Starting phenix.real_space_refine on Wed Jun 18 06:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4m_29725/06_2025/8g4m_29725.cif" } resolution = 2.95 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= 0.013 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 135 5.16 5 C 12837 2.51 5 N 3409 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20584 Number of models: 1 Model: "" Number of chains: 61 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 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: "O" 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: "P" 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: "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: 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: "S" 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: "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: 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: "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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 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: "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: 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: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 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: "g" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" 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: "l" 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: "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: 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: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 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: "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: 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: "s" 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: "t" 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: "u" 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: "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: 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: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: "z" 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: "0" 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: "1" 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: "2" 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: "C" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 Time building chain proxies: 14.10, per 1000 atoms: 0.68 Number of scatterers: 20584 At special positions: 0 Unit cell: (130.31, 132.8, 144.42, 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 135 16.00 O 4203 8.00 N 3409 7.00 C 12837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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 C 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 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 G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 I 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" 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 H 99 " - pdb=" SG CYS H 100D" 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 J 99 " - pdb=" SG CYS J 100D" 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 t 4 " - " MAN t 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN I 392 " " NAG 1 1 " - " ASN I 448 " " NAG 2 1 " - " ASN I 160 " " NAG A 701 " - " ASN A 637 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 234 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG I 601 " - " ASN I 339 " " NAG I 602 " - " ASN I 355 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 197 " " 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 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN G 88 " " NAG b 1 " - " ASN G 133 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN G 197 " " 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 392 " " NAG m 1 " - " ASN G 448 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN I 88 " " NAG p 1 " - " ASN I 133 " " NAG q 1 " - " ASN I 156 " " NAG r 1 " - " ASN I 197 " " NAG s 1 " - " ASN I 234 " " NAG t 1 " - " ASN I 262 " " NAG u 1 " - " ASN I 276 " " NAG v 1 " - " ASN I 295 " " NAG w 1 " - " ASN I 301 " " NAG x 1 " - " ASN I 332 " " NAG y 1 " - " ASN I 363 " " NAG z 1 " - " ASN I 386 " Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 2.8 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 45 sheets defined 20.5% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.882A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.542A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.616A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.675A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.771A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.532A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.560A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.592A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.839A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.618A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.736A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.713A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.577A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.632A pdb=" N ALA I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.931A 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: 4.030A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.917A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.164A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.471A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.744A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.755A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.513A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.932A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.690A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.248A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.640A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 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 259 through 261 removed outlier: 6.452A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.586A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.657A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.263A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.470A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.617A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.544A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.633A 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 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.656A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.171A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.508A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.430A 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: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.561A 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 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.041A pdb=" N ARG D 38 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.279A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.070A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.438A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.342A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.113A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.059A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.141A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2046 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: 7.99 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6415 1.34 - 1.46: 5264 1.46 - 1.58: 9118 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 20977 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" C1 NAG p 2 " pdb=" O5 NAG p 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 20972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27952 2.19 - 4.39: 435 4.39 - 6.58: 71 6.58 - 8.77: 0 8.77 - 10.97: 1 Bond angle restraints: 28459 Sorted by residual: angle pdb=" C2 NAG b 2 " pdb=" N2 NAG b 2 " pdb=" C7 NAG b 2 " ideal model delta sigma weight residual 124.56 135.53 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " ideal model delta sigma weight residual 110.40 115.22 -4.82 1.70e+00 3.46e-01 8.03e+00 angle pdb=" N GLY I 389 " pdb=" CA GLY I 389 " pdb=" C GLY I 389 " ideal model delta sigma weight residual 114.66 111.25 3.41 1.24e+00 6.50e-01 7.56e+00 angle pdb=" C GLY K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " pdb=" CD1 ILE B 635 " ideal model delta sigma weight residual 113.80 119.50 -5.70 2.10e+00 2.27e-01 7.38e+00 ... (remaining 28454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12568 21.78 - 43.56: 1097 43.56 - 65.34: 302 65.34 - 87.12: 79 87.12 - 108.90: 52 Dihedral angle restraints: 14098 sinusoidal: 7105 harmonic: 6993 Sorted by residual: dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.45 62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS D 99 " pdb=" SG CYS D 99 " pdb=" SG CYS D 100D" pdb=" CB CYS D 100D" ideal model delta sinusoidal sigma weight residual 93.00 153.67 -60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -139.44 53.44 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 14095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3030 0.059 - 0.119: 419 0.119 - 0.178: 66 0.178 - 0.238: 6 0.238 - 0.297: 8 Chirality restraints: 3529 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3526 not shown) Planarity restraints: 3521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 18 " -0.176 9.50e-02 1.11e+02 7.93e-02 4.15e+00 pdb=" NE ARG K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K 18 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG K 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 55 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" CG ASP J 55 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP J 55 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP J 55 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 635 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ILE B 635 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE B 635 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 636 " 0.006 2.00e-02 2.50e+03 ... (remaining 3518 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 537 2.69 - 3.24: 19246 3.24 - 3.79: 31779 3.79 - 4.35: 44438 4.35 - 4.90: 74271 Nonbonded interactions: 170271 Sorted by model distance: nonbonded pdb=" N GLU K 81 " pdb=" OE1 GLU K 81 " model vdw 2.132 3.120 nonbonded pdb=" N GLU E 81 " pdb=" OE1 GLU E 81 " model vdw 2.136 3.120 nonbonded pdb=" OE1 GLN I 258 " pdb=" OG1 THR I 387 " model vdw 2.140 3.040 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.161 3.040 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.188 3.040 ... (remaining 170266 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 '2' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 514 through 664 or resid 701)) selection = chain 'B' selection = (chain 'F' and (resid 514 through 664 or resid 701)) } ncs_group { reference = (chain 'C' and (resid 31 through 505 or resid 601 through 602)) selection = (chain 'G' and (resid 31 through 505 or resid 601 through 602)) 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 'a' selection = chain 'e' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = chain 't' } 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: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 50.770 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.240 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 : 0.004 0.040 21141 Z= 0.216 Angle : 0.659 10.968 28906 Z= 0.282 Chirality : 0.047 0.297 3529 Planarity : 0.003 0.079 3466 Dihedral : 18.251 108.900 9471 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 21.18 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2384 helix: 1.74 (0.29), residues: 412 sheet: 0.15 (0.19), residues: 771 loop : 0.22 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 96 HIS 0.003 0.000 HIS G 105 PHE 0.007 0.001 PHE D 100G TYR 0.012 0.001 TYR D 100E ARG 0.009 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 55) link_NAG-ASN : angle 1.63079 ( 165) link_ALPHA1-6 : bond 0.00391 ( 5) link_ALPHA1-6 : angle 1.75237 ( 15) link_BETA1-4 : bond 0.00357 ( 50) link_BETA1-4 : angle 1.50162 ( 150) link_ALPHA1-2 : bond 0.00595 ( 3) link_ALPHA1-2 : angle 2.70991 ( 9) link_ALPHA1-3 : bond 0.00286 ( 6) link_ALPHA1-3 : angle 1.79232 ( 18) hydrogen bonds : bond 0.20304 ( 744) hydrogen bonds : angle 8.34713 ( 2046) SS BOND : bond 0.00149 ( 45) SS BOND : angle 0.42175 ( 90) covalent geometry : bond 0.00447 (20977) covalent geometry : angle 0.63825 (28459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8458 (tpp) cc_final: 0.8173 (mpp) REVERT: A 601 LYS cc_start: 0.8922 (mttm) cc_final: 0.8625 (mttp) REVERT: G 475 MET cc_start: 0.8732 (mmm) cc_final: 0.7608 (mpp) REVERT: B 655 LYS cc_start: 0.8419 (tptm) cc_final: 0.8210 (tptp) REVERT: F 599 SER cc_start: 0.9376 (t) cc_final: 0.9055 (m) REVERT: D 3 GLN cc_start: 0.8140 (mm110) cc_final: 0.7566 (mp10) REVERT: D 13 GLN cc_start: 0.8777 (mp10) cc_final: 0.8514 (tp40) REVERT: D 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7307 (t0) REVERT: D 83 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8905 (ptp-170) REVERT: D 100 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8084 (mtp85) REVERT: D 107 THR cc_start: 0.9026 (t) cc_final: 0.8788 (p) REVERT: E 5 THR cc_start: 0.9172 (m) cc_final: 0.8960 (p) REVERT: H 38 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8575 (ptt-90) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7890 (t0) REVERT: H 85 GLU cc_start: 0.8953 (pm20) cc_final: 0.8688 (pm20) REVERT: H 89 VAL cc_start: 0.8596 (t) cc_final: 0.8225 (p) REVERT: H 107 THR cc_start: 0.8795 (t) cc_final: 0.8449 (p) REVERT: L 24 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: L 70 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8272 (mm-30) REVERT: J 13 GLN cc_start: 0.8563 (mm110) cc_final: 0.8267 (mm110) REVERT: J 43 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8439 (mppt) REVERT: J 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7683 (t70) REVERT: K 79 GLN cc_start: 0.8369 (mt0) cc_final: 0.8148 (mt0) outliers start: 51 outliers final: 39 residues processed: 306 average time/residue: 1.4360 time to fit residues: 493.2314 Evaluate side-chains 258 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 388 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 651 ASN G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051471 restraints weight = 48277.129| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.47 r_work: 0.2514 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21141 Z= 0.227 Angle : 0.636 9.230 28906 Z= 0.305 Chirality : 0.045 0.293 3529 Planarity : 0.003 0.034 3466 Dihedral : 12.677 95.369 5120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 20.56 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2384 helix: 2.33 (0.29), residues: 384 sheet: 0.09 (0.19), residues: 759 loop : 0.19 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.004 0.001 HIS G 330 PHE 0.012 0.001 PHE C 383 TYR 0.019 0.002 TYR E 49 ARG 0.006 0.001 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 55) link_NAG-ASN : angle 1.88382 ( 165) link_ALPHA1-6 : bond 0.00188 ( 5) link_ALPHA1-6 : angle 1.97008 ( 15) link_BETA1-4 : bond 0.00352 ( 50) link_BETA1-4 : angle 1.52908 ( 150) link_ALPHA1-2 : bond 0.01114 ( 3) link_ALPHA1-2 : angle 2.32318 ( 9) link_ALPHA1-3 : bond 0.00972 ( 6) link_ALPHA1-3 : angle 1.99773 ( 18) hydrogen bonds : bond 0.04844 ( 744) hydrogen bonds : angle 5.87359 ( 2046) SS BOND : bond 0.00308 ( 45) SS BOND : angle 0.79706 ( 90) covalent geometry : bond 0.00529 (20977) covalent geometry : angle 0.60758 (28459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 2.083 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9140 (mttm) cc_final: 0.8819 (mtmm) REVERT: G 475 MET cc_start: 0.8825 (mmm) cc_final: 0.7994 (mpp) REVERT: B 632 ASP cc_start: 0.9140 (t0) cc_final: 0.8847 (t0) REVERT: B 655 LYS cc_start: 0.8810 (tptm) cc_final: 0.8514 (tptm) REVERT: I 92 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: I 114 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: F 599 SER cc_start: 0.9502 (t) cc_final: 0.9224 (p) REVERT: F 621 GLU cc_start: 0.9035 (tt0) cc_final: 0.8563 (pt0) REVERT: F 655 LYS cc_start: 0.7917 (tptt) cc_final: 0.7631 (ttmt) REVERT: D 13 GLN cc_start: 0.8840 (mp10) cc_final: 0.8372 (mm-40) REVERT: D 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7507 (t0) REVERT: D 89 VAL cc_start: 0.9015 (t) cc_final: 0.8738 (p) REVERT: D 100 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8184 (mtp85) REVERT: D 107 THR cc_start: 0.9011 (t) cc_final: 0.8808 (p) REVERT: E 79 GLN cc_start: 0.8196 (mt0) cc_final: 0.7915 (mp-120) REVERT: H 85 GLU cc_start: 0.9176 (pm20) cc_final: 0.8921 (pm20) REVERT: H 89 VAL cc_start: 0.8945 (t) cc_final: 0.8589 (p) REVERT: L 24 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7945 (ttp80) REVERT: J 13 GLN cc_start: 0.8703 (mm110) cc_final: 0.8442 (mm110) REVERT: J 72 ASP cc_start: 0.8446 (t0) cc_final: 0.7984 (t70) REVERT: K 17 GLU cc_start: 0.8822 (pt0) cc_final: 0.8610 (pm20) REVERT: K 24 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8139 (ttp80) REVERT: K 79 GLN cc_start: 0.8708 (mt0) cc_final: 0.8199 (mt0) outliers start: 64 outliers final: 24 residues processed: 291 average time/residue: 1.6370 time to fit residues: 531.3630 Evaluate side-chains 243 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 105 HIS G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN H 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051672 restraints weight = 47728.959| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.41 r_work: 0.2531 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21141 Z= 0.177 Angle : 0.598 9.480 28906 Z= 0.284 Chirality : 0.045 0.253 3529 Planarity : 0.003 0.039 3466 Dihedral : 11.039 90.724 5089 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.76 % Allowed : 21.42 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.78 (0.18), residues: 2384 helix: 2.90 (0.29), residues: 358 sheet: 0.11 (0.19), residues: 756 loop : 0.19 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.003 0.001 HIS G 330 PHE 0.011 0.001 PHE C 383 TYR 0.017 0.001 TYR J 100E ARG 0.008 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 55) link_NAG-ASN : angle 1.86023 ( 165) link_ALPHA1-6 : bond 0.00390 ( 5) link_ALPHA1-6 : angle 1.87598 ( 15) link_BETA1-4 : bond 0.00340 ( 50) link_BETA1-4 : angle 1.53274 ( 150) link_ALPHA1-2 : bond 0.01077 ( 3) link_ALPHA1-2 : angle 2.41583 ( 9) link_ALPHA1-3 : bond 0.01108 ( 6) link_ALPHA1-3 : angle 1.60253 ( 18) hydrogen bonds : bond 0.04171 ( 744) hydrogen bonds : angle 5.38483 ( 2046) SS BOND : bond 0.00253 ( 45) SS BOND : angle 0.65560 ( 90) covalent geometry : bond 0.00408 (20977) covalent geometry : angle 0.56971 (28459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 228 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9195 (mttm) cc_final: 0.8919 (mttp) REVERT: G 475 MET cc_start: 0.8780 (mmm) cc_final: 0.8025 (mpp) REVERT: B 632 ASP cc_start: 0.9179 (t0) cc_final: 0.8901 (t0) REVERT: B 655 LYS cc_start: 0.8806 (tptm) cc_final: 0.8497 (tptm) REVERT: I 92 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8573 (tp30) REVERT: I 114 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: F 599 SER cc_start: 0.9507 (t) cc_final: 0.9244 (p) REVERT: F 621 GLU cc_start: 0.8996 (tt0) cc_final: 0.8763 (pt0) REVERT: F 655 LYS cc_start: 0.7944 (tptt) cc_final: 0.7595 (ttpt) REVERT: D 13 GLN cc_start: 0.8850 (mp10) cc_final: 0.8350 (mm-40) REVERT: D 34 MET cc_start: 0.9124 (mmt) cc_final: 0.8879 (tpp) REVERT: D 72 ASP cc_start: 0.8225 (t0) cc_final: 0.7511 (t0) REVERT: D 85 GLU cc_start: 0.9264 (pm20) cc_final: 0.9036 (pm20) REVERT: D 86 ASP cc_start: 0.9089 (m-30) cc_final: 0.8563 (m-30) REVERT: D 89 VAL cc_start: 0.9039 (t) cc_final: 0.8786 (p) REVERT: D 100 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8272 (mtp85) REVERT: E 79 GLN cc_start: 0.8271 (mt0) cc_final: 0.8011 (mp-120) REVERT: H 46 GLU cc_start: 0.8481 (tt0) cc_final: 0.8266 (tt0) REVERT: L 24 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7880 (ttm-80) REVERT: L 39 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7967 (mmtm) REVERT: L 81 GLU cc_start: 0.8480 (pp20) cc_final: 0.8219 (pp20) REVERT: L 105 GLU cc_start: 0.5491 (tp30) cc_final: 0.5156 (tm-30) REVERT: J 13 GLN cc_start: 0.8722 (mm110) cc_final: 0.8467 (mm110) REVERT: J 43 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8611 (mppt) REVERT: J 72 ASP cc_start: 0.8461 (t0) cc_final: 0.7990 (t70) REVERT: K 79 GLN cc_start: 0.8492 (mt0) cc_final: 0.8167 (mt0) outliers start: 79 outliers final: 33 residues processed: 288 average time/residue: 1.4960 time to fit residues: 481.9058 Evaluate side-chains 245 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 147 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 80 ASN G 114 GLN F 656 ASN H 13 GLN H 81 GLN J 39 GLN K 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051927 restraints weight = 48214.878| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.54 r_work: 0.2532 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21141 Z= 0.154 Angle : 0.589 9.544 28906 Z= 0.277 Chirality : 0.044 0.251 3529 Planarity : 0.003 0.040 3466 Dihedral : 9.955 85.422 5089 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.38 % Allowed : 21.99 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2384 helix: 2.98 (0.28), residues: 358 sheet: 0.14 (0.18), residues: 750 loop : 0.15 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.002 0.001 HIS G 330 PHE 0.012 0.001 PHE G 383 TYR 0.016 0.001 TYR J 100E ARG 0.008 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 55) link_NAG-ASN : angle 1.83522 ( 165) link_ALPHA1-6 : bond 0.00506 ( 5) link_ALPHA1-6 : angle 1.86099 ( 15) link_BETA1-4 : bond 0.00369 ( 50) link_BETA1-4 : angle 1.53713 ( 150) link_ALPHA1-2 : bond 0.01029 ( 3) link_ALPHA1-2 : angle 2.43795 ( 9) link_ALPHA1-3 : bond 0.01154 ( 6) link_ALPHA1-3 : angle 1.64885 ( 18) hydrogen bonds : bond 0.03808 ( 744) hydrogen bonds : angle 5.11963 ( 2046) SS BOND : bond 0.00242 ( 45) SS BOND : angle 0.58462 ( 90) covalent geometry : bond 0.00353 (20977) covalent geometry : angle 0.56030 (28459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: A 601 LYS cc_start: 0.9192 (mttm) cc_final: 0.8883 (mtmm) REVERT: G 141 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (p0) REVERT: G 475 MET cc_start: 0.8765 (mmm) cc_final: 0.8033 (mpp) REVERT: B 632 ASP cc_start: 0.9148 (t0) cc_final: 0.8855 (t0) REVERT: B 655 LYS cc_start: 0.8727 (tptm) cc_final: 0.8437 (tptm) REVERT: I 92 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: F 599 SER cc_start: 0.9489 (t) cc_final: 0.9250 (p) REVERT: F 655 LYS cc_start: 0.7949 (tptt) cc_final: 0.7612 (ttpt) REVERT: D 13 GLN cc_start: 0.8878 (mp10) cc_final: 0.8370 (mm-40) REVERT: D 34 MET cc_start: 0.9113 (mmp) cc_final: 0.8876 (tpp) REVERT: D 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7474 (t0) REVERT: D 86 ASP cc_start: 0.9056 (m-30) cc_final: 0.8505 (m-30) REVERT: D 89 VAL cc_start: 0.9063 (t) cc_final: 0.8829 (p) REVERT: D 100 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8309 (mtp85) REVERT: E 79 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (mp-120) REVERT: H 46 GLU cc_start: 0.8484 (tt0) cc_final: 0.7968 (pt0) REVERT: L 24 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7879 (ttm-80) REVERT: L 105 GLU cc_start: 0.5476 (tp30) cc_final: 0.5132 (tm-30) REVERT: J 13 GLN cc_start: 0.8734 (mm110) cc_final: 0.8467 (mm110) REVERT: J 43 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8577 (mppt) REVERT: J 72 ASP cc_start: 0.8466 (t0) cc_final: 0.7997 (t70) REVERT: J 105 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8847 (mm-40) outliers start: 71 outliers final: 36 residues processed: 282 average time/residue: 1.4687 time to fit residues: 464.4312 Evaluate side-chains 253 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 203 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 13 GLN H 13 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.051389 restraints weight = 48560.123| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.42 r_work: 0.2523 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21141 Z= 0.198 Angle : 0.603 9.606 28906 Z= 0.283 Chirality : 0.045 0.260 3529 Planarity : 0.003 0.032 3466 Dihedral : 9.243 80.308 5088 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 22.47 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2384 helix: 2.73 (0.29), residues: 371 sheet: 0.13 (0.18), residues: 753 loop : 0.16 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 96 HIS 0.003 0.001 HIS G 330 PHE 0.012 0.001 PHE G 383 TYR 0.016 0.001 TYR J 100E ARG 0.008 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 55) link_NAG-ASN : angle 1.91223 ( 165) link_ALPHA1-6 : bond 0.00549 ( 5) link_ALPHA1-6 : angle 1.83997 ( 15) link_BETA1-4 : bond 0.00351 ( 50) link_BETA1-4 : angle 1.57546 ( 150) link_ALPHA1-2 : bond 0.00961 ( 3) link_ALPHA1-2 : angle 2.48123 ( 9) link_ALPHA1-3 : bond 0.01085 ( 6) link_ALPHA1-3 : angle 1.66424 ( 18) hydrogen bonds : bond 0.03914 ( 744) hydrogen bonds : angle 5.05058 ( 2046) SS BOND : bond 0.00271 ( 45) SS BOND : angle 0.63616 ( 90) covalent geometry : bond 0.00458 (20977) covalent geometry : angle 0.57259 (28459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 2.085 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8903 (pp) REVERT: C 189 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (pttm) REVERT: C 348 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: A 601 LYS cc_start: 0.9208 (mttm) cc_final: 0.8932 (mttp) REVERT: G 475 MET cc_start: 0.8723 (mmm) cc_final: 0.7997 (mpp) REVERT: B 584 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8603 (mt-10) REVERT: B 632 ASP cc_start: 0.9194 (t0) cc_final: 0.8888 (t0) REVERT: B 655 LYS cc_start: 0.8737 (tptm) cc_final: 0.8443 (tptm) REVERT: I 114 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: F 599 SER cc_start: 0.9499 (t) cc_final: 0.9244 (p) REVERT: F 621 GLU cc_start: 0.9045 (pt0) cc_final: 0.8763 (pt0) REVERT: F 655 LYS cc_start: 0.7986 (tptt) cc_final: 0.7670 (ttpt) REVERT: D 6 GLU cc_start: 0.8015 (mp0) cc_final: 0.7227 (pm20) REVERT: D 13 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8450 (mm-40) REVERT: D 34 MET cc_start: 0.9160 (mmp) cc_final: 0.8913 (tpp) REVERT: D 72 ASP cc_start: 0.8225 (t0) cc_final: 0.7475 (t0) REVERT: D 86 ASP cc_start: 0.9016 (m-30) cc_final: 0.8487 (m-30) REVERT: D 89 VAL cc_start: 0.9060 (t) cc_final: 0.8798 (p) REVERT: D 100 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8374 (mtp85) REVERT: D 100 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8843 (p90) REVERT: E 54 ARG cc_start: 0.8700 (ttm110) cc_final: 0.8252 (ttm-80) REVERT: H 46 GLU cc_start: 0.8530 (tt0) cc_final: 0.8037 (pt0) REVERT: L 105 GLU cc_start: 0.5424 (tp30) cc_final: 0.5090 (tm-30) REVERT: J 13 GLN cc_start: 0.8738 (mm110) cc_final: 0.8474 (mm110) REVERT: J 72 ASP cc_start: 0.8495 (t0) cc_final: 0.8021 (t70) REVERT: J 100 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.8949 (p) REVERT: J 105 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8896 (mm-40) REVERT: K 103 LYS cc_start: 0.8793 (tppp) cc_final: 0.8321 (tppp) outliers start: 77 outliers final: 38 residues processed: 284 average time/residue: 1.4300 time to fit residues: 457.8168 Evaluate side-chains 256 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 153 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 114 GLN F 656 ASN D 3 GLN H 13 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.052121 restraints weight = 48005.062| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.52 r_work: 0.2535 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21141 Z= 0.145 Angle : 0.595 9.548 28906 Z= 0.278 Chirality : 0.044 0.270 3529 Planarity : 0.003 0.036 3466 Dihedral : 8.705 74.990 5085 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.14 % Allowed : 23.42 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.81 (0.18), residues: 2384 helix: 3.06 (0.28), residues: 360 sheet: 0.14 (0.18), residues: 753 loop : 0.14 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 103 HIS 0.002 0.000 HIS G 330 PHE 0.012 0.001 PHE G 383 TYR 0.015 0.001 TYR J 100E ARG 0.010 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 55) link_NAG-ASN : angle 1.84220 ( 165) link_ALPHA1-6 : bond 0.00678 ( 5) link_ALPHA1-6 : angle 1.81553 ( 15) link_BETA1-4 : bond 0.00385 ( 50) link_BETA1-4 : angle 1.55965 ( 150) link_ALPHA1-2 : bond 0.01004 ( 3) link_ALPHA1-2 : angle 2.51293 ( 9) link_ALPHA1-3 : bond 0.01159 ( 6) link_ALPHA1-3 : angle 1.59436 ( 18) hydrogen bonds : bond 0.03640 ( 744) hydrogen bonds : angle 4.92270 ( 2046) SS BOND : bond 0.00231 ( 45) SS BOND : angle 0.59889 ( 90) covalent geometry : bond 0.00333 (20977) covalent geometry : angle 0.56651 (28459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8871 (pp) REVERT: C 189 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7556 (pttm) REVERT: C 348 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8318 (mp10) REVERT: A 601 LYS cc_start: 0.9195 (mttm) cc_final: 0.8883 (mtmm) REVERT: G 475 MET cc_start: 0.8699 (mmm) cc_final: 0.7977 (mpp) REVERT: B 632 ASP cc_start: 0.9164 (t0) cc_final: 0.8841 (t0) REVERT: B 655 LYS cc_start: 0.8702 (tptm) cc_final: 0.8416 (tptm) REVERT: I 114 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: F 599 SER cc_start: 0.9473 (t) cc_final: 0.9234 (p) REVERT: F 621 GLU cc_start: 0.9022 (pt0) cc_final: 0.8693 (pt0) REVERT: F 655 LYS cc_start: 0.8042 (tptt) cc_final: 0.7740 (ttpt) REVERT: D 13 GLN cc_start: 0.9045 (mp10) cc_final: 0.8704 (tp40) REVERT: D 34 MET cc_start: 0.9141 (mmp) cc_final: 0.8907 (tpp) REVERT: D 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7451 (t0) REVERT: D 86 ASP cc_start: 0.9020 (m-30) cc_final: 0.8478 (m-30) REVERT: D 89 VAL cc_start: 0.9060 (t) cc_final: 0.8797 (p) REVERT: D 100 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8363 (mtp85) REVERT: E 32 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.6164 (mmtm) REVERT: E 54 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8216 (ttm-80) REVERT: H 46 GLU cc_start: 0.8511 (tt0) cc_final: 0.8030 (pt0) REVERT: L 24 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7789 (ttm-80) REVERT: L 39 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8094 (mmtm) REVERT: L 105 GLU cc_start: 0.5498 (tp30) cc_final: 0.5201 (tm-30) REVERT: J 13 GLN cc_start: 0.8741 (mm110) cc_final: 0.8478 (mm110) REVERT: J 43 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8499 (mppt) REVERT: J 72 ASP cc_start: 0.8467 (t0) cc_final: 0.8013 (t70) REVERT: J 100 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8936 (p) REVERT: J 105 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8920 (mm-40) REVERT: K 103 LYS cc_start: 0.8772 (tppp) cc_final: 0.8287 (tppp) outliers start: 66 outliers final: 34 residues processed: 277 average time/residue: 1.4890 time to fit residues: 462.6033 Evaluate side-chains 253 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 210 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 105 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051893 restraints weight = 47927.037| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.53 r_work: 0.2534 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21141 Z= 0.155 Angle : 0.596 9.581 28906 Z= 0.278 Chirality : 0.044 0.272 3529 Planarity : 0.003 0.030 3466 Dihedral : 8.183 68.266 5080 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.19 % Allowed : 23.66 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2384 helix: 2.89 (0.28), residues: 369 sheet: 0.16 (0.18), residues: 753 loop : 0.17 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 PHE 0.012 0.001 PHE G 383 TYR 0.016 0.001 TYR D 100E ARG 0.010 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 55) link_NAG-ASN : angle 1.83974 ( 165) link_ALPHA1-6 : bond 0.00721 ( 5) link_ALPHA1-6 : angle 1.73170 ( 15) link_BETA1-4 : bond 0.00386 ( 50) link_BETA1-4 : angle 1.57015 ( 150) link_ALPHA1-2 : bond 0.00935 ( 3) link_ALPHA1-2 : angle 2.48571 ( 9) link_ALPHA1-3 : bond 0.01111 ( 6) link_ALPHA1-3 : angle 1.55090 ( 18) hydrogen bonds : bond 0.03638 ( 744) hydrogen bonds : angle 4.85851 ( 2046) SS BOND : bond 0.00229 ( 45) SS BOND : angle 0.60615 ( 90) covalent geometry : bond 0.00359 (20977) covalent geometry : angle 0.56733 (28459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8881 (pp) REVERT: C 348 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: A 601 LYS cc_start: 0.9201 (mttm) cc_final: 0.8920 (mttp) REVERT: G 475 MET cc_start: 0.8697 (mmm) cc_final: 0.7987 (mpp) REVERT: B 584 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 632 ASP cc_start: 0.9161 (t0) cc_final: 0.8888 (t0) REVERT: B 655 LYS cc_start: 0.8693 (tptm) cc_final: 0.8386 (tptm) REVERT: I 114 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: I 231 LYS cc_start: 0.9454 (mttt) cc_final: 0.9206 (mttm) REVERT: F 599 SER cc_start: 0.9459 (t) cc_final: 0.9232 (p) REVERT: F 621 GLU cc_start: 0.9019 (pt0) cc_final: 0.8695 (pt0) REVERT: F 655 LYS cc_start: 0.8008 (tptt) cc_final: 0.7707 (ttpt) REVERT: D 13 GLN cc_start: 0.9104 (mp10) cc_final: 0.8670 (mm-40) REVERT: D 34 MET cc_start: 0.9147 (mmp) cc_final: 0.8915 (tpp) REVERT: D 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7458 (t0) REVERT: D 86 ASP cc_start: 0.9012 (m-30) cc_final: 0.8436 (m-30) REVERT: D 89 VAL cc_start: 0.9061 (t) cc_final: 0.8802 (p) REVERT: D 100 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8357 (mtp85) REVERT: E 32 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6083 (mmtm) REVERT: E 54 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8244 (ttm-80) REVERT: H 46 GLU cc_start: 0.8472 (tt0) cc_final: 0.8019 (pt0) REVERT: H 105 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8496 (mm-40) REVERT: L 24 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7763 (ttm-80) REVERT: L 105 GLU cc_start: 0.5422 (tp30) cc_final: 0.5109 (tm-30) REVERT: J 13 GLN cc_start: 0.8752 (mm110) cc_final: 0.8480 (mm110) REVERT: J 43 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8524 (mppt) REVERT: J 72 ASP cc_start: 0.8476 (t0) cc_final: 0.8012 (t70) REVERT: J 100 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8953 (p) REVERT: J 105 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8949 (mm-40) REVERT: K 17 GLU cc_start: 0.8662 (pm20) cc_final: 0.8349 (pm20) REVERT: K 24 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7852 (mtm-85) REVERT: K 103 LYS cc_start: 0.8764 (tppp) cc_final: 0.8235 (tppp) outliers start: 67 outliers final: 38 residues processed: 274 average time/residue: 1.4472 time to fit residues: 443.6375 Evaluate side-chains 259 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 17 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.052010 restraints weight = 48158.186| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.54 r_work: 0.2536 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21141 Z= 0.152 Angle : 0.603 9.583 28906 Z= 0.280 Chirality : 0.044 0.274 3529 Planarity : 0.003 0.045 3466 Dihedral : 7.772 61.088 5080 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 24.51 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2384 helix: 2.90 (0.28), residues: 369 sheet: 0.19 (0.19), residues: 753 loop : 0.16 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 103 HIS 0.002 0.001 HIS G 105 PHE 0.012 0.001 PHE G 383 TYR 0.014 0.001 TYR J 100E ARG 0.013 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 55) link_NAG-ASN : angle 1.81987 ( 165) link_ALPHA1-6 : bond 0.00770 ( 5) link_ALPHA1-6 : angle 1.60613 ( 15) link_BETA1-4 : bond 0.00394 ( 50) link_BETA1-4 : angle 1.58038 ( 150) link_ALPHA1-2 : bond 0.00933 ( 3) link_ALPHA1-2 : angle 2.47914 ( 9) link_ALPHA1-3 : bond 0.01127 ( 6) link_ALPHA1-3 : angle 1.50403 ( 18) hydrogen bonds : bond 0.03574 ( 744) hydrogen bonds : angle 4.78801 ( 2046) SS BOND : bond 0.00225 ( 45) SS BOND : angle 0.64190 ( 90) covalent geometry : bond 0.00351 (20977) covalent geometry : angle 0.57575 (28459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8872 (pp) REVERT: C 348 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: A 601 LYS cc_start: 0.9196 (mttm) cc_final: 0.8905 (mttp) REVERT: G 475 MET cc_start: 0.8719 (mmm) cc_final: 0.8013 (mpp) REVERT: B 584 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 632 ASP cc_start: 0.9130 (t70) cc_final: 0.8847 (t0) REVERT: B 655 LYS cc_start: 0.8665 (tptm) cc_final: 0.8384 (tptm) REVERT: I 114 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: I 231 LYS cc_start: 0.9449 (mttt) cc_final: 0.9201 (mttm) REVERT: F 599 SER cc_start: 0.9460 (t) cc_final: 0.9248 (p) REVERT: F 621 GLU cc_start: 0.8989 (pt0) cc_final: 0.8640 (pt0) REVERT: F 655 LYS cc_start: 0.8004 (tptt) cc_final: 0.7698 (ttpt) REVERT: D 13 GLN cc_start: 0.9081 (mp10) cc_final: 0.8634 (mm-40) REVERT: D 34 MET cc_start: 0.9155 (mmp) cc_final: 0.8928 (tpp) REVERT: D 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7477 (t0) REVERT: D 89 VAL cc_start: 0.9072 (t) cc_final: 0.8800 (p) REVERT: D 100 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8373 (mtp85) REVERT: E 32 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.6091 (mmtm) REVERT: E 54 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8268 (ttm-80) REVERT: H 46 GLU cc_start: 0.8476 (tt0) cc_final: 0.8052 (pt0) REVERT: H 105 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8512 (mm-40) REVERT: L 24 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7798 (ttm-80) REVERT: J 13 GLN cc_start: 0.8761 (mm110) cc_final: 0.8492 (mm110) REVERT: J 43 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8466 (mppt) REVERT: J 72 ASP cc_start: 0.8479 (t0) cc_final: 0.8019 (t70) REVERT: J 100 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.8964 (p) REVERT: J 105 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8966 (mm-40) REVERT: K 17 GLU cc_start: 0.8643 (pm20) cc_final: 0.8335 (pm20) REVERT: K 24 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7806 (mtm-85) REVERT: K 74 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8383 (p) REVERT: K 103 LYS cc_start: 0.8774 (tppp) cc_final: 0.8252 (tppp) outliers start: 55 outliers final: 37 residues processed: 263 average time/residue: 1.5739 time to fit residues: 464.4193 Evaluate side-chains 259 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 172 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 216 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 105 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052867 restraints weight = 48004.774| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.54 r_work: 0.2557 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21141 Z= 0.122 Angle : 0.592 9.792 28906 Z= 0.274 Chirality : 0.043 0.276 3529 Planarity : 0.003 0.051 3466 Dihedral : 7.090 56.871 5080 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.33 % Allowed : 24.75 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2384 helix: 2.93 (0.28), residues: 369 sheet: 0.22 (0.19), residues: 753 loop : 0.19 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 479 HIS 0.002 0.000 HIS G 105 PHE 0.011 0.001 PHE G 383 TYR 0.012 0.001 TYR J 100E ARG 0.012 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 55) link_NAG-ASN : angle 1.74467 ( 165) link_ALPHA1-6 : bond 0.00847 ( 5) link_ALPHA1-6 : angle 1.54432 ( 15) link_BETA1-4 : bond 0.00424 ( 50) link_BETA1-4 : angle 1.57825 ( 150) link_ALPHA1-2 : bond 0.00936 ( 3) link_ALPHA1-2 : angle 2.44170 ( 9) link_ALPHA1-3 : bond 0.01168 ( 6) link_ALPHA1-3 : angle 1.38124 ( 18) hydrogen bonds : bond 0.03384 ( 744) hydrogen bonds : angle 4.67531 ( 2046) SS BOND : bond 0.00262 ( 45) SS BOND : angle 0.61937 ( 90) covalent geometry : bond 0.00278 (20977) covalent geometry : angle 0.56513 (28459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 2.331 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8855 (pp) REVERT: C 348 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: A 601 LYS cc_start: 0.9194 (mttm) cc_final: 0.8896 (mttp) REVERT: G 475 MET cc_start: 0.8673 (mmm) cc_final: 0.7969 (mpp) REVERT: B 584 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 632 ASP cc_start: 0.9030 (t70) cc_final: 0.8752 (t0) REVERT: I 114 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: I 231 LYS cc_start: 0.9439 (mttt) cc_final: 0.9194 (mttm) REVERT: F 599 SER cc_start: 0.9451 (t) cc_final: 0.9236 (p) REVERT: F 621 GLU cc_start: 0.8993 (pt0) cc_final: 0.8597 (pt0) REVERT: F 655 LYS cc_start: 0.7947 (tptt) cc_final: 0.7610 (ttpt) REVERT: D 13 GLN cc_start: 0.9090 (mp10) cc_final: 0.8648 (mm-40) REVERT: D 72 ASP cc_start: 0.8216 (t0) cc_final: 0.7469 (t0) REVERT: D 86 ASP cc_start: 0.8913 (m-30) cc_final: 0.8418 (m-30) REVERT: D 89 VAL cc_start: 0.9072 (t) cc_final: 0.8821 (p) REVERT: D 100 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8321 (mtp85) REVERT: E 32 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.6140 (mmtm) REVERT: E 54 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8235 (ttm-80) REVERT: E 103 LYS cc_start: 0.8757 (tppp) cc_final: 0.8439 (tptp) REVERT: H 46 GLU cc_start: 0.8430 (tt0) cc_final: 0.8024 (pt0) REVERT: H 105 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8536 (mm-40) REVERT: L 24 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7832 (ttm-80) REVERT: J 13 GLN cc_start: 0.8779 (mm110) cc_final: 0.8519 (mm110) REVERT: J 43 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8470 (mppt) REVERT: J 72 ASP cc_start: 0.8473 (t0) cc_final: 0.8013 (t70) REVERT: J 105 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8975 (mm-40) REVERT: K 17 GLU cc_start: 0.8627 (pm20) cc_final: 0.8323 (pm20) REVERT: K 24 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7816 (mtm-85) REVERT: K 74 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8401 (p) REVERT: K 103 LYS cc_start: 0.8753 (tppp) cc_final: 0.8245 (tppp) outliers start: 49 outliers final: 32 residues processed: 265 average time/residue: 1.5563 time to fit residues: 459.8163 Evaluate side-chains 258 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 47 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN B 651 ASN F 656 ASN D 3 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.050231 restraints weight = 48723.132| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.54 r_work: 0.2492 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 21141 Z= 0.306 Angle : 0.685 10.382 28906 Z= 0.320 Chirality : 0.046 0.267 3529 Planarity : 0.004 0.060 3466 Dihedral : 7.150 56.743 5080 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.28 % Allowed : 25.13 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2384 helix: 2.66 (0.29), residues: 371 sheet: 0.18 (0.19), residues: 738 loop : 0.06 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 103 HIS 0.004 0.001 HIS G 330 PHE 0.015 0.002 PHE C 383 TYR 0.019 0.002 TYR D 100E ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 55) link_NAG-ASN : angle 2.03093 ( 165) link_ALPHA1-6 : bond 0.00706 ( 5) link_ALPHA1-6 : angle 1.50742 ( 15) link_BETA1-4 : bond 0.00349 ( 50) link_BETA1-4 : angle 1.69932 ( 150) link_ALPHA1-2 : bond 0.00798 ( 3) link_ALPHA1-2 : angle 2.40279 ( 9) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 1.55698 ( 18) hydrogen bonds : bond 0.04160 ( 744) hydrogen bonds : angle 4.95292 ( 2046) SS BOND : bond 0.00374 ( 45) SS BOND : angle 0.83500 ( 90) covalent geometry : bond 0.00713 (20977) covalent geometry : angle 0.65639 (28459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9214 (mttm) cc_final: 0.8936 (mttp) REVERT: G 166 ARG cc_start: 0.4355 (tmt170) cc_final: 0.4038 (tmt170) REVERT: G 475 MET cc_start: 0.8763 (mmm) cc_final: 0.8017 (mpp) REVERT: B 584 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8634 (mt-10) REVERT: B 632 ASP cc_start: 0.9105 (t70) cc_final: 0.8801 (t0) REVERT: B 633 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8831 (mtpt) REVERT: I 114 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: F 599 SER cc_start: 0.9492 (t) cc_final: 0.9240 (p) REVERT: F 621 GLU cc_start: 0.9001 (pt0) cc_final: 0.8606 (pt0) REVERT: F 655 LYS cc_start: 0.8012 (tptt) cc_final: 0.7686 (ttmt) REVERT: D 72 ASP cc_start: 0.8229 (t0) cc_final: 0.7498 (t0) REVERT: D 89 VAL cc_start: 0.9062 (t) cc_final: 0.8808 (p) REVERT: D 100 ARG cc_start: 0.8793 (mtm-85) cc_final: 0.8378 (mtp85) REVERT: E 32 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.6097 (mmtm) REVERT: E 54 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8310 (ttm-80) REVERT: H 46 GLU cc_start: 0.8532 (tt0) cc_final: 0.8131 (pt0) REVERT: H 105 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8612 (mm-40) REVERT: L 24 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7864 (ttm-80) REVERT: L 70 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8276 (mm-30) REVERT: J 13 GLN cc_start: 0.8754 (mm110) cc_final: 0.8489 (mm110) REVERT: J 43 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8496 (mppt) REVERT: J 72 ASP cc_start: 0.8506 (t0) cc_final: 0.8041 (t70) REVERT: J 100 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8950 (p) REVERT: J 105 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8959 (mm-40) REVERT: K 17 GLU cc_start: 0.8641 (pm20) cc_final: 0.8319 (pm20) REVERT: K 74 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8374 (p) REVERT: K 103 LYS cc_start: 0.8725 (tppp) cc_final: 0.8201 (tppp) outliers start: 48 outliers final: 31 residues processed: 253 average time/residue: 1.5429 time to fit residues: 435.4120 Evaluate side-chains 245 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 142 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 216 optimal weight: 0.0870 chunk 179 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 152 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 13 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.052379 restraints weight = 48151.666| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.55 r_work: 0.2547 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21141 Z= 0.126 Angle : 0.610 9.870 28906 Z= 0.284 Chirality : 0.043 0.275 3529 Planarity : 0.003 0.056 3466 Dihedral : 6.684 56.892 5078 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 25.70 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2384 helix: 2.84 (0.28), residues: 369 sheet: 0.17 (0.19), residues: 744 loop : 0.12 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.002 0.001 HIS D 35 PHE 0.011 0.001 PHE G 383 TYR 0.021 0.001 TYR E 49 ARG 0.011 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 55) link_NAG-ASN : angle 1.75155 ( 165) link_ALPHA1-6 : bond 0.00889 ( 5) link_ALPHA1-6 : angle 1.45144 ( 15) link_BETA1-4 : bond 0.00414 ( 50) link_BETA1-4 : angle 1.60819 ( 150) link_ALPHA1-2 : bond 0.00891 ( 3) link_ALPHA1-2 : angle 2.48391 ( 9) link_ALPHA1-3 : bond 0.01154 ( 6) link_ALPHA1-3 : angle 1.25691 ( 18) hydrogen bonds : bond 0.03450 ( 744) hydrogen bonds : angle 4.73350 ( 2046) SS BOND : bond 0.00217 ( 45) SS BOND : angle 0.60356 ( 90) covalent geometry : bond 0.00288 (20977) covalent geometry : angle 0.58404 (28459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12499.34 seconds wall clock time: 214 minutes 44.69 seconds (12884.69 seconds total)