Starting phenix.real_space_refine on Fri Feb 6 04:41:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.map" model { file = "/net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nc0_49239/02_2026/9nc0_49239.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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 126 5.16 5 C 13956 2.51 5 N 3606 2.21 5 O 4793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22481 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3618 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1181 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3618 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1181 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "G" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3618 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 22, 'TRANS': 434} Chain breaks: 1 Chain: "F" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1181 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 130 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 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: "r" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 130 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 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: "0" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "3" 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: "4" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "5" 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: "6" 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: "7" 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: "8" 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: "9" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 130 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "AA" 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: "BA" 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: "CA" 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: "DA" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 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 Time building chain proxies: 5.80, per 1000 atoms: 0.26 Number of scatterers: 22481 At special positions: 0 Unit cell: (156.2, 149.6, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4793 8.00 N 3606 7.00 C 13956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.10 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.01 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.10 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.09 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.11 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.14 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.10 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.07 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 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 D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.08 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.01 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.11 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.09 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 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 J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.09 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 9 4 " - " MAN 9 5 " " MAN 9 5 " - " MAN 9 6 " " MAN 9 8 " - " MAN 9 9 " " MAN Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN Z 8 " - " MAN Z 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 4 " - " MAN 0 5 " " BMA 7 3 " - " MAN 7 4 " " BMA 9 3 " - " MAN 9 4 " " MAN 9 7 " - " MAN 9 11 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 7 " - " MAN Z 11 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 5 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 11 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " MAN 0 6 " - " MAN 0 7 " " BMA 4 3 " - " MAN 4 4 " " BMA 7 3 " - " MAN 7 5 " " BMA 9 3 " - " MAN 9 7 " " MAN 9 7 " - " MAN 9 8 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 7 " - " MAN Z 8 " " BMA h 3 " - " MAN h 5 " " BMA m 3 " - " MAN m 4 " " BMA p 3 " - " MAN p 5 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 8 " " BMA z 3 " - " MAN z 5 " BETA1-2 " MAN 9 7 " - " NAG 9 10 " " MAN Z 7 " - " NAG Z 10 " " MAN r 7 " - " NAG r 10 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG 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 x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " NAG-ASN " NAG 0 1 " - " ASN E 262 " " NAG 1 1 " - " ASN E 276 " " NAG 2 1 " - " ASN E 289 " " NAG 3 1 " - " ASN E 295 " " NAG 4 1 " - " ASN E 301 " " NAG 5 1 " - " ASN E 332 " " NAG 6 1 " - " ASN E 339 " " NAG 7 1 " - " ASN E 362 " " NAG 8 1 " - " ASN E 392 " " NAG 9 1 " - " ASN E 386 " " NAG A 601 " - " ASN A 187B" " NAG A 602 " - " ASN A 356 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 463 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 187B" " NAG C 602 " - " ASN C 356 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 463 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 187B" " NAG E 602 " - " ASN E 356 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 463 " " NAG F 701 " - " ASN F 611 " " NAG M 1 " - " ASN A 130 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 289 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 339 " " NAG X 1 " - " ASN A 362 " " NAG Y 1 " - " ASN A 392 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 396 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN A 88 " " NAG d 1 " - " ASN B 625 " " NAG e 1 " - " ASN C 130 " " NAG f 1 " - " ASN C 156 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 241 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 276 " " NAG k 1 " - " ASN C 289 " " NAG l 1 " - " ASN C 295 " " NAG m 1 " - " ASN C 301 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 339 " " NAG p 1 " - " ASN C 362 " " NAG q 1 " - " ASN C 392 " " NAG r 1 " - " ASN C 386 " " NAG s 1 " - " ASN C 396 " " NAG t 1 " - " ASN C 448 " " NAG u 1 " - " ASN C 88 " " NAG v 1 " - " ASN D 625 " " NAG w 1 " - " ASN E 130 " " NAG x 1 " - " ASN E 156 " " NAG y 1 " - " ASN E 197 " " NAG z 1 " - " ASN E 241 " " NAGAA 1 " - " ASN E 396 " " NAGBA 1 " - " ASN E 448 " " NAGCA 1 " - " ASN E 88 " " NAGDA 1 " - " ASN F 625 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 940.6 milliseconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4686 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 23.6% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.531A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.931A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.745A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.856A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 555 removed outlier: 3.510A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 555 " --> pdb=" O GLN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 597 removed outlier: 3.727A pdb=" N LEU B 568 " --> pdb=" O HIS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.504A pdb=" N ASN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.777A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) 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: 3.644A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.854A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.648A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.727A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.833A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.592A pdb=" N GLY D 521 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 555 removed outlier: 3.683A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN D 550 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN D 552 " --> pdb=" O ILE D 548 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 597 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.762A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.774A pdb=" N LEU D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.650A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.753A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.537A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.736A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.846A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.825A pdb=" N GLY F 521 " --> pdb=" O MET F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 555 removed outlier: 3.542A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY F 547 " --> pdb=" O ASN F 543 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 549 " --> pdb=" O LEU F 545 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN F 552 " --> pdb=" O ILE F 548 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 555 " --> pdb=" O GLN F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 597 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.770A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.769A pdb=" N LEU F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.648A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.523A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.899A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132A Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.230A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.414A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 11 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.533A pdb=" N ALA C 497 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.914A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 132A Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 184 Processing sheet with id=AC1, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.177A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.518A pdb=" N ASN C 301 " --> pdb=" O ILE C 322A" (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 11 current: chain 'G' and resid 46 through 52 removed outlier: 3.582A pdb=" N ASN G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 56 through 59 current: chain 'G' and resid 100J through 103 Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 53 through 54 current: chain 'I' and resid 97 through 98 Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 499 removed outlier: 3.536A pdb=" N ALA E 497 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.892A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'E' and resid 130 through 132A Processing sheet with id=AD3, first strand: chain 'E' and resid 181 through 184 Processing sheet with id=AD4, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.172A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.507A pdb=" N ASN E 301 " --> pdb=" O ILE E 322A" (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE E 322A" --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 309 " --> pdb=" O ARG E 315 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 322A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AD6, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 11 current: chain 'J' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100J through 103 Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 53 through 54 current: chain 'K' and resid 97 through 98 594 hydrogen bonds defined for protein. 1572 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: 3.87 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4277 1.33 - 1.45: 6213 1.45 - 1.58: 12243 1.58 - 1.70: 0 1.70 - 1.83: 174 Bond restraints: 22907 Sorted by residual: bond pdb=" NE ARG G 94 " pdb=" CZ ARG G 94 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.68e+00 bond pdb=" NE ARG H 94 " pdb=" CZ ARG H 94 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 7.15e+00 bond pdb=" NE ARG J 94 " pdb=" CZ ARG J 94 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 7.07e+00 bond pdb=" CD GLU E 91 " pdb=" OE1 GLU E 91 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.69e+00 bond pdb=" CG ASP A 185 " pdb=" OD1 ASP A 185 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.59e+00 ... (remaining 22902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 27732 2.00 - 3.99: 2762 3.99 - 5.99: 497 5.99 - 7.98: 107 7.98 - 9.98: 9 Bond angle restraints: 31107 Sorted by residual: angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 125.87 -6.21 7.20e-01 1.93e+00 7.44e+01 angle pdb=" C GLY H 96 " pdb=" N PRO H 97 " pdb=" CA PRO H 97 " ideal model delta sigma weight residual 120.03 128.52 -8.49 9.90e-01 1.02e+00 7.35e+01 angle pdb=" C GLY J 96 " pdb=" N PRO J 97 " pdb=" CA PRO J 97 " ideal model delta sigma weight residual 120.03 128.35 -8.32 9.90e-01 1.02e+00 7.07e+01 angle pdb=" C GLY G 96 " pdb=" N PRO G 97 " pdb=" CA PRO G 97 " ideal model delta sigma weight residual 119.85 128.28 -8.43 1.01e+00 9.80e-01 6.96e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.59 -5.93 7.20e-01 1.93e+00 6.78e+01 ... (remaining 31102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 15552 21.77 - 43.55: 339 43.55 - 65.32: 121 65.32 - 87.10: 191 87.10 - 108.87: 121 Dihedral angle restraints: 16324 sinusoidal: 9064 harmonic: 7260 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 47.95 45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.98 42.98 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -127.59 41.59 1 1.00e+01 1.00e-02 2.42e+01 ... (remaining 16321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 4025 0.272 - 0.545: 34 0.545 - 0.817: 6 0.817 - 1.090: 1 1.090 - 1.362: 4 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C1 MAN r 8 " pdb=" O6 MAN r 7 " pdb=" C2 MAN r 8 " pdb=" O5 MAN r 8 " both_signs ideal model delta sigma weight residual False 2.40 1.04 1.36 2.00e-02 2.50e+03 4.64e+03 chirality pdb=" C1 NAG 9 2 " pdb=" O4 NAG 9 1 " pdb=" C2 NAG 9 2 " pdb=" O5 NAG 9 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.25e+03 chirality pdb=" C1 NAG r 2 " pdb=" O4 NAG r 1 " pdb=" C2 NAG r 2 " pdb=" O5 NAG r 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.52e+03 ... (remaining 4067 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 332 " 0.071 2.00e-02 2.50e+03 7.19e-02 6.46e+01 pdb=" CG ASN E 332 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 332 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN E 332 " -0.110 2.00e-02 2.50e+03 pdb=" C1 NAG 5 1 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " -0.067 2.00e-02 2.50e+03 6.77e-02 5.72e+01 pdb=" CG ASN C 332 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " 0.103 2.00e-02 2.50e+03 pdb=" C1 NAG n 1 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.066 2.00e-02 2.50e+03 6.66e-02 5.55e+01 pdb=" CG ASN A 332 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.101 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.081 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 214 2.63 - 3.20: 20010 3.20 - 3.77: 31773 3.77 - 4.33: 46006 4.33 - 4.90: 71824 Nonbonded interactions: 169827 Sorted by model distance: nonbonded pdb=" O3 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.064 3.040 nonbonded pdb=" O3 NAG r 2 " pdb=" O7 NAG r 2 " model vdw 2.070 3.040 nonbonded pdb=" C3 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.261 3.470 nonbonded pdb=" O3 NAG s 2 " pdb=" O7 NAG s 2 " model vdw 2.265 3.040 nonbonded pdb=" O3 NAG a 2 " pdb=" O7 NAG a 2 " model vdw 2.268 3.040 ... (remaining 169822 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' and (resid 2 or resid 5 through 7)) selection = (chain 'Q' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain '1' selection = chain '2' selection = chain '5' selection = chain '6' selection = chain 'AA' selection = chain 'CA' selection = chain 'DA' selection = chain 'M' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain '8' selection = chain 'BA' selection = chain 'O' selection = chain 'T' selection = chain 'Y' selection = chain 'b' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'q' selection = chain 't' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'N' selection = chain 'U' selection = chain 'm' } ncs_group { reference = chain '7' selection = chain 'P' selection = chain 'X' selection = chain 'h' selection = chain 'i' selection = chain 'p' selection = chain 'z' } ncs_group { reference = chain '9' selection = chain 'Z' selection = chain 'r' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.890 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.140 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.012 0.114 23148 Z= 0.657 Angle : 1.399 16.115 31791 Z= 0.822 Chirality : 0.091 1.362 4070 Planarity : 0.005 0.019 3687 Dihedral : 17.328 108.870 11521 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.16), residues: 2478 helix: 0.36 (0.21), residues: 447 sheet: 1.64 (0.19), residues: 648 loop : 2.78 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 54 TYR 0.033 0.004 TYR A 173 PHE 0.019 0.003 PHE H 45 TRP 0.027 0.005 TRP C 69 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01158 (22907) covalent geometry : angle 1.33699 (31107) SS BOND : bond 0.04332 ( 39) SS BOND : angle 2.91810 ( 78) hydrogen bonds : bond 0.23970 ( 594) hydrogen bonds : angle 6.79201 ( 1572) link_ALPHA1-2 : bond 0.01611 ( 10) link_ALPHA1-2 : angle 2.51559 ( 30) link_ALPHA1-3 : bond 0.01743 ( 18) link_ALPHA1-3 : angle 3.60370 ( 54) link_ALPHA1-6 : bond 0.00992 ( 18) link_ALPHA1-6 : angle 2.76014 ( 54) link_BETA1-2 : bond 0.00379 ( 3) link_BETA1-2 : angle 3.51810 ( 9) link_BETA1-4 : bond 0.01061 ( 84) link_BETA1-4 : angle 3.09578 ( 252) link_NAG-ASN : bond 0.07090 ( 69) link_NAG-ASN : angle 3.20408 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.7788 (m) cc_final: 0.7493 (p) REVERT: A 104 MET cc_start: 0.7614 (ttm) cc_final: 0.7394 (ttt) REVERT: B 626 MET cc_start: 0.7803 (mtp) cc_final: 0.7523 (mtt) REVERT: H 82 LEU cc_start: 0.7104 (mt) cc_final: 0.6761 (mt) REVERT: L 5 THR cc_start: 0.7857 (p) cc_final: 0.7544 (p) REVERT: L 61 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7019 (mtm110) REVERT: L 79 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7635 (mt-10) REVERT: L 82 ASP cc_start: 0.7936 (m-30) cc_final: 0.7728 (p0) REVERT: C 90 THR cc_start: 0.7875 (m) cc_final: 0.7448 (p) REVERT: C 318 TYR cc_start: 0.6784 (m-80) cc_final: 0.6274 (m-80) REVERT: C 486 TYR cc_start: 0.7720 (m-80) cc_final: 0.7429 (m-80) REVERT: D 626 MET cc_start: 0.7987 (mtp) cc_final: 0.7516 (mtp) REVERT: G 3 GLN cc_start: 0.7991 (tp40) cc_final: 0.7564 (tm-30) REVERT: G 4 LEU cc_start: 0.7808 (mt) cc_final: 0.7518 (mp) REVERT: G 17 SER cc_start: 0.6861 (p) cc_final: 0.5982 (m) REVERT: G 57 LYS cc_start: 0.8384 (mttt) cc_final: 0.8128 (mtpp) REVERT: G 64 GLN cc_start: 0.8356 (pt0) cc_final: 0.8088 (pp30) REVERT: G 82 SER cc_start: 0.8273 (m) cc_final: 0.7498 (t) REVERT: G 82 LEU cc_start: 0.7464 (mt) cc_final: 0.7107 (mt) REVERT: G 91 TYR cc_start: 0.6854 (m-80) cc_final: 0.6653 (m-80) REVERT: I 28 ILE cc_start: 0.8279 (mm) cc_final: 0.7868 (tp) REVERT: I 61 ARG cc_start: 0.8134 (ptp-170) cc_final: 0.7842 (mtm180) REVERT: I 82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7554 (m-30) REVERT: I 88 CYS cc_start: 0.4699 (p) cc_final: 0.4341 (p) REVERT: I 104 LEU cc_start: 0.6854 (tp) cc_final: 0.6602 (tp) REVERT: E 90 THR cc_start: 0.8000 (m) cc_final: 0.7485 (p) REVERT: F 626 MET cc_start: 0.7751 (mtp) cc_final: 0.7385 (mtp) REVERT: J 17 SER cc_start: 0.6203 (p) cc_final: 0.5139 (m) REVERT: J 64 GLN cc_start: 0.8499 (pt0) cc_final: 0.8122 (pp30) REVERT: J 82 SER cc_start: 0.7543 (m) cc_final: 0.7116 (t) REVERT: K 5 THR cc_start: 0.7615 (p) cc_final: 0.7231 (p) REVERT: K 28 ILE cc_start: 0.8231 (mm) cc_final: 0.7907 (tp) REVERT: K 61 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.6583 (mtm110) REVERT: K 79 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7613 (mt-10) REVERT: K 82 ASP cc_start: 0.7750 (m-30) cc_final: 0.6411 (m-30) REVERT: K 104 LEU cc_start: 0.7073 (tp) cc_final: 0.6858 (tt) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.1825 time to fit residues: 163.9809 Evaluate side-chains 299 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 374 HIS A 377 ASN B 551 GLN H 3 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 374 HIS D 567 GLN E 374 HIS E 377 ASN E 478 ASN F 651 ASN J 23 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.219438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.194011 restraints weight = 30550.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.193487 restraints weight = 37641.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.194051 restraints weight = 32717.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.193683 restraints weight = 28681.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.194572 restraints weight = 25821.515| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23148 Z= 0.186 Angle : 0.903 22.708 31791 Z= 0.409 Chirality : 0.053 0.615 4070 Planarity : 0.005 0.035 3687 Dihedral : 13.993 81.467 6799 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 2.44 % Allowed : 7.05 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.16), residues: 2478 helix: 1.79 (0.25), residues: 450 sheet: 1.40 (0.18), residues: 705 loop : 1.98 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 54 TYR 0.023 0.002 TYR K 96 PHE 0.026 0.002 PHE K 71 TRP 0.018 0.001 TRP H 100 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (22907) covalent geometry : angle 0.79426 (31107) SS BOND : bond 0.00461 ( 39) SS BOND : angle 2.41055 ( 78) hydrogen bonds : bond 0.07718 ( 594) hydrogen bonds : angle 5.79172 ( 1572) link_ALPHA1-2 : bond 0.01182 ( 10) link_ALPHA1-2 : angle 1.88222 ( 30) link_ALPHA1-3 : bond 0.00796 ( 18) link_ALPHA1-3 : angle 3.43844 ( 54) link_ALPHA1-6 : bond 0.01070 ( 18) link_ALPHA1-6 : angle 2.40939 ( 54) link_BETA1-2 : bond 0.00349 ( 3) link_BETA1-2 : angle 0.88932 ( 9) link_BETA1-4 : bond 0.00954 ( 84) link_BETA1-4 : angle 2.40391 ( 252) link_NAG-ASN : bond 0.01050 ( 69) link_NAG-ASN : angle 4.01829 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8040 (ttm) cc_final: 0.7763 (ttt) REVERT: A 154 MET cc_start: 0.6428 (mmt) cc_final: 0.5928 (mmt) REVERT: A 318 TYR cc_start: 0.5981 (m-80) cc_final: 0.5340 (m-80) REVERT: C 90 THR cc_start: 0.7363 (m) cc_final: 0.7077 (p) REVERT: C 447 SER cc_start: 0.9000 (m) cc_final: 0.8788 (m) REVERT: D 607 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8404 (m) REVERT: G 38 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6992 (ppt170) REVERT: G 77 THR cc_start: 0.7787 (m) cc_final: 0.7549 (p) REVERT: I 28 ILE cc_start: 0.7743 (mm) cc_final: 0.7369 (tp) REVERT: I 61 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7276 (mtm180) REVERT: E 318 TYR cc_start: 0.6168 (m-80) cc_final: 0.5838 (m-80) REVERT: E 332 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7368 (p0) REVERT: E 424 VAL cc_start: 0.7856 (m) cc_final: 0.7541 (p) REVERT: F 635 ILE cc_start: 0.8340 (pt) cc_final: 0.8071 (tt) REVERT: J 59 PHE cc_start: 0.7849 (m-80) cc_final: 0.7505 (m-80) outliers start: 54 outliers final: 30 residues processed: 397 average time/residue: 0.1691 time to fit residues: 102.7667 Evaluate side-chains 285 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 607 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 58 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 651 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 478 ASN F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.210308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.185033 restraints weight = 31462.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184196 restraints weight = 37844.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185171 restraints weight = 35922.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183983 restraints weight = 31324.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.184665 restraints weight = 30491.126| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23148 Z= 0.161 Angle : 0.800 12.352 31791 Z= 0.365 Chirality : 0.049 0.418 4070 Planarity : 0.005 0.086 3687 Dihedral : 11.456 74.149 6799 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 2.71 % Allowed : 8.13 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.16), residues: 2478 helix: 1.88 (0.25), residues: 447 sheet: 1.29 (0.18), residues: 723 loop : 1.49 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.031 0.002 TYR L 96 PHE 0.030 0.002 PHE E 376 TRP 0.013 0.001 TRP A 427 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00339 (22907) covalent geometry : angle 0.72788 (31107) SS BOND : bond 0.00530 ( 39) SS BOND : angle 1.80237 ( 78) hydrogen bonds : bond 0.06175 ( 594) hydrogen bonds : angle 5.48649 ( 1572) link_ALPHA1-2 : bond 0.00998 ( 10) link_ALPHA1-2 : angle 1.75716 ( 30) link_ALPHA1-3 : bond 0.00790 ( 18) link_ALPHA1-3 : angle 2.94006 ( 54) link_ALPHA1-6 : bond 0.01178 ( 18) link_ALPHA1-6 : angle 2.09474 ( 54) link_BETA1-2 : bond 0.00393 ( 3) link_BETA1-2 : angle 1.13140 ( 9) link_BETA1-4 : bond 0.00834 ( 84) link_BETA1-4 : angle 2.06498 ( 252) link_NAG-ASN : bond 0.00586 ( 69) link_NAG-ASN : angle 2.89780 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6658 (mmt) cc_final: 0.6207 (mmt) REVERT: A 229 ASN cc_start: 0.7017 (OUTLIER) cc_final: 0.6765 (t0) REVERT: A 318 TYR cc_start: 0.5727 (m-80) cc_final: 0.5255 (m-80) REVERT: C 90 THR cc_start: 0.7343 (m) cc_final: 0.7126 (p) REVERT: I 28 ILE cc_start: 0.7618 (mm) cc_final: 0.7297 (tp) REVERT: I 61 ARG cc_start: 0.7265 (ptp-170) cc_final: 0.6980 (ptt90) REVERT: I 96 TYR cc_start: 0.5906 (t80) cc_final: 0.5548 (t80) REVERT: F 635 ILE cc_start: 0.8321 (pt) cc_final: 0.8063 (tt) REVERT: J 59 PHE cc_start: 0.7894 (m-80) cc_final: 0.7545 (m-80) REVERT: K 28 ILE cc_start: 0.7848 (mm) cc_final: 0.7498 (tp) outliers start: 60 outliers final: 39 residues processed: 320 average time/residue: 0.1631 time to fit residues: 80.9481 Evaluate side-chains 279 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 127 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 47 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 156 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 246 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.208862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.183611 restraints weight = 31099.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.183109 restraints weight = 35977.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.183103 restraints weight = 36636.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182815 restraints weight = 29676.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183071 restraints weight = 28285.968| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23148 Z= 0.164 Angle : 0.770 17.594 31791 Z= 0.354 Chirality : 0.049 0.436 4070 Planarity : 0.004 0.053 3687 Dihedral : 10.140 111.494 6799 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.62 % Allowed : 8.58 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 2478 helix: 2.12 (0.25), residues: 429 sheet: 1.11 (0.18), residues: 723 loop : 1.09 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 54 TYR 0.027 0.002 TYR L 96 PHE 0.018 0.002 PHE K 71 TRP 0.011 0.001 TRP E 427 HIS 0.009 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00362 (22907) covalent geometry : angle 0.70503 (31107) SS BOND : bond 0.00557 ( 39) SS BOND : angle 2.28179 ( 78) hydrogen bonds : bond 0.05736 ( 594) hydrogen bonds : angle 5.34308 ( 1572) link_ALPHA1-2 : bond 0.00924 ( 10) link_ALPHA1-2 : angle 1.72201 ( 30) link_ALPHA1-3 : bond 0.00815 ( 18) link_ALPHA1-3 : angle 2.97594 ( 54) link_ALPHA1-6 : bond 0.01210 ( 18) link_ALPHA1-6 : angle 2.06517 ( 54) link_BETA1-2 : bond 0.00387 ( 3) link_BETA1-2 : angle 1.17548 ( 9) link_BETA1-4 : bond 0.00756 ( 84) link_BETA1-4 : angle 1.88808 ( 252) link_NAG-ASN : bond 0.00499 ( 69) link_NAG-ASN : angle 2.46859 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6686 (mmt) cc_final: 0.6222 (mmt) REVERT: L 62 PHE cc_start: 0.7228 (m-10) cc_final: 0.6939 (m-10) REVERT: C 200 VAL cc_start: 0.9175 (t) cc_final: 0.8937 (m) REVERT: C 416 ILE cc_start: 0.6637 (mt) cc_final: 0.6261 (pt) REVERT: D 535 MET cc_start: 0.7425 (mmp) cc_final: 0.7119 (mmm) REVERT: I 28 ILE cc_start: 0.7582 (mm) cc_final: 0.7246 (tp) REVERT: I 96 TYR cc_start: 0.5755 (t80) cc_final: 0.5169 (t80) REVERT: F 635 ILE cc_start: 0.8435 (pt) cc_final: 0.8125 (tt) REVERT: K 28 ILE cc_start: 0.7849 (mm) cc_final: 0.7514 (tp) outliers start: 58 outliers final: 40 residues processed: 296 average time/residue: 0.1743 time to fit residues: 78.7120 Evaluate side-chains 276 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 168 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 258 GLN A 374 HIS B 651 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.208643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.183635 restraints weight = 31184.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183011 restraints weight = 37329.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.184213 restraints weight = 35138.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183765 restraints weight = 27202.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.184202 restraints weight = 27963.676| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23148 Z= 0.134 Angle : 0.715 12.437 31791 Z= 0.325 Chirality : 0.047 0.436 4070 Planarity : 0.004 0.048 3687 Dihedral : 8.698 65.022 6799 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.53 % Allowed : 9.44 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.16), residues: 2478 helix: 2.24 (0.25), residues: 429 sheet: 1.01 (0.18), residues: 723 loop : 0.89 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 54 TYR 0.027 0.001 TYR L 96 PHE 0.017 0.001 PHE C 376 TRP 0.013 0.001 TRP C 427 HIS 0.012 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (22907) covalent geometry : angle 0.64915 (31107) SS BOND : bond 0.00451 ( 39) SS BOND : angle 1.92357 ( 78) hydrogen bonds : bond 0.05035 ( 594) hydrogen bonds : angle 5.08575 ( 1572) link_ALPHA1-2 : bond 0.00919 ( 10) link_ALPHA1-2 : angle 1.70539 ( 30) link_ALPHA1-3 : bond 0.00854 ( 18) link_ALPHA1-3 : angle 2.90989 ( 54) link_ALPHA1-6 : bond 0.01258 ( 18) link_ALPHA1-6 : angle 1.91551 ( 54) link_BETA1-2 : bond 0.00411 ( 3) link_BETA1-2 : angle 1.16122 ( 9) link_BETA1-4 : bond 0.00732 ( 84) link_BETA1-4 : angle 1.80408 ( 252) link_NAG-ASN : bond 0.00438 ( 69) link_NAG-ASN : angle 2.46909 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6522 (mmt) cc_final: 0.6101 (mmt) REVERT: D 535 MET cc_start: 0.7331 (mmp) cc_final: 0.7060 (mmm) REVERT: D 540 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: I 28 ILE cc_start: 0.7578 (mm) cc_final: 0.7184 (tp) REVERT: F 635 ILE cc_start: 0.8435 (pt) cc_final: 0.8142 (tt) REVERT: K 28 ILE cc_start: 0.7839 (mm) cc_final: 0.7532 (tp) REVERT: K 81 GLU cc_start: 0.6731 (pm20) cc_final: 0.6219 (pm20) outliers start: 56 outliers final: 36 residues processed: 286 average time/residue: 0.1719 time to fit residues: 75.0229 Evaluate side-chains 271 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 193 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 233 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 163 optimal weight: 0.3980 chunk 177 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 246 GLN A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 562 GLN B 651 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.205842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180231 restraints weight = 31449.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.179234 restraints weight = 40325.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179947 restraints weight = 38669.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179297 restraints weight = 30497.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.179800 restraints weight = 29100.951| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23148 Z= 0.145 Angle : 0.715 17.744 31791 Z= 0.329 Chirality : 0.047 0.439 4070 Planarity : 0.004 0.051 3687 Dihedral : 8.034 61.426 6799 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.71 % Allowed : 9.89 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2478 helix: 2.16 (0.26), residues: 432 sheet: 0.92 (0.19), residues: 705 loop : 0.67 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 54 TYR 0.018 0.001 TYR L 96 PHE 0.019 0.002 PHE L 62 TRP 0.011 0.001 TRP E 427 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (22907) covalent geometry : angle 0.65640 (31107) SS BOND : bond 0.00506 ( 39) SS BOND : angle 2.33180 ( 78) hydrogen bonds : bond 0.05027 ( 594) hydrogen bonds : angle 4.96941 ( 1572) link_ALPHA1-2 : bond 0.00838 ( 10) link_ALPHA1-2 : angle 1.72680 ( 30) link_ALPHA1-3 : bond 0.00861 ( 18) link_ALPHA1-3 : angle 2.83784 ( 54) link_ALPHA1-6 : bond 0.01307 ( 18) link_ALPHA1-6 : angle 1.93749 ( 54) link_BETA1-2 : bond 0.00400 ( 3) link_BETA1-2 : angle 1.23889 ( 9) link_BETA1-4 : bond 0.00742 ( 84) link_BETA1-4 : angle 1.68922 ( 252) link_NAG-ASN : bond 0.00407 ( 69) link_NAG-ASN : angle 2.17800 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6671 (mmt) cc_final: 0.6207 (mmt) REVERT: D 540 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: I 28 ILE cc_start: 0.7555 (mm) cc_final: 0.7160 (tp) REVERT: I 61 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7752 (ptt-90) REVERT: I 97 THR cc_start: 0.7729 (m) cc_final: 0.7366 (p) REVERT: F 635 ILE cc_start: 0.8417 (pt) cc_final: 0.8128 (tt) REVERT: K 28 ILE cc_start: 0.7800 (mm) cc_final: 0.7498 (tp) REVERT: K 82 ASP cc_start: 0.7381 (p0) cc_final: 0.6467 (p0) outliers start: 60 outliers final: 42 residues processed: 295 average time/residue: 0.1650 time to fit residues: 74.4980 Evaluate side-chains 270 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 147 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN I 49 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.201832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.176255 restraints weight = 31498.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.175206 restraints weight = 41410.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.175735 restraints weight = 37879.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175241 restraints weight = 28644.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175728 restraints weight = 27682.307| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23148 Z= 0.169 Angle : 0.742 13.031 31791 Z= 0.344 Chirality : 0.048 0.439 4070 Planarity : 0.004 0.050 3687 Dihedral : 7.859 59.802 6799 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.57 % Allowed : 10.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2478 helix: 1.60 (0.25), residues: 465 sheet: 0.86 (0.20), residues: 660 loop : 0.47 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 54 TYR 0.020 0.002 TYR L 96 PHE 0.018 0.002 PHE I 62 TRP 0.009 0.001 TRP C 338 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (22907) covalent geometry : angle 0.68273 (31107) SS BOND : bond 0.00525 ( 39) SS BOND : angle 2.29187 ( 78) hydrogen bonds : bond 0.05377 ( 594) hydrogen bonds : angle 5.02830 ( 1572) link_ALPHA1-2 : bond 0.00799 ( 10) link_ALPHA1-2 : angle 1.72620 ( 30) link_ALPHA1-3 : bond 0.00835 ( 18) link_ALPHA1-3 : angle 2.79969 ( 54) link_ALPHA1-6 : bond 0.01305 ( 18) link_ALPHA1-6 : angle 1.93627 ( 54) link_BETA1-2 : bond 0.00366 ( 3) link_BETA1-2 : angle 1.30974 ( 9) link_BETA1-4 : bond 0.00722 ( 84) link_BETA1-4 : angle 1.66861 ( 252) link_NAG-ASN : bond 0.00428 ( 69) link_NAG-ASN : angle 2.36180 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7389 (pm20) cc_final: 0.7120 (pm20) REVERT: A 154 MET cc_start: 0.6596 (mmt) cc_final: 0.6115 (mmt) REVERT: A 192 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6821 (ttt180) REVERT: D 535 MET cc_start: 0.7735 (mmp) cc_final: 0.7390 (mmm) REVERT: I 28 ILE cc_start: 0.7508 (mm) cc_final: 0.7051 (tp) REVERT: I 61 ARG cc_start: 0.7960 (ptt90) cc_final: 0.7300 (ptt-90) REVERT: I 79 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6181 (mt-10) REVERT: I 97 THR cc_start: 0.7749 (m) cc_final: 0.7345 (p) REVERT: F 635 ILE cc_start: 0.8361 (pt) cc_final: 0.8100 (tt) REVERT: K 75 ILE cc_start: 0.8418 (pt) cc_final: 0.8162 (pt) outliers start: 57 outliers final: 46 residues processed: 281 average time/residue: 0.1728 time to fit residues: 73.9177 Evaluate side-chains 271 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 85 optimal weight: 0.0270 chunk 214 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 651 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.200891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.176822 restraints weight = 31575.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174536 restraints weight = 54662.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175599 restraints weight = 51554.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.176052 restraints weight = 39272.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175867 restraints weight = 37532.787| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23148 Z= 0.176 Angle : 0.767 20.039 31791 Z= 0.356 Chirality : 0.048 0.438 4070 Planarity : 0.004 0.094 3687 Dihedral : 7.787 58.669 6799 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.57 % Allowed : 10.52 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2478 helix: 1.68 (0.26), residues: 447 sheet: 0.75 (0.20), residues: 660 loop : 0.30 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 54 TYR 0.018 0.002 TYR L 96 PHE 0.037 0.002 PHE K 98 TRP 0.010 0.001 TRP E 338 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00407 (22907) covalent geometry : angle 0.70182 (31107) SS BOND : bond 0.00602 ( 39) SS BOND : angle 2.83501 ( 78) hydrogen bonds : bond 0.05416 ( 594) hydrogen bonds : angle 5.02383 ( 1572) link_ALPHA1-2 : bond 0.00754 ( 10) link_ALPHA1-2 : angle 1.71982 ( 30) link_ALPHA1-3 : bond 0.00808 ( 18) link_ALPHA1-3 : angle 2.77737 ( 54) link_ALPHA1-6 : bond 0.01261 ( 18) link_ALPHA1-6 : angle 1.91970 ( 54) link_BETA1-2 : bond 0.00336 ( 3) link_BETA1-2 : angle 1.34813 ( 9) link_BETA1-4 : bond 0.00720 ( 84) link_BETA1-4 : angle 1.65291 ( 252) link_NAG-ASN : bond 0.00468 ( 69) link_NAG-ASN : angle 2.53560 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7336 (pm20) cc_final: 0.7043 (pm20) REVERT: A 154 MET cc_start: 0.6606 (mmt) cc_final: 0.6192 (mmt) REVERT: A 192 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.6956 (ttt180) REVERT: D 518 MET cc_start: 0.5159 (mmt) cc_final: 0.4490 (mmt) REVERT: D 535 MET cc_start: 0.7687 (mmp) cc_final: 0.7214 (mmm) REVERT: I 28 ILE cc_start: 0.7610 (mm) cc_final: 0.7141 (tp) REVERT: I 61 ARG cc_start: 0.7797 (ptt90) cc_final: 0.7168 (ptt-90) REVERT: I 97 THR cc_start: 0.7773 (m) cc_final: 0.7444 (p) REVERT: E 318 TYR cc_start: 0.6667 (m-80) cc_final: 0.6314 (m-80) REVERT: F 635 ILE cc_start: 0.8357 (pt) cc_final: 0.8109 (tt) REVERT: K 79 GLU cc_start: 0.6243 (pm20) cc_final: 0.5961 (pm20) outliers start: 57 outliers final: 51 residues processed: 273 average time/residue: 0.1683 time to fit residues: 70.2664 Evaluate side-chains 269 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 140 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 651 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.201526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.176800 restraints weight = 31374.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176041 restraints weight = 41096.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.175897 restraints weight = 38178.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175079 restraints weight = 31278.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.175782 restraints weight = 29761.639| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23148 Z= 0.148 Angle : 0.732 17.367 31791 Z= 0.339 Chirality : 0.047 0.437 4070 Planarity : 0.004 0.068 3687 Dihedral : 7.595 59.239 6799 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.30 % Allowed : 11.11 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2478 helix: 1.56 (0.26), residues: 465 sheet: 0.78 (0.20), residues: 660 loop : 0.30 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 54 TYR 0.015 0.001 TYR L 96 PHE 0.026 0.002 PHE K 98 TRP 0.011 0.001 TRP E 427 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (22907) covalent geometry : angle 0.66535 (31107) SS BOND : bond 0.00399 ( 39) SS BOND : angle 2.80078 ( 78) hydrogen bonds : bond 0.05110 ( 594) hydrogen bonds : angle 4.93814 ( 1572) link_ALPHA1-2 : bond 0.00820 ( 10) link_ALPHA1-2 : angle 1.71429 ( 30) link_ALPHA1-3 : bond 0.00810 ( 18) link_ALPHA1-3 : angle 2.74736 ( 54) link_ALPHA1-6 : bond 0.01270 ( 18) link_ALPHA1-6 : angle 1.87569 ( 54) link_BETA1-2 : bond 0.00333 ( 3) link_BETA1-2 : angle 1.34532 ( 9) link_BETA1-4 : bond 0.00713 ( 84) link_BETA1-4 : angle 1.64291 ( 252) link_NAG-ASN : bond 0.00421 ( 69) link_NAG-ASN : angle 2.47944 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7341 (pm20) cc_final: 0.6901 (pm20) REVERT: A 192 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.6881 (ttt180) REVERT: D 518 MET cc_start: 0.5235 (mmt) cc_final: 0.4478 (mmt) REVERT: D 535 MET cc_start: 0.7750 (mmp) cc_final: 0.7371 (mmm) REVERT: I 28 ILE cc_start: 0.7665 (mm) cc_final: 0.7172 (tp) REVERT: I 97 THR cc_start: 0.7953 (m) cc_final: 0.7614 (p) REVERT: F 635 ILE cc_start: 0.8335 (pt) cc_final: 0.8097 (tt) REVERT: J 100 MET cc_start: 0.6996 (mmt) cc_final: 0.6756 (mmt) outliers start: 51 outliers final: 44 residues processed: 272 average time/residue: 0.1593 time to fit residues: 67.1110 Evaluate side-chains 261 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 101 optimal weight: 0.0030 chunk 49 optimal weight: 0.0020 chunk 233 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN L 49 HIS ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.202515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.177135 restraints weight = 31311.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176706 restraints weight = 38783.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176423 restraints weight = 36364.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.176002 restraints weight = 29362.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.176341 restraints weight = 28073.883| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23148 Z= 0.131 Angle : 0.710 15.786 31791 Z= 0.328 Chirality : 0.046 0.436 4070 Planarity : 0.004 0.073 3687 Dihedral : 7.391 59.902 6799 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.17 % Allowed : 11.52 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2478 helix: 1.63 (0.26), residues: 465 sheet: 0.83 (0.20), residues: 660 loop : 0.29 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 54 TYR 0.014 0.001 TYR L 96 PHE 0.027 0.002 PHE A 159 TRP 0.019 0.001 TRP G 47 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00283 (22907) covalent geometry : angle 0.64707 (31107) SS BOND : bond 0.00418 ( 39) SS BOND : angle 2.60665 ( 78) hydrogen bonds : bond 0.04651 ( 594) hydrogen bonds : angle 4.76046 ( 1572) link_ALPHA1-2 : bond 0.00814 ( 10) link_ALPHA1-2 : angle 1.72978 ( 30) link_ALPHA1-3 : bond 0.00790 ( 18) link_ALPHA1-3 : angle 2.71225 ( 54) link_ALPHA1-6 : bond 0.01298 ( 18) link_ALPHA1-6 : angle 1.86310 ( 54) link_BETA1-2 : bond 0.00339 ( 3) link_BETA1-2 : angle 1.33166 ( 9) link_BETA1-4 : bond 0.00702 ( 84) link_BETA1-4 : angle 1.62230 ( 252) link_NAG-ASN : bond 0.00392 ( 69) link_NAG-ASN : angle 2.33589 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7234 (pm20) cc_final: 0.6780 (pm20) REVERT: A 192 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6789 (ttt180) REVERT: B 661 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7292 (mt) REVERT: L 97 THR cc_start: 0.9115 (m) cc_final: 0.8855 (p) REVERT: D 518 MET cc_start: 0.5250 (mmt) cc_final: 0.4514 (mmt) REVERT: D 535 MET cc_start: 0.7757 (mmp) cc_final: 0.7405 (mmm) REVERT: I 28 ILE cc_start: 0.7674 (mm) cc_final: 0.7162 (tp) REVERT: I 97 THR cc_start: 0.7813 (m) cc_final: 0.7544 (p) REVERT: E 383 PHE cc_start: 0.7080 (m-80) cc_final: 0.6870 (m-80) REVERT: F 535 MET cc_start: 0.7236 (mmm) cc_final: 0.6378 (mtp) REVERT: F 635 ILE cc_start: 0.8275 (pt) cc_final: 0.8065 (tt) REVERT: J 100 MET cc_start: 0.6948 (mmt) cc_final: 0.6692 (mmt) outliers start: 48 outliers final: 42 residues processed: 265 average time/residue: 0.1629 time to fit residues: 66.4954 Evaluate side-chains 266 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 163 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.202542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.181373 restraints weight = 31118.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180207 restraints weight = 43704.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.180787 restraints weight = 43919.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.180109 restraints weight = 34172.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180634 restraints weight = 33092.386| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 23148 Z= 0.187 Angle : 0.860 59.195 31791 Z= 0.452 Chirality : 0.046 0.436 4070 Planarity : 0.005 0.154 3687 Dihedral : 7.394 59.899 6799 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.21 % Allowed : 11.65 % Favored : 86.13 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2478 helix: 1.56 (0.26), residues: 465 sheet: 0.83 (0.20), residues: 660 loop : 0.29 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 54 TYR 0.015 0.001 TYR L 96 PHE 0.023 0.002 PHE A 159 TRP 0.020 0.001 TRP G 47 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00376 (22907) covalent geometry : angle 0.81078 (31107) SS BOND : bond 0.00528 ( 39) SS BOND : angle 2.74124 ( 78) hydrogen bonds : bond 0.04799 ( 594) hydrogen bonds : angle 4.77133 ( 1572) link_ALPHA1-2 : bond 0.00777 ( 10) link_ALPHA1-2 : angle 1.73309 ( 30) link_ALPHA1-3 : bond 0.00796 ( 18) link_ALPHA1-3 : angle 2.71217 ( 54) link_ALPHA1-6 : bond 0.01292 ( 18) link_ALPHA1-6 : angle 1.92126 ( 54) link_BETA1-2 : bond 0.00331 ( 3) link_BETA1-2 : angle 1.33168 ( 9) link_BETA1-4 : bond 0.00701 ( 84) link_BETA1-4 : angle 1.62181 ( 252) link_NAG-ASN : bond 0.00394 ( 69) link_NAG-ASN : angle 2.33334 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3236.55 seconds wall clock time: 57 minutes 22.74 seconds (3442.74 seconds total)