REVERT: E 83 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7081 (mm) REVERT: H 28 LYS cc_start: 0.9239 (ptmm) cc_final: 0.8990 (pmtt) REVERT: H 31 ASP cc_start: 0.8774 (t0) cc_final: 0.8199 (t0) REVERT: H 32 TYR cc_start: 0.7973 (m-80) cc_final: 0.7475 (m-80) REVERT: H 64 ARG cc_start: 0.6392 (ttp-170) cc_final: 0.6022 (mtm-85) REVERT: H 94 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7945 (ptt180) REVERT: H 95 LEU cc_start: 0.8450 (tp) cc_final: 0.8113 (tm) REVERT: H 96 GLN cc_start: 0.7686 (mt0) cc_final: 0.7265 (mt0) REVERT: H 100 TYR cc_start: 0.7428 (p90) cc_final: 0.6924 (p90) REVERT: H 101 ASP cc_start: 0.9055 (p0) cc_final: 0.8285 (p0) REVERT: L 32 TYR cc_start: 0.6704 (m-80) cc_final: 0.5873 (m-80) REVERT: L 83 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6996 (mm) REVERT: L 93 HIS cc_start: 0.8552 (m90) cc_final: 0.8147 (m-70) REVERT: J 28 LYS cc_start: 0.9230 (ptmm) cc_final: 0.8981 (pmtt) REVERT: J 31 ASP cc_start: 0.8797 (t0) cc_final: 0.8304 (t0) REVERT: J 32 TYR cc_start: 0.7907 (m-80) cc_final: 0.7503 (m-10) REVERT: J 94 ARG cc_start: 0.8332 (ptt180) cc_final: 0.8060 (ptt180) REVERT: J 96 GLN cc_start: 0.7874 (tt0) cc_final: 0.7276 (tp-100) REVERT: K 30 ASN cc_start: 0.6785 (t0) cc_final: 0.6381 (t0) REVERT: K 45 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7972 (mmpt) REVERT: K 50 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8568 (tptp) REVERT: K 83 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6851 (mm) outliers start: 74 outliers final: 44 residues processed: 304 average time/residue: 1.2526 time to fit residues: 436.7269 Evaluate side-chains 295 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR 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 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 426 MET Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 27 TYR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 LEU 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 71 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 167 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064998 restraints weight = 40521.967| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.60 r_work: 0.2740 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21840 Z= 0.139 Angle : 0.632 9.717 29925 Z= 0.296 Chirality : 0.044 0.256 3774 Planarity : 0.003 0.054 3504 Dihedral : 7.503 56.223 5850 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.32 % Allowed : 23.03 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2406 helix: 1.60 (0.26), residues: 459 sheet: 0.22 (0.18), residues: 738 loop : 0.25 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 PHE 0.017 0.001 PHE E 55 TYR 0.034 0.001 TYR K 49 ARG 0.008 0.000 ARG I 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 63) link_NAG-ASN : angle 1.88549 ( 189) link_ALPHA1-6 : bond 0.00992 ( 9) link_ALPHA1-6 : angle 1.66603 ( 27) link_BETA1-4 : bond 0.00633 ( 75) link_BETA1-4 : angle 1.88236 ( 225) link_ALPHA1-2 : bond 0.00488 ( 3) link_ALPHA1-2 : angle 1.78767 ( 9) link_ALPHA1-3 : bond 0.01135 ( 9) link_ALPHA1-3 : angle 1.59462 ( 27) hydrogen bonds : bond 0.03323 ( 771) hydrogen bonds : angle 4.83565 ( 2178) SS BOND : bond 0.00251 ( 42) SS BOND : angle 0.81868 ( 84) covalent geometry : bond 0.00312 (21639) covalent geometry : angle 0.59133 (29364) *********************** 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 316 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 2.447 Fit side-chains 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: 0.8480 (OUTLIER) cc_final: 0.8168 (pp) REVERT: F 571 TRP cc_start: 0.7463 (m-10) cc_final: 0.7244 (m-10) REVERT: F 655 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7170 (ptpp) REVERT: G 114 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: G 356 ASN cc_start: 0.8789 (p0) cc_final: 0.8489 (p0) REVERT: G 504 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6854 (mmt90) REVERT: I 356 ASN cc_start: 0.8775 (p0) cc_final: 0.8491 (p0) REVERT: I 504 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6745 (mmt90) REVERT: D 28 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8852 (pmtt) REVERT: D 31 ASP cc_start: 0.8842 (t0) cc_final: 0.8097 (OUTLIER) REVERT: D 32 TYR cc_start: 0.8151 (m-80) cc_final: 0.7169 (m-10) REVERT: D 59 TYR cc_start: 0.7295 (m-80) cc_final: 0.7038 (m-80) REVERT: D 96 GLN cc_start: 0.7901 (mt0) cc_final: 0.7495 (mt0) REVERT: E 30 ASN cc_start: 0.6755 (t0) cc_final: 0.6252 (t0) REVERT: E 32 TYR cc_start: 0.6777 (m-80) cc_final: 0.5918 (m-80) REVERT: E 83 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7087 (mm) REVERT: H 23 LYS cc_start: 0.8927 (tppp) cc_final: 0.8707 (tppt) REVERT: H 27 TYR cc_start: 0.6726 (p90) cc_final: 0.6473 (p90) REVERT: H 31 ASP cc_start: 0.8730 (t0) cc_final: 0.8312 (t0) REVERT: H 32 TYR cc_start: 0.7982 (m-80) cc_final: 0.7677 (m-10) REVERT: H 64 ARG cc_start: 0.6386 (ttp-170) cc_final: 0.6024 (mtm-85) REVERT: H 95 LEU cc_start: 0.8499 (tp) cc_final: 0.8114 (tm) REVERT: H 96 GLN cc_start: 0.7679 (mt0) cc_final: 0.7250 (mt0) REVERT: H 100 TYR cc_start: 0.7530 (p90) cc_final: 0.7080 (p90) REVERT: L 32 TYR cc_start: 0.6692 (m-80) cc_final: 0.5781 (m-80) REVERT: L 83 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6984 (mm) REVERT: L 93 HIS cc_start: 0.8564 (m90) cc_final: 0.8148 (m-70) REVERT: J 28 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8982 (pmtt) REVERT: J 94 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8080 (ptt180) REVERT: J 95 LEU cc_start: 0.8491 (tp) cc_final: 0.8163 (tm) REVERT: K 30 ASN cc_start: 0.6763 (t0) cc_final: 0.6385 (t0) REVERT: K 50 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8551 (tptp) REVERT: K 83 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6961 (mm) outliers start: 71 outliers final: 46 residues processed: 295 average time/residue: 1.2557 time to fit residues: 425.2080 Evaluate side-chains 293 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE 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 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 381 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 426 MET Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 97 LEU Chi-restraints excluded: chain H residue 109 VAL 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 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 138 optimal weight: 0.0030 chunk 182 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 197 optimal weight: 30.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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** J 30 ASN ** 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 = 0.118270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064805 restraints weight = 40504.588| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.63 r_work: 0.2733 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2316 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= 0.148 Angle : 0.647 9.723 29925 Z= 0.304 Chirality : 0.044 0.256 3774 Planarity : 0.004 0.082 3504 Dihedral : 7.337 56.338 5850 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.04 % Allowed : 23.41 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2406 helix: 1.60 (0.26), residues: 459 sheet: 0.21 (0.18), residues: 738 loop : 0.27 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.002 0.001 HIS C 249 PHE 0.014 0.001 PHE E 55 TYR 0.030 0.001 TYR E 49 ARG 0.019 0.000 ARG C 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 63) link_NAG-ASN : angle 1.90335 ( 189) link_ALPHA1-6 : bond 0.01014 ( 9) link_ALPHA1-6 : angle 1.65369 ( 27) link_BETA1-4 : bond 0.00627 ( 75) link_BETA1-4 : angle 1.85744 ( 225) link_ALPHA1-2 : bond 0.00470 ( 3) link_ALPHA1-2 : angle 1.78825 ( 9) link_ALPHA1-3 : bond 0.01111 ( 9) link_ALPHA1-3 : angle 1.58031 ( 27) hydrogen bonds : bond 0.03362 ( 771) hydrogen bonds : angle 4.85364 ( 2178) SS BOND : bond 0.00253 ( 42) SS BOND : angle 0.81137 ( 84) covalent geometry : bond 0.00338 (21639) covalent geometry : angle 0.60767 (29364) *********************** 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 309 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 2.980 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8536 (pt0) cc_final: 0.8273 (pm20) REVERT: C 356 ASN cc_start: 0.8855 (p0) cc_final: 0.8550 (p0) REVERT: C 416 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8205 (pp) REVERT: C 504 ARG cc_start: 0.7160 (mmm160) cc_final: 0.6666 (mmt-90) REVERT: F 571 TRP cc_start: 0.7484 (m-10) cc_final: 0.7258 (m-10) REVERT: F 621 GLU cc_start: 0.8653 (pt0) cc_final: 0.8331 (pm20) REVERT: F 655 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7334 (ptpt) REVERT: G 114 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: G 356 ASN cc_start: 0.8782 (p0) cc_final: 0.8482 (p0) REVERT: G 504 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6910 (mmt90) REVERT: I 356 ASN cc_start: 0.8766 (p0) cc_final: 0.8460 (p0) REVERT: I 504 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6792 (mmt90) REVERT: D 23 LYS cc_start: 0.8878 (tppp) cc_final: 0.8624 (tppt) REVERT: D 28 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8894 (pmtt) REVERT: D 31 ASP cc_start: 0.8847 (t0) cc_final: 0.8177 (OUTLIER) REVERT: D 32 TYR cc_start: 0.8176 (m-80) cc_final: 0.7260 (m-10) REVERT: D 59 TYR cc_start: 0.7275 (m-80) cc_final: 0.7064 (m-80) REVERT: D 96 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: E 30 ASN cc_start: 0.6792 (t0) cc_final: 0.6314 (t0) REVERT: E 32 TYR cc_start: 0.6803 (m-80) cc_final: 0.5850 (m-80) REVERT: E 83 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7055 (mm) REVERT: H 23 LYS cc_start: 0.8930 (tppp) cc_final: 0.8719 (tppt) REVERT: H 31 ASP cc_start: 0.8773 (t0) cc_final: 0.8353 (t0) REVERT: H 32 TYR cc_start: 0.8059 (m-80) cc_final: 0.7680 (m-10) REVERT: H 64 ARG cc_start: 0.6385 (ttp-170) cc_final: 0.6022 (mtm-85) REVERT: H 96 GLN cc_start: 0.7703 (mt0) cc_final: 0.7228 (mt0) REVERT: H 100 TYR cc_start: 0.7621 (p90) cc_final: 0.7256 (p90) REVERT: L 32 TYR cc_start: 0.6639 (m-80) cc_final: 0.5733 (m-80) REVERT: L 33 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8792 (tm) REVERT: L 83 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7020 (mm) REVERT: L 93 HIS cc_start: 0.8571 (m90) cc_final: 0.8154 (m-70) REVERT: J 31 ASP cc_start: 0.8772 (t0) cc_final: 0.8323 (t0) REVERT: J 32 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: J 95 LEU cc_start: 0.8463 (tp) cc_final: 0.8132 (tm) REVERT: K 30 ASN cc_start: 0.6759 (t0) cc_final: 0.6378 (t0) REVERT: K 50 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8491 (tptp) REVERT: K 83 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6945 (mm) outliers start: 65 outliers final: 42 residues processed: 290 average time/residue: 1.2821 time to fit residues: 430.5826 Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE 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 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 F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 333 VAL 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 333 VAL Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 97 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 33 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 1.9990 chunk 175 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 237 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** J 30 ASN ** 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 = 0.3929 r_free = 0.3929 target = 0.118245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064716 restraints weight = 40362.266| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.64 r_work: 0.2733 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2402 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= 0.146 Angle : 0.649 9.740 29925 Z= 0.305 Chirality : 0.044 0.256 3774 Planarity : 0.004 0.064 3504 Dihedral : 7.131 56.269 5850 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.95 % Allowed : 23.55 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2406 helix: 1.43 (0.26), residues: 477 sheet: 0.24 (0.19), residues: 738 loop : 0.29 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 96 HIS 0.002 0.001 HIS I 249 PHE 0.015 0.001 PHE J 63 TYR 0.040 0.002 TYR L 49 ARG 0.015 0.000 ARG C 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 63) link_NAG-ASN : angle 1.89123 ( 189) link_ALPHA1-6 : bond 0.01042 ( 9) link_ALPHA1-6 : angle 1.63629 ( 27) link_BETA1-4 : bond 0.00625 ( 75) link_BETA1-4 : angle 1.81929 ( 225) link_ALPHA1-2 : bond 0.00456 ( 3) link_ALPHA1-2 : angle 1.78665 ( 9) link_ALPHA1-3 : bond 0.01082 ( 9) link_ALPHA1-3 : angle 1.54939 ( 27) hydrogen bonds : bond 0.03364 ( 771) hydrogen bonds : angle 4.85629 ( 2178) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.86191 ( 84) covalent geometry : bond 0.00335 (21639) covalent geometry : angle 0.61107 (29364) *********************** 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 312 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8525 (pt0) cc_final: 0.8248 (pm20) REVERT: B 621 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: C 356 ASN cc_start: 0.8847 (p0) cc_final: 0.8545 (p0) REVERT: C 416 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (pp) REVERT: C 504 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6740 (mmt90) REVERT: F 571 TRP cc_start: 0.7494 (m-10) cc_final: 0.7269 (m-10) REVERT: F 621 GLU cc_start: 0.8641 (pt0) cc_final: 0.8316 (pm20) REVERT: F 655 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7306 (ptpt) REVERT: G 114 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: G 356 ASN cc_start: 0.8774 (p0) cc_final: 0.8474 (p0) REVERT: G 504 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6963 (mmt90) REVERT: I 232 LYS cc_start: 0.8891 (tppt) cc_final: 0.8583 (mmtp) REVERT: I 356 ASN cc_start: 0.8759 (p0) cc_final: 0.8454 (p0) REVERT: I 504 ARG cc_start: 0.7281 (mmm160) cc_final: 0.6821 (mmt90) REVERT: D 31 ASP cc_start: 0.8821 (t0) cc_final: 0.8140 (t0) REVERT: D 32 TYR cc_start: 0.8164 (m-80) cc_final: 0.7227 (m-10) REVERT: D 59 TYR cc_start: 0.7270 (m-80) cc_final: 0.7064 (m-80) REVERT: D 95 LEU cc_start: 0.8507 (tp) cc_final: 0.8204 (tm) REVERT: D 96 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: E 30 ASN cc_start: 0.6820 (t0) cc_final: 0.6379 (t0) REVERT: E 32 TYR cc_start: 0.6754 (m-80) cc_final: 0.5854 (m-80) REVERT: E 83 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7133 (mm) REVERT: H 23 LYS cc_start: 0.9006 (tppp) cc_final: 0.8797 (tppt) REVERT: H 31 ASP cc_start: 0.8775 (t0) cc_final: 0.8369 (t0) REVERT: H 32 TYR cc_start: 0.8055 (m-80) cc_final: 0.7675 (m-80) REVERT: H 64 ARG cc_start: 0.6396 (ttp-170) cc_final: 0.6037 (mtm-85) REVERT: H 95 LEU cc_start: 0.8419 (tp) cc_final: 0.8039 (tm) REVERT: H 96 GLN cc_start: 0.7739 (mt0) cc_final: 0.7301 (mt0) REVERT: H 100 TYR cc_start: 0.7576 (p90) cc_final: 0.6696 (p90) REVERT: L 32 TYR cc_start: 0.6622 (m-80) cc_final: 0.5697 (m-80) REVERT: L 33 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8698 (tm) REVERT: L 50 LYS cc_start: 0.8657 (tppp) cc_final: 0.8437 (tppp) REVERT: L 83 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7024 (mm) REVERT: L 93 HIS cc_start: 0.8574 (m90) cc_final: 0.8189 (m-70) REVERT: J 95 LEU cc_start: 0.8454 (tp) cc_final: 0.7958 (tm) REVERT: J 96 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: K 30 ASN cc_start: 0.6826 (t0) cc_final: 0.6409 (t0) REVERT: K 45 LYS cc_start: 0.8400 (mmpt) cc_final: 0.8171 (mmpt) REVERT: K 50 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8418 (tptp) REVERT: K 83 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6970 (mm) outliers start: 63 outliers final: 43 residues processed: 292 average time/residue: 1.2549 time to fit residues: 421.7840 Evaluate side-chains 295 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 621 GLU 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 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 C residue 426 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 333 VAL 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 333 VAL Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 97 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 33 LEU 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 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 49 TYR 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 66 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 140 optimal weight: 0.2980 chunk 237 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.117209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063521 restraints weight = 40486.438| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.61 r_work: 0.2701 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21840 Z= 0.229 Angle : 0.692 9.869 29925 Z= 0.326 Chirality : 0.046 0.261 3774 Planarity : 0.004 0.077 3504 Dihedral : 7.188 57.462 5850 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.57 % Allowed : 24.02 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2406 helix: 1.35 (0.26), residues: 477 sheet: 0.25 (0.18), residues: 741 loop : 0.25 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.003 0.001 HIS C 249 PHE 0.015 0.001 PHE I 383 TYR 0.049 0.002 TYR K 49 ARG 0.015 0.000 ARG C 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 63) link_NAG-ASN : angle 1.97862 ( 189) link_ALPHA1-6 : bond 0.00996 ( 9) link_ALPHA1-6 : angle 1.58747 ( 27) link_BETA1-4 : bond 0.00634 ( 75) link_BETA1-4 : angle 1.86951 ( 225) link_ALPHA1-2 : bond 0.00359 ( 3) link_ALPHA1-2 : angle 1.79423 ( 9) link_ALPHA1-3 : bond 0.01021 ( 9) link_ALPHA1-3 : angle 1.56849 ( 27) hydrogen bonds : bond 0.03813 ( 771) hydrogen bonds : angle 4.99259 ( 2178) SS BOND : bond 0.00275 ( 42) SS BOND : angle 0.98782 ( 84) covalent geometry : bond 0.00540 (21639) covalent geometry : angle 0.65406 (29364) ********************** 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 301 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8862 (p0) cc_final: 0.8548 (p0) REVERT: C 504 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6797 (mmt90) REVERT: F 571 TRP cc_start: 0.7554 (m-10) cc_final: 0.7316 (m-10) REVERT: F 655 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7279 (ptpt) REVERT: G 114 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: G 356 ASN cc_start: 0.8798 (p0) cc_final: 0.8496 (p0) REVERT: G 504 ARG cc_start: 0.7307 (mmm160) cc_final: 0.6998 (mmt90) REVERT: I 232 LYS cc_start: 0.8896 (tppt) cc_final: 0.8548 (mmtp) REVERT: I 356 ASN cc_start: 0.8814 (p0) cc_final: 0.8475 (p0) REVERT: I 504 ARG cc_start: 0.7330 (mmm160) cc_final: 0.6887 (mmt90) REVERT: D 23 LYS cc_start: 0.8823 (tppp) cc_final: 0.8579 (tppt) REVERT: D 31 ASP cc_start: 0.8595 (t0) cc_final: 0.8278 (t0) REVERT: D 32 TYR cc_start: 0.8081 (m-80) cc_final: 0.7592 (m-10) REVERT: D 59 TYR cc_start: 0.7287 (m-80) cc_final: 0.7066 (m-80) REVERT: D 96 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: E 30 ASN cc_start: 0.6839 (t0) cc_final: 0.6319 (t0) REVERT: E 32 TYR cc_start: 0.6637 (m-80) cc_final: 0.5750 (m-80) REVERT: E 83 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 23 LYS cc_start: 0.8977 (tppp) cc_final: 0.8772 (tppt) REVERT: H 31 ASP cc_start: 0.8777 (t0) cc_final: 0.8363 (t0) REVERT: H 32 TYR cc_start: 0.8066 (m-80) cc_final: 0.7786 (m-80) REVERT: H 95 LEU cc_start: 0.8471 (tp) cc_final: 0.8117 (tm) REVERT: H 96 GLN cc_start: 0.7740 (mt0) cc_final: 0.7284 (mt0) REVERT: L 32 TYR cc_start: 0.6628 (m-80) cc_final: 0.5580 (m-80) REVERT: L 33 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8779 (tm) REVERT: L 83 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7052 (mm) REVERT: L 93 HIS cc_start: 0.8549 (m90) cc_final: 0.8155 (m-70) REVERT: J 31 ASP cc_start: 0.8851 (t0) cc_final: 0.8454 (t0) REVERT: J 32 TYR cc_start: 0.7734 (m-10) cc_final: 0.7041 (m-10) REVERT: K 30 ASN cc_start: 0.6941 (t0) cc_final: 0.6504 (t0) REVERT: K 45 LYS cc_start: 0.8433 (mmpt) cc_final: 0.8223 (mmpt) REVERT: K 83 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7061 (mm) REVERT: K 106 MET cc_start: 0.4123 (pp-130) cc_final: 0.3588 (pmm) outliers start: 55 outliers final: 41 residues processed: 283 average time/residue: 1.2978 time to fit residues: 420.4728 Evaluate side-chains 291 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 639 THR Chi-restraints excluded: chain F residue 655 LYS 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 333 VAL 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 333 VAL Chi-restraints excluded: chain I residue 381 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET 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 97 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 33 LEU 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 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 188 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 237 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 411 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN K 30 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.118225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065106 restraints weight = 40408.364| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.57 r_work: 0.2739 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21840 Z= 0.137 Angle : 0.653 9.672 29925 Z= 0.308 Chirality : 0.044 0.253 3774 Planarity : 0.004 0.080 3504 Dihedral : 6.950 55.794 5850 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.29 % Allowed : 24.20 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2406 helix: 1.41 (0.26), residues: 477 sheet: 0.28 (0.19), residues: 738 loop : 0.28 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 35 HIS 0.002 0.001 HIS I 249 PHE 0.021 0.001 PHE J 100A TYR 0.036 0.001 TYR L 49 ARG 0.013 0.000 ARG I 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 63) link_NAG-ASN : angle 1.86140 ( 189) link_ALPHA1-6 : bond 0.01045 ( 9) link_ALPHA1-6 : angle 1.62299 ( 27) link_BETA1-4 : bond 0.00611 ( 75) link_BETA1-4 : angle 1.76693 ( 225) link_ALPHA1-2 : bond 0.00431 ( 3) link_ALPHA1-2 : angle 1.79184 ( 9) link_ALPHA1-3 : bond 0.01050 ( 9) link_ALPHA1-3 : angle 1.49279 ( 27) hydrogen bonds : bond 0.03272 ( 771) hydrogen bonds : angle 4.86901 ( 2178) SS BOND : bond 0.00213 ( 42) SS BOND : angle 0.80566 ( 84) covalent geometry : bond 0.00313 (21639) covalent geometry : angle 0.61699 (29364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20123.12 seconds wall clock time: 350 minutes 49.73 seconds (21049.73 seconds total)