Starting phenix.real_space_refine on Wed Nov 20 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_29396.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_29396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_29396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_29396.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr6_29396/11_2024/8fr6_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 14.37, per 1000 atoms: 0.68 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: 6.19 Conformation dependent library (CDL) restraints added in 2.8 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: 2.67 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: 8.48 Time building geometry restraints manager: 6.89 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: 0.00 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: 5.740 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: 0.040 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 49.680 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.180 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.920 ------------------------------------------------------------------------------- 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 21639 Z= 0.298 Angle : 0.792 7.085 29364 Z= 0.333 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 *********************** 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 : 2.254 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: 1.3030 time to fit residues: 448.0175 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 : 2.363 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 21639 Z= 0.364 Angle : 0.712 9.724 29364 Z= 0.343 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 *********************** 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 : 2.531 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8871 (p0) cc_final: 0.8528 (p0) REVERT: F 655 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7629 (ptpp) REVERT: G 114 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: G 356 ASN cc_start: 0.8844 (p0) cc_final: 0.8554 (p0) REVERT: I 356 ASN cc_start: 0.8820 (p0) cc_final: 0.8468 (p0) REVERT: D 89 VAL cc_start: 0.7153 (t) cc_final: 0.6832 (m) REVERT: E 75 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5226 (mp) REVERT: H 32 TYR cc_start: 0.7812 (m-80) cc_final: 0.7285 (m-10) REVERT: L 75 ILE cc_start: 0.5595 (OUTLIER) cc_final: 0.5127 (mp) REVERT: L 94 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7865 (mt) REVERT: J 31 ASP cc_start: 0.7702 (t0) cc_final: 0.7461 (t0) REVERT: J 89 VAL cc_start: 0.7149 (t) cc_final: 0.6837 (m) REVERT: K 75 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.5193 (mp) outliers start: 64 outliers final: 26 residues processed: 288 average time/residue: 1.1872 time to fit residues: 396.8885 Evaluate side-chains 277 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain K residue 27 VAL 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 121 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 30.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 D 96 GLN E 30 ASN H 30 ASN H 43 HIS H 96 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21639 Z= 0.265 Angle : 0.644 9.652 29364 Z= 0.309 Chirality : 0.047 0.254 3774 Planarity : 0.004 0.043 3504 Dihedral : 11.331 67.041 5856 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.34 % Allowed : 22.05 % 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: 0.48 (0.17), residues: 2406 helix: 1.35 (0.26), residues: 456 sheet: 0.13 (0.18), residues: 759 loop : 0.18 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 96 HIS 0.003 0.001 HIS C 249 PHE 0.013 0.001 PHE H 63 TYR 0.029 0.002 TYR D 27 ARG 0.008 0.000 ARG D 94 *********************** 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 305 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8819 (p0) cc_final: 0.8462 (p0) REVERT: C 416 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8473 (pp) REVERT: G 114 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: G 356 ASN cc_start: 0.8796 (p0) cc_final: 0.8501 (p0) REVERT: I 356 ASN cc_start: 0.8779 (p0) cc_final: 0.8457 (p0) REVERT: D 32 TYR cc_start: 0.7775 (m-80) cc_final: 0.7510 (m-10) REVERT: D 89 VAL cc_start: 0.7132 (t) cc_final: 0.6821 (m) REVERT: E 75 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.4979 (mp) REVERT: H 32 TYR cc_start: 0.7814 (m-80) cc_final: 0.7607 (m-80) REVERT: H 64 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7535 (mtm-85) REVERT: H 89 VAL cc_start: 0.7244 (t) cc_final: 0.6954 (m) REVERT: L 75 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.4967 (mp) REVERT: K 75 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.5090 (mp) outliers start: 50 outliers final: 20 residues processed: 285 average time/residue: 1.2179 time to fit residues: 400.0632 Evaluate side-chains 270 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 B residue 518 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 309 ILE 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 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 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 97 LEU 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 215 optimal weight: 30.0000 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 50.0000 chunk 231 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 62 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21639 Z= 0.243 Angle : 0.618 9.706 29364 Z= 0.299 Chirality : 0.046 0.254 3774 Planarity : 0.004 0.047 3504 Dihedral : 9.103 58.245 5851 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.39 % Allowed : 22.57 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.26), residues: 456 sheet: 0.13 (0.18), residues: 753 loop : 0.16 (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 0.013 0.001 PHE C 53 TYR 0.031 0.002 TYR K 49 ARG 0.012 0.001 ARG C 504 *********************** 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: 51 poor density : 259 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8796 (p0) cc_final: 0.8455 (p0) REVERT: C 416 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8442 (pp) REVERT: C 504 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6692 (mmt90) REVERT: F 655 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7572 (ptpp) REVERT: G 114 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: G 356 ASN cc_start: 0.8776 (p0) cc_final: 0.8460 (p0) REVERT: G 504 ARG cc_start: 0.7075 (mmm160) cc_final: 0.6787 (mmt90) REVERT: I 356 ASN cc_start: 0.8762 (p0) cc_final: 0.8471 (p0) REVERT: I 504 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6762 (mmt90) REVERT: D 32 TYR cc_start: 0.7841 (m-80) cc_final: 0.7522 (m-10) REVERT: H 64 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7545 (mtm-85) REVERT: L 75 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.4905 (mp) outliers start: 51 outliers final: 28 residues processed: 291 average time/residue: 1.2725 time to fit residues: 424.6199 Evaluate side-chains 271 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 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 655 LYS Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 40.0000 chunk 160 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 58 optimal weight: 0.0870 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN E 30 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21639 Z= 0.228 Angle : 0.621 10.875 29364 Z= 0.301 Chirality : 0.045 0.256 3774 Planarity : 0.004 0.048 3504 Dihedral : 8.426 56.702 5850 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.18 % Allowed : 22.38 % Favored : 74.44 % 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: 0.53 (0.17), residues: 2406 helix: 1.50 (0.26), residues: 456 sheet: 0.13 (0.18), residues: 756 loop : 0.18 (0.18), residues: 1194 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 D 63 TYR 0.030 0.002 TYR L 49 ARG 0.008 0.000 ARG E 61 *********************** 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: 68 poor density : 251 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8779 (p0) cc_final: 0.8430 (p0) REVERT: C 416 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8417 (pp) REVERT: C 504 ARG cc_start: 0.7103 (mmm160) cc_final: 0.6730 (mmt90) REVERT: F 655 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (ptpt) REVERT: G 114 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: G 356 ASN cc_start: 0.8748 (p0) cc_final: 0.8444 (p0) REVERT: G 504 ARG cc_start: 0.7104 (mmm160) cc_final: 0.6874 (mmt90) REVERT: I 356 ASN cc_start: 0.8731 (p0) cc_final: 0.8434 (p0) REVERT: I 504 ARG cc_start: 0.7070 (mmm160) cc_final: 0.6781 (mmt90) REVERT: H 64 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7560 (mtm-85) REVERT: L 75 ILE cc_start: 0.5391 (OUTLIER) cc_final: 0.4966 (mp) outliers start: 68 outliers final: 32 residues processed: 293 average time/residue: 1.2510 time to fit residues: 421.0396 Evaluate side-chains 274 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 518 VAL Chi-restraints excluded: chain B residue 620 SER 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 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 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 E residue 69 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 42 VAL 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 78 optimal weight: 0.0980 chunk 208 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21639 Z= 0.228 Angle : 0.614 9.743 29364 Z= 0.298 Chirality : 0.045 0.257 3774 Planarity : 0.004 0.048 3504 Dihedral : 7.967 56.667 5850 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.42 % Allowed : 22.38 % Favored : 74.20 % 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: 1.54 (0.26), residues: 456 sheet: 0.14 (0.18), residues: 753 loop : 0.22 (0.19), 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 0.013 0.001 PHE C 53 TYR 0.055 0.002 TYR L 49 ARG 0.005 0.000 ARG E 61 *********************** 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 318 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 2.403 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8769 (p0) cc_final: 0.8423 (p0) REVERT: C 416 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (pp) REVERT: F 571 TRP cc_start: 0.7575 (m-10) cc_final: 0.7360 (m-10) REVERT: F 655 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7726 (ptpt) REVERT: G 114 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: G 356 ASN cc_start: 0.8734 (p0) cc_final: 0.8434 (p0) REVERT: G 504 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6917 (mmt90) REVERT: I 356 ASN cc_start: 0.8732 (p0) cc_final: 0.8434 (p0) REVERT: I 504 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6862 (mmt90) REVERT: D 32 TYR cc_start: 0.7840 (m-80) cc_final: 0.7506 (m-10) REVERT: H 64 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7550 (mtm-85) REVERT: J 32 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7450 (m-10) outliers start: 73 outliers final: 40 residues processed: 291 average time/residue: 1.3030 time to fit residues: 436.1598 Evaluate side-chains 281 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 518 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 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 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 109 VAL 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 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 231 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 141 optimal weight: 0.0020 chunk 106 optimal weight: 0.7980 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21639 Z= 0.209 Angle : 0.611 9.720 29364 Z= 0.296 Chirality : 0.044 0.256 3774 Planarity : 0.004 0.063 3504 Dihedral : 7.561 56.364 5850 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 23.46 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.17), residues: 2406 helix: 1.58 (0.26), residues: 456 sheet: 0.17 (0.18), residues: 747 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 0.001 HIS I 249 PHE 0.013 0.001 PHE J 63 TYR 0.030 0.002 TYR J 27 ARG 0.017 0.000 ARG C 504 *********************** 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 313 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 232 LYS cc_start: 0.8774 (tppp) cc_final: 0.8473 (mmtp) REVERT: C 268 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: C 356 ASN cc_start: 0.8751 (p0) cc_final: 0.8416 (p0) REVERT: C 416 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8369 (pp) REVERT: C 504 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6800 (mmt90) REVERT: F 571 TRP cc_start: 0.7561 (m-10) cc_final: 0.7342 (m-10) REVERT: F 655 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7728 (ptpt) REVERT: G 114 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: G 356 ASN cc_start: 0.8720 (p0) cc_final: 0.8422 (p0) REVERT: I 232 LYS cc_start: 0.8858 (tppt) cc_final: 0.8551 (mmtp) REVERT: I 356 ASN cc_start: 0.8702 (p0) cc_final: 0.8394 (p0) REVERT: I 504 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6893 (mmt90) REVERT: D 59 TYR cc_start: 0.7718 (m-80) cc_final: 0.7498 (m-80) REVERT: E 30 ASN cc_start: 0.5732 (t0) cc_final: 0.5423 (t0) REVERT: H 64 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7540 (mtm-85) REVERT: L 49 TYR cc_start: 0.7031 (p90) cc_final: 0.6805 (p90) REVERT: J 32 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7478 (m-10) outliers start: 68 outliers final: 39 residues processed: 290 average time/residue: 1.3004 time to fit residues: 432.3694 Evaluate side-chains 278 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 518 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 C residue 66 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 268 GLU 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 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 109 VAL 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 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21639 Z= 0.175 Angle : 0.616 10.357 29364 Z= 0.300 Chirality : 0.044 0.256 3774 Planarity : 0.004 0.063 3504 Dihedral : 7.268 55.635 5850 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.76 % Allowed : 24.06 % Favored : 73.17 % 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: 0.69 (0.18), residues: 2406 helix: 1.63 (0.26), residues: 456 sheet: 0.26 (0.18), residues: 744 loop : 0.25 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 96 HIS 0.002 0.000 HIS G 249 PHE 0.017 0.001 PHE J 29 TYR 0.040 0.002 TYR D 32 ARG 0.012 0.000 ARG C 504 *********************** 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 299 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8745 (p0) cc_final: 0.8423 (p0) REVERT: C 416 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (pp) REVERT: C 504 ARG cc_start: 0.7066 (mmm160) cc_final: 0.6788 (mmt90) REVERT: F 571 TRP cc_start: 0.7534 (m-10) cc_final: 0.7299 (m-10) REVERT: F 655 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7571 (ptpp) REVERT: G 356 ASN cc_start: 0.8688 (p0) cc_final: 0.8369 (p0) REVERT: I 232 LYS cc_start: 0.8859 (tppt) cc_final: 0.8509 (mmtp) REVERT: I 268 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: I 356 ASN cc_start: 0.8668 (p0) cc_final: 0.8373 (p0) REVERT: I 504 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6904 (mmt90) REVERT: E 30 ASN cc_start: 0.5714 (t0) cc_final: 0.5471 (t0) REVERT: H 64 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7524 (mtm-85) outliers start: 59 outliers final: 36 residues processed: 283 average time/residue: 1.2705 time to fit residues: 413.5111 Evaluate side-chains 269 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain B residue 518 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 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 333 VAL 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 268 GLU 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 109 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 30.0000 overall best weight: 1.0402 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21639 Z= 0.243 Angle : 0.634 9.791 29364 Z= 0.308 Chirality : 0.044 0.260 3774 Planarity : 0.004 0.076 3504 Dihedral : 7.143 56.513 5850 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.39 % Allowed : 24.67 % Favored : 72.94 % 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: 0.67 (0.18), residues: 2406 helix: 1.62 (0.26), residues: 456 sheet: 0.24 (0.18), residues: 747 loop : 0.25 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 96 HIS 0.002 0.001 HIS E 93 PHE 0.013 0.001 PHE D 29 TYR 0.032 0.002 TYR H 27 ARG 0.011 0.000 ARG C 504 *********************** 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 291 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: C 356 ASN cc_start: 0.8753 (p0) cc_final: 0.8425 (p0) REVERT: C 416 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 504 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6867 (mmt90) REVERT: F 571 TRP cc_start: 0.7583 (m-10) cc_final: 0.7352 (m-10) REVERT: F 655 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7737 (ptpt) REVERT: G 356 ASN cc_start: 0.8700 (p0) cc_final: 0.8378 (p0) REVERT: I 232 LYS cc_start: 0.8857 (tppt) cc_final: 0.8511 (mmtp) REVERT: I 268 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: I 356 ASN cc_start: 0.8674 (p0) cc_final: 0.8357 (p0) REVERT: I 504 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6972 (mmt90) REVERT: D 32 TYR cc_start: 0.7357 (m-10) cc_final: 0.7104 (m-10) REVERT: E 30 ASN cc_start: 0.5698 (t0) cc_final: 0.5287 (t0) REVERT: H 64 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7550 (mtm-85) REVERT: J 32 TYR cc_start: 0.7643 (m-10) cc_final: 0.7218 (m-10) outliers start: 51 outliers final: 31 residues processed: 274 average time/residue: 1.3242 time to fit residues: 414.5102 Evaluate side-chains 268 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 396 ILE Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 268 GLU 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 109 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0980 chunk 227 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 239 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: