Starting phenix.real_space_refine on Fri Mar 6 00:17:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udj_20739/03_2026/6udj_20739.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 16575 2.51 5 N 4383 2.21 5 O 5499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26592 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "N" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1050 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "M" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "P" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "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: 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: "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: 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: "e" 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: "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: 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: "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: 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: 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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: "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: 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: "4" 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: "5" 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: "6" 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: "7" 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: "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: 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: "AA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 5.94, per 1000 atoms: 0.22 Number of scatterers: 26592 At special positions: 0 Unit cell: (153.265, 150.094, 154.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5499 8.00 N 4383 7.00 C 16575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.05 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 598 " - pdb=" SG CYS M 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.05 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.06 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.04 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS P 501 " distance=2.04 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.05 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.04 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.06 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.04 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.04 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA 3 3 " - " MAN 3 6 " " MAN 3 4 " - " MAN 3 5 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 6 " " MAN b 4 " - " MAN b 5 " " BMA i 3 " - " MAN i 4 " " BMA l 3 " - " MAN l 4 " " BMA p 3 " - " MAN p 6 " " MAN p 4 " - " MAN p 5 " " BMA w 3 " - " MAN w 4 " " BMA z 3 " - " MAN z 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 5 3 " - " MAN 5 4 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 9 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA X 3 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA i 3 " - " MAN i 5 " " BMA l 3 " - " MAN l 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 5 " " BMA z 3 " - " MAN z 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " 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 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG 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 n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN P 160 " " NAG 1 1 " - " ASN P 197 " " NAG 2 1 " - " ASN P 234 " " NAG 3 1 " - " ASN P 276 " " NAG 4 1 " - " ASN P 295 " " NAG 5 1 " - " ASN P 301 " " NAG 6 1 " - " ASN P 386 " " NAG 7 1 " - " ASN P 392 " " NAG 8 1 " - " ASN P 363 " " NAG 9 1 " - " ASN P 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG C 703 " - " ASN C 618 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 630 " - " ASN G 339 " " NAG G 631 " - " ASN G 355 " " NAG J 630 " - " ASN J 339 " " NAG J 631 " - " ASN J 355 " " NAG M 701 " - " ASN M 611 " " NAG M 702 " - " ASN M 637 " " NAG M 703 " - " ASN M 618 " " NAG P 630 " - " ASN P 339 " " NAG P 631 " - " ASN P 355 " " NAG S 1 " - " ASN G 332 " " NAG T 1 " - " ASN J 332 " " NAG U 1 " - " ASN P 332 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 133 " " NAG X 1 " - " ASN G 156 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 276 " " NAG c 1 " - " ASN G 295 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN G 386 " " NAG f 1 " - " ASN G 392 " " NAG g 1 " - " ASN G 363 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 262 " " NAG j 1 " - " ASN J 88 " " NAG k 1 " - " ASN J 133 " " NAG l 1 " - " ASN J 156 " " NAG m 1 " - " ASN J 160 " " NAG n 1 " - " ASN J 197 " " NAG o 1 " - " ASN J 234 " " NAG p 1 " - " ASN J 276 " " NAG q 1 " - " ASN J 295 " " NAG r 1 " - " ASN J 301 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 392 " " NAG u 1 " - " ASN J 363 " " NAG v 1 " - " ASN J 448 " " NAG w 1 " - " ASN J 262 " " NAG x 1 " - " ASN P 88 " " NAG y 1 " - " ASN P 133 " " NAG z 1 " - " ASN P 156 " " NAGAA 1 " - " ASN P 262 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 987.7 milliseconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 63 sheets defined 15.9% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 4.098A pdb=" N ASN A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.951A pdb=" N THR A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 100D through 100H Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.907A pdb=" N ASN K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.878A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 100D through 100H Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.808A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100D through 100H Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.812A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.953A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.967A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35C Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.602A pdb=" N SER D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.604A pdb=" N SER N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.651A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 3.915A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 661 removed outlier: 3.532A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 115 removed outlier: 3.693A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 481 Processing helix chain 'M' and resid 529 through 534 Processing helix chain 'M' and resid 536 through 542 removed outlier: 3.689A pdb=" N GLN M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 570 through 596 removed outlier: 4.015A pdb=" N LYS M 574 " --> pdb=" O VAL M 570 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA M 578 " --> pdb=" O LYS M 574 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG M 579 " --> pdb=" O GLN M 575 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL M 580 " --> pdb=" O LEU M 576 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP M 589 " --> pdb=" O ARG M 585 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 625 Processing helix chain 'M' and resid 627 through 636 Processing helix chain 'M' and resid 638 through 661 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 98 through 115 removed outlier: 3.675A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 354 removed outlier: 3.908A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE J 353 " --> pdb=" O LEU J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.130A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.438A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.689A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.989A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.582A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 98 through 115 removed outlier: 3.639A pdb=" N GLU P 102 " --> pdb=" O ASN P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 4.018A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE P 353 " --> pdb=" O LEU P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 373 Processing helix chain 'P' and resid 475 through 484 removed outlier: 4.227A pdb=" N GLU P 482 " --> pdb=" O ASN P 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 72 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.780A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.035A pdb=" N THR A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.728A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.966A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.859A pdb=" N LEU E 33 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.942A pdb=" N THR E 97 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.826A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 13 removed outlier: 4.024A pdb=" N THR O 97 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.874A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP I 35 " --> pdb=" O VAL I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.874A pdb=" N THR I 97 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.541A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.920A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS D 92 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY D 106 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR D 90 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA D 108 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY D 88 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 35E" --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL D 50 " --> pdb=" O THR D 35E" (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 14 removed outlier: 6.555A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AC7, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.967A pdb=" N TRP N 103 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG N 94 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY N 105 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS N 92 " --> pdb=" O GLY N 105 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR N 35E" --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL N 50 " --> pdb=" O THR N 35E" (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 9 through 14 removed outlier: 6.356A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 18 through 22 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.963A pdb=" N TRP H 103 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG H 94 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLY H 105 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS H 92 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 35E" --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL H 50 " --> pdb=" O THR H 35E" (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.323A pdb=" N CYS C 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR G 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.726A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.388A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.734A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.768A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 315 through 323 removed outlier: 6.611A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.796A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.734A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 603 through 609 removed outlier: 8.318A pdb=" N CYS M 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR J 40 " --> pdb=" O CYS M 604 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR M 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL J 38 " --> pdb=" O THR M 606 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL M 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.639A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AE9, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AF1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AF2, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.123A pdb=" N ALA J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR J 435 " --> pdb=" O ALA J 200 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.558A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 393 through 395 removed outlier: 6.474A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 271 through 274 removed outlier: 6.804A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 315 through 323 removed outlier: 6.601A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 374 through 378 removed outlier: 4.039A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.631A pdb=" N VAL P 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 45 through 47 removed outlier: 4.482A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 53 through 55 Processing sheet with id=AG2, first strand: chain 'P' and resid 91 through 94 Processing sheet with id=AG3, first strand: chain 'P' and resid 169 through 177 Processing sheet with id=AG4, first strand: chain 'P' and resid 200 through 203 removed outlier: 6.133A pdb=" N ALA P 200 " --> pdb=" O ALA P 433 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR P 435 " --> pdb=" O ALA P 200 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR P 202 " --> pdb=" O TYR P 435 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 259 through 261 removed outlier: 6.254A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 393 through 395 removed outlier: 5.499A pdb=" N GLY P 441 " --> pdb=" O ASN P 300 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN P 300 " --> pdb=" O GLY P 441 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 271 through 274 removed outlier: 6.770A pdb=" N ASN P 301 " --> pdb=" O ILE P 322 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE P 322 " --> pdb=" O ASN P 301 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR P 303 " --> pdb=" O GLY P 321 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 315 through 323 removed outlier: 6.601A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR P 303 " --> pdb=" O GLY P 321 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE P 322 " --> pdb=" O ASN P 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN P 301 " --> pdb=" O ILE P 322 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN P 293 " --> pdb=" O SER P 334 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER P 334 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE P 382 " --> pdb=" O LYS P 421 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 374 through 378 removed outlier: 4.067A pdb=" N PHE P 382 " --> pdb=" O LYS P 421 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER P 334 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN P 293 " --> pdb=" O SER P 334 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN P 300 " --> pdb=" O GLY P 441 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY P 441 " --> pdb=" O ASN P 300 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 2844 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: 6.48 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6727 1.33 - 1.46: 8608 1.46 - 1.60: 11584 1.60 - 1.73: 1 1.73 - 1.86: 179 Bond restraints: 27099 Sorted by residual: bond pdb=" C ALA G 204 " pdb=" N CYS G 205 " ideal model delta sigma weight residual 1.331 1.210 0.121 1.63e-02 3.76e+03 5.51e+01 bond pdb=" C ALA J 204 " pdb=" N CYS J 205 " ideal model delta sigma weight residual 1.328 1.232 0.095 1.67e-02 3.59e+03 3.27e+01 bond pdb=" CG1 ILE P 443 " pdb=" CD1 ILE P 443 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.04e+01 bond pdb=" C TRP P 427 " pdb=" O TRP P 427 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 9.03e+00 bond pdb=" C TRP J 427 " pdb=" O TRP J 427 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.34e-02 5.57e+03 8.83e+00 ... (remaining 27094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 35125 2.50 - 4.99: 1397 4.99 - 7.49: 207 7.49 - 9.98: 46 9.98 - 12.48: 11 Bond angle restraints: 36786 Sorted by residual: angle pdb=" C ARG N 100 " pdb=" N ALA N 100A" pdb=" CA ALA N 100A" ideal model delta sigma weight residual 120.06 128.21 -8.15 1.19e+00 7.06e-01 4.69e+01 angle pdb=" C GLY I 50 " pdb=" N THR I 51 " pdb=" CA THR I 51 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" C TRP J 427 " pdb=" N GLN J 428 " pdb=" CA GLN J 428 " ideal model delta sigma weight residual 122.07 131.11 -9.04 1.43e+00 4.89e-01 3.99e+01 angle pdb=" C ARG H 100 " pdb=" N ALA H 100A" pdb=" CA ALA H 100A" ideal model delta sigma weight residual 120.09 127.89 -7.80 1.25e+00 6.40e-01 3.90e+01 angle pdb=" C ARG D 100 " pdb=" N ALA D 100A" pdb=" CA ALA D 100A" ideal model delta sigma weight residual 120.09 127.41 -7.32 1.25e+00 6.40e-01 3.43e+01 ... (remaining 36781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 16865 22.14 - 44.28: 1001 44.28 - 66.41: 210 66.41 - 88.55: 194 88.55 - 110.69: 102 Dihedral angle restraints: 18372 sinusoidal: 9522 harmonic: 8850 Sorted by residual: dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -165.14 79.14 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA GLN E 27 " pdb=" C GLN E 27 " pdb=" N GLY E 27A" pdb=" CA GLY E 27A" ideal model delta harmonic sigma weight residual 180.00 137.33 42.67 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN I 27 " pdb=" C GLN I 27 " pdb=" N GLY I 27A" pdb=" CA GLY I 27A" ideal model delta harmonic sigma weight residual 180.00 137.45 42.55 0 5.00e+00 4.00e-02 7.24e+01 ... (remaining 18369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3291 0.068 - 0.136: 1074 0.136 - 0.205: 171 0.205 - 0.273: 32 0.273 - 0.341: 22 Chirality restraints: 4590 Sorted by residual: chirality pdb=" CB THR J 123 " pdb=" CA THR J 123 " pdb=" OG1 THR J 123 " pdb=" CG2 THR J 123 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C5 BMA w 3 " pdb=" C4 BMA w 3 " pdb=" C6 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4587 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 51 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C THR O 51 " -0.056 2.00e-02 2.50e+03 pdb=" O THR O 51 " 0.021 2.00e-02 2.50e+03 pdb=" N SER O 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 51 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR E 51 " -0.056 2.00e-02 2.50e+03 pdb=" O THR E 51 " 0.021 2.00e-02 2.50e+03 pdb=" N SER E 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 312 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO G 313 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO G 313 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 313 " 0.043 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5354 2.78 - 3.31: 21843 3.31 - 3.84: 45892 3.84 - 4.37: 54480 4.37 - 4.90: 90530 Nonbonded interactions: 218099 Sorted by model distance: nonbonded pdb=" O ASN J 355 " pdb=" OG SER J 397 " model vdw 2.252 3.040 nonbonded pdb=" O LYS J 421 " pdb=" O HOH J 701 " model vdw 2.262 3.040 nonbonded pdb=" O LYS G 421 " pdb=" O HOH G 701 " model vdw 2.274 3.040 nonbonded pdb=" O ASN G 355 " pdb=" OG SER G 397 " model vdw 2.286 3.040 nonbonded pdb=" NE2 GLN H 6 " pdb=" O GLY H 104 " model vdw 2.297 3.120 ... (remaining 218094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '7' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 't' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '5' selection = chain 'Z' selection = chain 'd' selection = chain 'n' selection = chain 'r' } ncs_group { reference = chain '3' selection = chain 'b' selection = chain 'p' } ncs_group { reference = chain '6' selection = chain '8' selection = chain '9' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'AA' selection = chain 'X' selection = chain 'i' selection = chain 'l' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'B' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.160 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.010 0.126 27324 Z= 0.463 Angle : 1.205 12.480 37407 Z= 0.598 Chirality : 0.069 0.341 4590 Planarity : 0.007 0.077 4434 Dihedral : 18.534 110.691 12561 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 0.41 % Allowed : 5.18 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.93 (0.13), residues: 3018 helix: -2.30 (0.18), residues: 429 sheet: -0.64 (0.15), residues: 975 loop : -1.35 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 54 TYR 0.023 0.003 TYR P 384 PHE 0.026 0.004 PHE J 159 TRP 0.027 0.004 TRP P 427 HIS 0.013 0.002 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.01025 (27099) covalent geometry : angle 1.15629 (36786) SS BOND : bond 0.01051 ( 45) SS BOND : angle 2.66131 ( 90) hydrogen bonds : bond 0.13707 ( 931) hydrogen bonds : angle 7.02696 ( 2844) Misc. bond : bond 0.00175 ( 3) link_ALPHA1-2 : bond 0.00404 ( 6) link_ALPHA1-2 : angle 2.63512 ( 18) link_ALPHA1-3 : bond 0.00584 ( 18) link_ALPHA1-3 : angle 1.66478 ( 54) link_ALPHA1-6 : bond 0.00719 ( 21) link_ALPHA1-6 : angle 1.90041 ( 63) link_BETA1-4 : bond 0.00898 ( 72) link_BETA1-4 : angle 2.95340 ( 216) link_NAG-ASN : bond 0.01012 ( 60) link_NAG-ASN : angle 3.42041 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 491 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 74 SER cc_start: 0.4983 (p) cc_final: 0.4754 (p) REVERT: K 91 TYR cc_start: 0.7989 (m-80) cc_final: 0.7626 (m-80) REVERT: O 61 ARG cc_start: 0.7816 (ptt-90) cc_final: 0.7554 (ptt-90) REVERT: O 79 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6466 (mp0) REVERT: O 106 LYS cc_start: 0.5962 (pttm) cc_final: 0.5733 (pmtt) REVERT: B 66 ASP cc_start: 0.8982 (t0) cc_final: 0.8717 (t0) REVERT: L 66 ASP cc_start: 0.9070 (t0) cc_final: 0.8726 (t0) REVERT: L 70 ARG cc_start: 0.7390 (mtp85) cc_final: 0.7157 (mtt-85) REVERT: R 63 SER cc_start: 0.8598 (m) cc_final: 0.8362 (m) REVERT: R 66 ASP cc_start: 0.8979 (t0) cc_final: 0.8631 (t0) REVERT: C 542 ARG cc_start: 0.8272 (ptt180) cc_final: 0.8037 (ptt-90) REVERT: C 647 GLU cc_start: 0.7517 (tt0) cc_final: 0.7271 (tt0) REVERT: C 653 GLN cc_start: 0.7297 (mt0) cc_final: 0.6916 (tt0) REVERT: G 35 TRP cc_start: 0.8467 (m-90) cc_final: 0.8265 (m100) REVERT: G 95 MET cc_start: 0.9367 (ptm) cc_final: 0.8969 (ptm) REVERT: G 340 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7398 (mt-10) REVERT: J 35 TRP cc_start: 0.8495 (m-90) cc_final: 0.8202 (m100) REVERT: J 95 MET cc_start: 0.9302 (ptm) cc_final: 0.8954 (ptm) REVERT: J 213 ILE cc_start: 0.9224 (mm) cc_final: 0.9013 (mp) REVERT: J 264 SER cc_start: 0.9096 (p) cc_final: 0.8815 (m) REVERT: F 536 THR cc_start: 0.8988 (p) cc_final: 0.8767 (p) REVERT: F 577 GLN cc_start: 0.6978 (pt0) cc_final: 0.6726 (pm20) REVERT: F 653 GLN cc_start: 0.7243 (mt0) cc_final: 0.6964 (tt0) REVERT: F 655 LYS cc_start: 0.7059 (ttmm) cc_final: 0.6474 (pttt) REVERT: P 95 MET cc_start: 0.9324 (ptm) cc_final: 0.8972 (ptm) REVERT: P 130 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8527 (mm-40) REVERT: P 173 TYR cc_start: 0.8995 (p90) cc_final: 0.8651 (p90) REVERT: P 217 TYR cc_start: 0.8884 (m-80) cc_final: 0.8675 (m-80) REVERT: P 426 MET cc_start: 0.8356 (tpp) cc_final: 0.8117 (tpt) REVERT: P 432 GLN cc_start: 0.8568 (mt0) cc_final: 0.8347 (mt0) outliers start: 11 outliers final: 4 residues processed: 500 average time/residue: 0.7243 time to fit residues: 411.1407 Evaluate side-chains 405 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 401 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain J residue 501 CYS Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.5980 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 30 ASN A 82AASN K 82AASN K 99 GLN D 6 GLN L 66CASN N 6 GLN R 66CASN H 6 GLN C 607 ASN C 652 GLN C 653 GLN G 85 HIS G 114 GLN G 280 ASN G 356 ASN G 377 ASN G 411 ASN G 422 GLN M 575 GLN M 607 ASN J 85 HIS J 103 GLN J 280 ASN J 356 ASN J 377 ASN J 411 ASN J 422 GLN F 607 ASN F 630 GLN F 653 GLN P 280 ASN P 411 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109738 restraints weight = 27658.589| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.26 r_work: 0.3001 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27324 Z= 0.134 Angle : 0.703 9.351 37407 Z= 0.338 Chirality : 0.047 0.193 4590 Planarity : 0.005 0.059 4434 Dihedral : 14.106 88.766 6940 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 10.51 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.92 (0.14), residues: 3018 helix: -0.30 (0.25), residues: 429 sheet: -0.26 (0.16), residues: 1002 loop : -0.87 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 96 TYR 0.012 0.001 TYR J 318 PHE 0.017 0.001 PHE G 383 TRP 0.020 0.001 TRP P 479 HIS 0.004 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00288 (27099) covalent geometry : angle 0.65982 (36786) SS BOND : bond 0.00437 ( 45) SS BOND : angle 1.40708 ( 90) hydrogen bonds : bond 0.04048 ( 931) hydrogen bonds : angle 5.46378 ( 2844) Misc. bond : bond 0.00094 ( 3) link_ALPHA1-2 : bond 0.00532 ( 6) link_ALPHA1-2 : angle 1.95082 ( 18) link_ALPHA1-3 : bond 0.01117 ( 18) link_ALPHA1-3 : angle 2.00222 ( 54) link_ALPHA1-6 : bond 0.00735 ( 21) link_ALPHA1-6 : angle 1.79666 ( 63) link_BETA1-4 : bond 0.00499 ( 72) link_BETA1-4 : angle 2.03342 ( 216) link_NAG-ASN : bond 0.00299 ( 60) link_NAG-ASN : angle 2.26510 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 438 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 74 SER cc_start: 0.5396 (p) cc_final: 0.5164 (p) REVERT: K 91 TYR cc_start: 0.7883 (m-80) cc_final: 0.7638 (m-80) REVERT: Q 34 TRP cc_start: 0.7796 (m100) cc_final: 0.7489 (m-90) REVERT: E 106 LYS cc_start: 0.4326 (pptt) cc_final: 0.3227 (pmtt) REVERT: O 61 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7600 (ptt180) REVERT: O 106 LYS cc_start: 0.5864 (pttm) cc_final: 0.5594 (pmtt) REVERT: B 26 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: B 85 ASP cc_start: 0.8259 (m-30) cc_final: 0.7970 (m-30) REVERT: D 100 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7703 (mtt90) REVERT: L 70 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7516 (mtt-85) REVERT: R 63 SER cc_start: 0.8658 (m) cc_final: 0.8420 (m) REVERT: R 66 ASP cc_start: 0.9125 (t0) cc_final: 0.8784 (t0) REVERT: R 85 ASP cc_start: 0.8452 (m-30) cc_final: 0.8208 (m-30) REVERT: H 99 ASP cc_start: 0.8972 (m-30) cc_final: 0.8662 (m-30) REVERT: C 542 ARG cc_start: 0.8477 (ptt180) cc_final: 0.8188 (ptt-90) REVERT: C 653 GLN cc_start: 0.7532 (mt0) cc_final: 0.7032 (tt0) REVERT: G 95 MET cc_start: 0.9448 (ptm) cc_final: 0.9230 (ptm) REVERT: G 271 MET cc_start: 0.9093 (mmm) cc_final: 0.8824 (mmp) REVERT: G 340 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8177 (mt-10) REVERT: M 621 GLU cc_start: 0.7250 (pt0) cc_final: 0.6897 (pt0) REVERT: M 647 GLU cc_start: 0.7994 (tt0) cc_final: 0.7787 (tt0) REVERT: M 655 LYS cc_start: 0.7089 (ttmm) cc_final: 0.6505 (ptpt) REVERT: J 35 TRP cc_start: 0.8498 (m-90) cc_final: 0.8214 (m100) REVERT: J 95 MET cc_start: 0.9450 (ptm) cc_final: 0.9153 (ptm) REVERT: J 264 SER cc_start: 0.9274 (p) cc_final: 0.9072 (m) REVERT: J 271 MET cc_start: 0.9024 (mmm) cc_final: 0.8699 (mmp) REVERT: F 536 THR cc_start: 0.8931 (p) cc_final: 0.8720 (p) REVERT: F 653 GLN cc_start: 0.7178 (mt0) cc_final: 0.6954 (tt0) REVERT: F 655 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6713 (ptpt) REVERT: P 130 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8898 (mm-40) REVERT: P 340 GLU cc_start: 0.8585 (tt0) cc_final: 0.8151 (tm-30) outliers start: 54 outliers final: 23 residues processed: 471 average time/residue: 0.7127 time to fit residues: 383.6948 Evaluate side-chains 431 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 407 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain M residue 653 GLN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 411 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 GLN C 630 GLN G 130 GLN G 293 GLN G 411 ASN M 543 ASN M 607 ASN M 630 GLN J 356 ASN J 377 ASN J 411 ASN F 575 GLN F 630 GLN P 183 GLN P 411 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102968 restraints weight = 27589.432| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.33 r_work: 0.2906 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 27324 Z= 0.374 Angle : 0.926 12.742 37407 Z= 0.443 Chirality : 0.057 0.245 4590 Planarity : 0.006 0.070 4434 Dihedral : 13.721 98.522 6936 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.17 % Allowed : 11.15 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.78 (0.15), residues: 3018 helix: 0.13 (0.26), residues: 411 sheet: -0.20 (0.15), residues: 1005 loop : -0.84 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 480 TYR 0.021 0.003 TYR G 318 PHE 0.020 0.003 PHE G 383 TRP 0.020 0.003 TRP P 479 HIS 0.013 0.002 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00871 (27099) covalent geometry : angle 0.87808 (36786) SS BOND : bond 0.00880 ( 45) SS BOND : angle 2.07816 ( 90) hydrogen bonds : bond 0.05612 ( 931) hydrogen bonds : angle 5.72054 ( 2844) Misc. bond : bond 0.00193 ( 3) link_ALPHA1-2 : bond 0.00635 ( 6) link_ALPHA1-2 : angle 2.47495 ( 18) link_ALPHA1-3 : bond 0.00956 ( 18) link_ALPHA1-3 : angle 1.74482 ( 54) link_ALPHA1-6 : bond 0.00940 ( 21) link_ALPHA1-6 : angle 1.82095 ( 63) link_BETA1-4 : bond 0.00633 ( 72) link_BETA1-4 : angle 2.55902 ( 216) link_NAG-ASN : bond 0.00745 ( 60) link_NAG-ASN : angle 2.78940 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 400 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 74 SER cc_start: 0.5250 (p) cc_final: 0.5014 (p) REVERT: K 91 TYR cc_start: 0.7954 (m-80) cc_final: 0.7621 (m-80) REVERT: K 99 GLN cc_start: 0.9164 (pt0) cc_final: 0.8876 (tt0) REVERT: E 106 LYS cc_start: 0.4542 (pptt) cc_final: 0.3259 (pmtt) REVERT: O 61 ARG cc_start: 0.7882 (ptt-90) cc_final: 0.7664 (ptt-90) REVERT: O 106 LYS cc_start: 0.5810 (pttm) cc_final: 0.5593 (pmtt) REVERT: D 100 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7864 (mtt90) REVERT: L 70 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7550 (mtt-85) REVERT: N 35 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9033 (mmpt) REVERT: R 63 SER cc_start: 0.8746 (m) cc_final: 0.8484 (m) REVERT: R 66 ASP cc_start: 0.9186 (t0) cc_final: 0.8881 (t0) REVERT: H 99 ASP cc_start: 0.9115 (m-30) cc_final: 0.8880 (m-30) REVERT: C 542 ARG cc_start: 0.8527 (ptt180) cc_final: 0.8223 (ptt-90) REVERT: C 647 GLU cc_start: 0.8062 (tt0) cc_final: 0.7848 (tt0) REVERT: C 652 GLN cc_start: 0.6435 (mt0) cc_final: 0.6174 (mp10) REVERT: C 653 GLN cc_start: 0.7446 (mt0) cc_final: 0.6986 (tt0) REVERT: G 95 MET cc_start: 0.9477 (ptm) cc_final: 0.9173 (ptm) REVERT: G 275 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8839 (tt0) REVERT: G 340 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8153 (mt-10) REVERT: M 621 GLU cc_start: 0.7377 (pt0) cc_final: 0.7118 (pt0) REVERT: M 655 LYS cc_start: 0.7051 (ttmm) cc_final: 0.6562 (ptpt) REVERT: J 35 TRP cc_start: 0.8545 (m-90) cc_final: 0.8200 (m100) REVERT: J 275 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: F 577 GLN cc_start: 0.7104 (pt0) cc_final: 0.6702 (pm20) REVERT: F 652 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6649 (tp40) REVERT: F 653 GLN cc_start: 0.7175 (mt0) cc_final: 0.6913 (tt0) REVERT: F 655 LYS cc_start: 0.7213 (ttmm) cc_final: 0.6738 (ptpt) REVERT: P 430 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9067 (mm) outliers start: 111 outliers final: 64 residues processed: 471 average time/residue: 0.6942 time to fit residues: 374.3729 Evaluate side-chains 461 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 392 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain M residue 653 GLN Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain J residue 490 LYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 231 LYS Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 490 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 7 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 180 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 211 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Q 99 GLN O 42 GLN C 575 GLN C 577 GLN G 293 GLN G 377 ASN G 411 ASN M 630 GLN J 356 ASN F 630 GLN P 293 GLN P 411 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108325 restraints weight = 27358.845| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.36 r_work: 0.3002 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27324 Z= 0.125 Angle : 0.677 9.837 37407 Z= 0.326 Chirality : 0.047 0.217 4590 Planarity : 0.004 0.054 4434 Dihedral : 11.693 89.387 6936 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.82 % Allowed : 13.36 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.35 (0.15), residues: 3018 helix: 0.58 (0.27), residues: 420 sheet: 0.06 (0.16), residues: 1002 loop : -0.58 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 96 TYR 0.014 0.001 TYR O 36 PHE 0.014 0.001 PHE P 383 TRP 0.018 0.001 TRP D 47 HIS 0.004 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00265 (27099) covalent geometry : angle 0.63842 (36786) SS BOND : bond 0.00287 ( 45) SS BOND : angle 1.37627 ( 90) hydrogen bonds : bond 0.03806 ( 931) hydrogen bonds : angle 5.20140 ( 2844) Misc. bond : bond 0.00083 ( 3) link_ALPHA1-2 : bond 0.00384 ( 6) link_ALPHA1-2 : angle 1.75968 ( 18) link_ALPHA1-3 : bond 0.01046 ( 18) link_ALPHA1-3 : angle 1.73471 ( 54) link_ALPHA1-6 : bond 0.00823 ( 21) link_ALPHA1-6 : angle 1.58047 ( 63) link_BETA1-4 : bond 0.00480 ( 72) link_BETA1-4 : angle 1.85301 ( 216) link_NAG-ASN : bond 0.00306 ( 60) link_NAG-ASN : angle 2.19697 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 423 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2439 (mtp) cc_final: 0.2156 (mtt) REVERT: A 34 TRP cc_start: 0.7925 (m100) cc_final: 0.7565 (m100) REVERT: K 74 SER cc_start: 0.5195 (p) cc_final: 0.4954 (p) REVERT: K 91 TYR cc_start: 0.7837 (m-80) cc_final: 0.7503 (m-80) REVERT: K 96 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7886 (ttm110) REVERT: E 106 LYS cc_start: 0.4391 (pptt) cc_final: 0.3207 (pmtt) REVERT: O 40 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7732 (ttm170) REVERT: I 40 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7783 (ttm170) REVERT: L 70 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7494 (mtt-85) REVERT: R 63 SER cc_start: 0.8664 (m) cc_final: 0.8397 (m) REVERT: R 66 ASP cc_start: 0.9135 (t0) cc_final: 0.8798 (t0) REVERT: H 99 ASP cc_start: 0.9070 (m-30) cc_final: 0.8805 (m-30) REVERT: C 542 ARG cc_start: 0.8477 (ptt180) cc_final: 0.8183 (ptt-90) REVERT: C 653 GLN cc_start: 0.7443 (mt0) cc_final: 0.7042 (tt0) REVERT: G 35 TRP cc_start: 0.8431 (m100) cc_final: 0.8176 (m100) REVERT: G 95 MET cc_start: 0.9439 (ptm) cc_final: 0.9154 (ptm) REVERT: G 271 MET cc_start: 0.9095 (mmm) cc_final: 0.8825 (mmp) REVERT: G 340 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8153 (mt-10) REVERT: M 621 GLU cc_start: 0.7284 (pt0) cc_final: 0.6958 (pt0) REVERT: M 655 LYS cc_start: 0.7218 (ttmm) cc_final: 0.6661 (ptpt) REVERT: J 35 TRP cc_start: 0.8521 (m-90) cc_final: 0.8252 (m100) REVERT: J 170 GLN cc_start: 0.8411 (tt0) cc_final: 0.7945 (tt0) REVERT: J 271 MET cc_start: 0.8940 (mmm) cc_final: 0.8710 (mmp) REVERT: J 464 THR cc_start: 0.8394 (p) cc_final: 0.8090 (p) REVERT: F 595 ILE cc_start: 0.8294 (pt) cc_final: 0.8037 (mp) REVERT: F 652 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6523 (tp40) REVERT: F 655 LYS cc_start: 0.7184 (ttmm) cc_final: 0.6505 (ptpt) REVERT: P 340 GLU cc_start: 0.8586 (tt0) cc_final: 0.8167 (tm-30) outliers start: 75 outliers final: 40 residues processed: 472 average time/residue: 0.7411 time to fit residues: 400.0682 Evaluate side-chains 448 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 405 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 281 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN G 411 ASN M 543 ASN M 575 GLN M 630 GLN J 356 ASN F 607 ASN P 293 GLN P 411 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105157 restraints weight = 27332.156| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.05 r_work: 0.2974 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27324 Z= 0.194 Angle : 0.737 10.067 37407 Z= 0.354 Chirality : 0.049 0.216 4590 Planarity : 0.005 0.054 4434 Dihedral : 11.256 92.330 6936 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.27 % Allowed : 13.85 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.28 (0.15), residues: 3018 helix: 0.90 (0.27), residues: 402 sheet: 0.06 (0.16), residues: 1005 loop : -0.57 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 77 TYR 0.014 0.002 TYR F 638 PHE 0.016 0.002 PHE P 383 TRP 0.020 0.002 TRP P 479 HIS 0.008 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00442 (27099) covalent geometry : angle 0.69589 (36786) SS BOND : bond 0.00589 ( 45) SS BOND : angle 1.70904 ( 90) hydrogen bonds : bond 0.04322 ( 931) hydrogen bonds : angle 5.23855 ( 2844) Misc. bond : bond 0.00110 ( 3) link_ALPHA1-2 : bond 0.00331 ( 6) link_ALPHA1-2 : angle 2.05639 ( 18) link_ALPHA1-3 : bond 0.00974 ( 18) link_ALPHA1-3 : angle 1.78896 ( 54) link_ALPHA1-6 : bond 0.00842 ( 21) link_ALPHA1-6 : angle 1.55536 ( 63) link_BETA1-4 : bond 0.00478 ( 72) link_BETA1-4 : angle 1.97421 ( 216) link_NAG-ASN : bond 0.00445 ( 60) link_NAG-ASN : angle 2.36242 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 404 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2507 (mtp) cc_final: 0.2269 (mtt) REVERT: A 34 TRP cc_start: 0.7959 (m100) cc_final: 0.7618 (m100) REVERT: A 96 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7949 (ttm110) REVERT: K 29 MET cc_start: 0.4126 (mmt) cc_final: 0.3821 (mtt) REVERT: K 74 SER cc_start: 0.5168 (p) cc_final: 0.4925 (p) REVERT: K 91 TYR cc_start: 0.7877 (m-80) cc_final: 0.7545 (m-80) REVERT: Q 96 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7970 (ttm110) REVERT: E 81 GLU cc_start: 0.7421 (pm20) cc_final: 0.6666 (pm20) REVERT: E 106 LYS cc_start: 0.4428 (pptt) cc_final: 0.3238 (pmtt) REVERT: O 10 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (mm) REVERT: O 40 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: I 40 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: L 70 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7487 (mtt-85) REVERT: N 35 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.8945 (mmpt) REVERT: R 63 SER cc_start: 0.8715 (m) cc_final: 0.8457 (m) REVERT: R 66 ASP cc_start: 0.9143 (t0) cc_final: 0.8811 (t0) REVERT: H 99 ASP cc_start: 0.9054 (m-30) cc_final: 0.8839 (m-30) REVERT: C 542 ARG cc_start: 0.8497 (ptt180) cc_final: 0.8218 (ptt-90) REVERT: C 653 GLN cc_start: 0.7475 (mt0) cc_final: 0.7051 (tt0) REVERT: G 35 TRP cc_start: 0.8508 (m100) cc_final: 0.8196 (m100) REVERT: G 95 MET cc_start: 0.9459 (ptm) cc_final: 0.9190 (ptm) REVERT: G 271 MET cc_start: 0.9077 (mmm) cc_final: 0.8794 (mmp) REVERT: G 340 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8130 (mt-10) REVERT: M 621 GLU cc_start: 0.7306 (pt0) cc_final: 0.6957 (pt0) REVERT: M 655 LYS cc_start: 0.7118 (ttmm) cc_final: 0.6647 (ptpt) REVERT: J 35 TRP cc_start: 0.8503 (m-90) cc_final: 0.8167 (m100) REVERT: J 170 GLN cc_start: 0.8438 (tt0) cc_final: 0.7984 (tt0) REVERT: J 271 MET cc_start: 0.9029 (mmm) cc_final: 0.8734 (mmp) REVERT: J 275 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: J 464 THR cc_start: 0.8426 (p) cc_final: 0.8105 (p) REVERT: F 577 GLN cc_start: 0.6591 (pt0) cc_final: 0.6312 (pm20) REVERT: F 595 ILE cc_start: 0.8461 (pt) cc_final: 0.7919 (mp) REVERT: F 652 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6510 (tp40) REVERT: F 655 LYS cc_start: 0.7145 (ttmm) cc_final: 0.6437 (ptpt) REVERT: F 658 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: P 340 GLU cc_start: 0.8579 (tt0) cc_final: 0.8165 (tm-30) REVERT: P 416 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8709 (mt) outliers start: 87 outliers final: 54 residues processed: 463 average time/residue: 0.7216 time to fit residues: 382.6724 Evaluate side-chains 466 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 404 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 281 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 240 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 99 GLN B 66CASN C 577 GLN G 377 ASN M 575 GLN M 630 GLN J 356 ASN P 411 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107352 restraints weight = 27331.000| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.40 r_work: 0.2948 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27324 Z= 0.206 Angle : 0.746 10.777 37407 Z= 0.357 Chirality : 0.049 0.224 4590 Planarity : 0.005 0.053 4434 Dihedral : 10.892 93.181 6936 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.83 % Allowed : 13.93 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.28 (0.15), residues: 3018 helix: 0.76 (0.27), residues: 411 sheet: 0.09 (0.16), residues: 1005 loop : -0.56 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 77 TYR 0.017 0.002 TYR G 217 PHE 0.016 0.002 PHE J 383 TRP 0.024 0.002 TRP P 479 HIS 0.008 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00469 (27099) covalent geometry : angle 0.70595 (36786) SS BOND : bond 0.00542 ( 45) SS BOND : angle 1.68723 ( 90) hydrogen bonds : bond 0.04413 ( 931) hydrogen bonds : angle 5.23605 ( 2844) Misc. bond : bond 0.00116 ( 3) link_ALPHA1-2 : bond 0.00329 ( 6) link_ALPHA1-2 : angle 2.03315 ( 18) link_ALPHA1-3 : bond 0.00989 ( 18) link_ALPHA1-3 : angle 1.84048 ( 54) link_ALPHA1-6 : bond 0.00843 ( 21) link_ALPHA1-6 : angle 1.54700 ( 63) link_BETA1-4 : bond 0.00501 ( 72) link_BETA1-4 : angle 1.93874 ( 216) link_NAG-ASN : bond 0.00499 ( 60) link_NAG-ASN : angle 2.38860 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 415 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2380 (mtp) cc_final: 0.2014 (mtt) REVERT: A 34 TRP cc_start: 0.7876 (m100) cc_final: 0.7460 (m100) REVERT: K 74 SER cc_start: 0.5195 (p) cc_final: 0.4965 (p) REVERT: K 91 TYR cc_start: 0.7801 (m-80) cc_final: 0.7527 (m-80) REVERT: K 96 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7822 (ttm110) REVERT: Q 29 MET cc_start: 0.3461 (mtt) cc_final: 0.3187 (mtm) REVERT: Q 96 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.8034 (ttm110) REVERT: E 81 GLU cc_start: 0.7421 (pm20) cc_final: 0.6702 (pm20) REVERT: E 106 LYS cc_start: 0.4426 (pptt) cc_final: 0.3106 (pmtt) REVERT: O 10 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8046 (mm) REVERT: O 40 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: I 40 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7725 (ttm170) REVERT: D 33 ASP cc_start: 0.8450 (p0) cc_final: 0.8203 (p0) REVERT: L 70 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7505 (mtt-85) REVERT: N 35 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.8962 (mmpt) REVERT: R 63 SER cc_start: 0.8722 (m) cc_final: 0.8462 (m) REVERT: R 66 ASP cc_start: 0.9153 (t0) cc_final: 0.8837 (t0) REVERT: C 542 ARG cc_start: 0.8484 (ptt180) cc_final: 0.8211 (ptt-90) REVERT: C 653 GLN cc_start: 0.7482 (mt0) cc_final: 0.7027 (tt0) REVERT: G 35 TRP cc_start: 0.8518 (m100) cc_final: 0.8254 (m100) REVERT: G 95 MET cc_start: 0.9467 (ptm) cc_final: 0.9204 (ptm) REVERT: G 271 MET cc_start: 0.9106 (mmm) cc_final: 0.8830 (mmp) REVERT: G 340 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8087 (mt-10) REVERT: M 621 GLU cc_start: 0.7336 (pt0) cc_final: 0.7040 (pt0) REVERT: J 35 TRP cc_start: 0.8506 (m-90) cc_final: 0.8159 (m100) REVERT: J 213 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8826 (mp) REVERT: J 271 MET cc_start: 0.9033 (mmm) cc_final: 0.8730 (mmp) REVERT: J 275 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8944 (tt0) REVERT: F 652 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: F 655 LYS cc_start: 0.7000 (ttmm) cc_final: 0.6354 (ptpt) REVERT: F 658 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: P 340 GLU cc_start: 0.8599 (tt0) cc_final: 0.8141 (tm-30) REVERT: P 416 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8746 (mt) outliers start: 102 outliers final: 63 residues processed: 477 average time/residue: 0.7384 time to fit residues: 403.3825 Evaluate side-chains 481 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 409 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 143 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN D 83 GLN C 575 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN G 377 ASN M 575 GLN M 630 GLN J 356 ASN P 411 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104549 restraints weight = 27382.261| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.04 r_work: 0.2964 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27324 Z= 0.224 Angle : 0.776 11.902 37407 Z= 0.372 Chirality : 0.050 0.229 4590 Planarity : 0.005 0.055 4434 Dihedral : 10.820 93.883 6936 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.98 % Allowed : 14.30 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 0.21 % 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: -0.30 (0.15), residues: 3018 helix: 0.75 (0.27), residues: 411 sheet: 0.09 (0.15), residues: 1005 loop : -0.59 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 77 TYR 0.017 0.002 TYR G 318 PHE 0.017 0.002 PHE J 383 TRP 0.026 0.002 TRP P 479 HIS 0.009 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00513 (27099) covalent geometry : angle 0.73256 (36786) SS BOND : bond 0.00604 ( 45) SS BOND : angle 2.23018 ( 90) hydrogen bonds : bond 0.04500 ( 931) hydrogen bonds : angle 5.25840 ( 2844) Misc. bond : bond 0.00121 ( 3) link_ALPHA1-2 : bond 0.00342 ( 6) link_ALPHA1-2 : angle 2.07666 ( 18) link_ALPHA1-3 : bond 0.00970 ( 18) link_ALPHA1-3 : angle 1.85868 ( 54) link_ALPHA1-6 : bond 0.00834 ( 21) link_ALPHA1-6 : angle 1.55001 ( 63) link_BETA1-4 : bond 0.00518 ( 72) link_BETA1-4 : angle 1.97710 ( 216) link_NAG-ASN : bond 0.00546 ( 60) link_NAG-ASN : angle 2.41407 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 404 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2432 (mtp) cc_final: 0.2118 (mtt) REVERT: A 34 TRP cc_start: 0.7937 (m100) cc_final: 0.7533 (m100) REVERT: K 74 SER cc_start: 0.5202 (p) cc_final: 0.4969 (p) REVERT: Q 29 MET cc_start: 0.3233 (mtt) cc_final: 0.2890 (mtm) REVERT: Q 35 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8121 (t) REVERT: Q 100 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7495 (mpt) REVERT: E 81 GLU cc_start: 0.7333 (pm20) cc_final: 0.6672 (pm20) REVERT: E 106 LYS cc_start: 0.4441 (pptt) cc_final: 0.3140 (pmtt) REVERT: O 10 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8031 (mm) REVERT: O 40 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7750 (ttm170) REVERT: I 40 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: L 70 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7491 (mtt-85) REVERT: N 35 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.8961 (mmpt) REVERT: R 63 SER cc_start: 0.8725 (m) cc_final: 0.8460 (m) REVERT: R 66 ASP cc_start: 0.9105 (t0) cc_final: 0.8812 (t0) REVERT: C 542 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8224 (ptt-90) REVERT: C 653 GLN cc_start: 0.7499 (mt0) cc_final: 0.7061 (tt0) REVERT: C 658 GLN cc_start: 0.7912 (tt0) cc_final: 0.7631 (tm-30) REVERT: G 35 TRP cc_start: 0.8549 (m100) cc_final: 0.8328 (m100) REVERT: G 95 MET cc_start: 0.9462 (ptm) cc_final: 0.9192 (ptm) REVERT: G 271 MET cc_start: 0.9098 (mmm) cc_final: 0.8822 (mmp) REVERT: G 340 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8078 (mt-10) REVERT: G 347 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8854 (tttt) REVERT: M 621 GLU cc_start: 0.7375 (pt0) cc_final: 0.7127 (pt0) REVERT: M 655 LYS cc_start: 0.7002 (tptt) cc_final: 0.6123 (mtmt) REVERT: J 35 TRP cc_start: 0.8570 (m-90) cc_final: 0.8247 (m100) REVERT: J 213 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8829 (mp) REVERT: J 271 MET cc_start: 0.9021 (mmm) cc_final: 0.8702 (mmp) REVERT: J 275 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8924 (tt0) REVERT: F 652 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6505 (tp40) REVERT: F 655 LYS cc_start: 0.6993 (ttmm) cc_final: 0.6384 (ptpt) REVERT: F 658 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: P 340 GLU cc_start: 0.8587 (tt0) cc_final: 0.8133 (tm-30) REVERT: P 416 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8719 (mt) outliers start: 106 outliers final: 68 residues processed: 475 average time/residue: 0.7091 time to fit residues: 386.2131 Evaluate side-chains 482 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 402 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain M residue 583 VAL Chi-restraints excluded: chain M residue 633 LYS Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN D 83 GLN C 575 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106467 restraints weight = 27585.360| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.35 r_work: 0.2981 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27324 Z= 0.155 Angle : 0.704 13.890 37407 Z= 0.339 Chirality : 0.047 0.233 4590 Planarity : 0.004 0.052 4434 Dihedral : 10.200 90.212 6936 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.19 % Allowed : 15.43 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 0.24 % 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: -0.16 (0.15), residues: 3018 helix: 0.91 (0.27), residues: 411 sheet: 0.19 (0.16), residues: 972 loop : -0.50 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 77 TYR 0.013 0.001 TYR J 318 PHE 0.014 0.002 PHE P 383 TRP 0.030 0.002 TRP P 479 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00346 (27099) covalent geometry : angle 0.66360 (36786) SS BOND : bond 0.00523 ( 45) SS BOND : angle 2.18180 ( 90) hydrogen bonds : bond 0.03953 ( 931) hydrogen bonds : angle 5.07747 ( 2844) Misc. bond : bond 0.00083 ( 3) link_ALPHA1-2 : bond 0.00304 ( 6) link_ALPHA1-2 : angle 1.85544 ( 18) link_ALPHA1-3 : bond 0.01016 ( 18) link_ALPHA1-3 : angle 1.82690 ( 54) link_ALPHA1-6 : bond 0.00816 ( 21) link_ALPHA1-6 : angle 1.49588 ( 63) link_BETA1-4 : bond 0.00488 ( 72) link_BETA1-4 : angle 1.74542 ( 216) link_NAG-ASN : bond 0.00345 ( 60) link_NAG-ASN : angle 2.23148 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 402 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2326 (mtp) cc_final: 0.1964 (mtt) REVERT: A 34 TRP cc_start: 0.7894 (m100) cc_final: 0.7471 (m100) REVERT: K 74 SER cc_start: 0.5288 (p) cc_final: 0.5066 (p) REVERT: K 96 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7827 (ttm110) REVERT: K 107 THR cc_start: 0.6555 (p) cc_final: 0.6128 (t) REVERT: Q 29 MET cc_start: 0.3078 (mtt) cc_final: 0.2618 (mtm) REVERT: E 81 GLU cc_start: 0.7418 (pm20) cc_final: 0.6766 (pm20) REVERT: E 106 LYS cc_start: 0.4418 (pptt) cc_final: 0.3126 (pmtt) REVERT: O 40 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7753 (ttm170) REVERT: I 40 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7713 (ttm170) REVERT: D 33 ASP cc_start: 0.8377 (p0) cc_final: 0.8139 (p0) REVERT: L 70 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7491 (mtt-85) REVERT: N 35 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8959 (mmpt) REVERT: R 63 SER cc_start: 0.8658 (m) cc_final: 0.8390 (m) REVERT: R 66 ASP cc_start: 0.9087 (t0) cc_final: 0.8763 (t0) REVERT: C 542 ARG cc_start: 0.8460 (ptt180) cc_final: 0.8210 (ptt-90) REVERT: C 647 GLU cc_start: 0.7768 (tt0) cc_final: 0.7475 (tt0) REVERT: C 653 GLN cc_start: 0.7471 (mt0) cc_final: 0.7056 (tt0) REVERT: C 658 GLN cc_start: 0.7920 (tt0) cc_final: 0.7665 (tm-30) REVERT: G 35 TRP cc_start: 0.8501 (m100) cc_final: 0.8239 (m100) REVERT: G 95 MET cc_start: 0.9463 (ptm) cc_final: 0.9245 (ptm) REVERT: G 271 MET cc_start: 0.9109 (mmm) cc_final: 0.8836 (mmp) REVERT: G 340 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8103 (mt-10) REVERT: G 347 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8856 (tttm) REVERT: M 621 GLU cc_start: 0.7359 (pt0) cc_final: 0.7116 (pt0) REVERT: J 35 TRP cc_start: 0.8472 (m-90) cc_final: 0.8123 (m100) REVERT: J 169 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8687 (mptp) REVERT: J 271 MET cc_start: 0.8949 (mmm) cc_final: 0.8722 (mmp) REVERT: J 275 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8952 (tt0) REVERT: F 652 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6489 (tp40) REVERT: F 655 LYS cc_start: 0.6962 (ttmm) cc_final: 0.6390 (mtpt) REVERT: F 658 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7400 (tp40) REVERT: F 660 LEU cc_start: 0.7661 (tt) cc_final: 0.7427 (tm) REVERT: P 340 GLU cc_start: 0.8588 (tt0) cc_final: 0.8154 (tm-30) REVERT: P 416 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8731 (mt) REVERT: P 430 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8962 (mm) outliers start: 85 outliers final: 58 residues processed: 462 average time/residue: 0.7215 time to fit residues: 380.9682 Evaluate side-chains 465 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 398 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain M residue 633 LYS Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 283 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 83 GLN C 577 GLN C 652 GLN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104315 restraints weight = 27513.797| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.06 r_work: 0.2962 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 27324 Z= 0.237 Angle : 0.793 17.542 37407 Z= 0.381 Chirality : 0.050 0.228 4590 Planarity : 0.005 0.056 4434 Dihedral : 10.459 93.874 6936 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.45 % Allowed : 15.28 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 0.24 % 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: -0.20 (0.15), residues: 3018 helix: 0.93 (0.27), residues: 402 sheet: 0.16 (0.16), residues: 1005 loop : -0.54 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 77 TYR 0.021 0.002 TYR F 638 PHE 0.016 0.002 PHE J 383 TRP 0.036 0.002 TRP P 479 HIS 0.010 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00545 (27099) covalent geometry : angle 0.74679 (36786) SS BOND : bond 0.00719 ( 45) SS BOND : angle 2.67737 ( 90) hydrogen bonds : bond 0.04563 ( 931) hydrogen bonds : angle 5.23063 ( 2844) Misc. bond : bond 0.00127 ( 3) link_ALPHA1-2 : bond 0.00342 ( 6) link_ALPHA1-2 : angle 2.13664 ( 18) link_ALPHA1-3 : bond 0.00945 ( 18) link_ALPHA1-3 : angle 1.89938 ( 54) link_ALPHA1-6 : bond 0.00832 ( 21) link_ALPHA1-6 : angle 1.51545 ( 63) link_BETA1-4 : bond 0.00532 ( 72) link_BETA1-4 : angle 1.99246 ( 216) link_NAG-ASN : bond 0.00513 ( 60) link_NAG-ASN : angle 2.42941 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 396 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.2220 (mtp) cc_final: 0.1858 (mtt) REVERT: A 34 TRP cc_start: 0.7984 (m100) cc_final: 0.7589 (m100) REVERT: K 74 SER cc_start: 0.5198 (p) cc_final: 0.4970 (p) REVERT: K 96 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7832 (ttm110) REVERT: K 107 THR cc_start: 0.6547 (p) cc_final: 0.6111 (t) REVERT: Q 29 MET cc_start: 0.3140 (mtt) cc_final: 0.2897 (mtm) REVERT: Q 100 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7513 (mpt) REVERT: E 81 GLU cc_start: 0.7354 (pm20) cc_final: 0.6615 (pm20) REVERT: E 106 LYS cc_start: 0.4454 (pptt) cc_final: 0.3165 (pmtt) REVERT: O 10 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8074 (mm) REVERT: O 40 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: I 40 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7717 (ttm170) REVERT: B 25 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6936 (mtt180) REVERT: L 70 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7520 (mtt-85) REVERT: N 35 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.8955 (mmpt) REVERT: R 63 SER cc_start: 0.8739 (m) cc_final: 0.8481 (m) REVERT: R 66 ASP cc_start: 0.9104 (t0) cc_final: 0.8815 (t0) REVERT: C 542 ARG cc_start: 0.8492 (ptt180) cc_final: 0.8215 (ptt-90) REVERT: C 653 GLN cc_start: 0.7501 (mt0) cc_final: 0.7062 (tt0) REVERT: G 35 TRP cc_start: 0.8568 (m100) cc_final: 0.8336 (m100) REVERT: G 95 MET cc_start: 0.9460 (ptm) cc_final: 0.9177 (ptm) REVERT: G 271 MET cc_start: 0.9096 (mmm) cc_final: 0.8819 (mmp) REVERT: G 340 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8092 (mt-10) REVERT: G 347 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8862 (tttt) REVERT: M 621 GLU cc_start: 0.7393 (pt0) cc_final: 0.7136 (pt0) REVERT: J 35 TRP cc_start: 0.8509 (m-90) cc_final: 0.8252 (m100) REVERT: J 169 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8655 (mptp) REVERT: J 275 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8964 (tt0) REVERT: F 652 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6493 (tp40) REVERT: F 655 LYS cc_start: 0.6971 (ttmm) cc_final: 0.6402 (mtpt) REVERT: F 658 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: F 660 LEU cc_start: 0.7744 (tt) cc_final: 0.7524 (tm) REVERT: P 340 GLU cc_start: 0.8583 (tt0) cc_final: 0.8132 (tm-30) REVERT: P 430 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9011 (mm) outliers start: 92 outliers final: 65 residues processed: 459 average time/residue: 0.7424 time to fit residues: 388.9652 Evaluate side-chains 474 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 397 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 96 ARG Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain M residue 633 LYS Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 78 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 chunk 263 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN D 83 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107411 restraints weight = 27469.576| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.32 r_work: 0.2983 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27324 Z= 0.157 Angle : 0.705 14.624 37407 Z= 0.339 Chirality : 0.047 0.235 4590 Planarity : 0.004 0.053 4434 Dihedral : 9.841 89.991 6936 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.93 % Allowed : 15.65 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.24 % 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: -0.06 (0.15), residues: 3018 helix: 1.08 (0.27), residues: 402 sheet: 0.25 (0.16), residues: 1002 loop : -0.46 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 77 TYR 0.014 0.001 TYR J 318 PHE 0.015 0.002 PHE P 383 TRP 0.033 0.002 TRP P 479 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00348 (27099) covalent geometry : angle 0.66441 (36786) SS BOND : bond 0.00529 ( 45) SS BOND : angle 2.16959 ( 90) hydrogen bonds : bond 0.03953 ( 931) hydrogen bonds : angle 5.04502 ( 2844) Misc. bond : bond 0.00085 ( 3) link_ALPHA1-2 : bond 0.00300 ( 6) link_ALPHA1-2 : angle 1.84467 ( 18) link_ALPHA1-3 : bond 0.00998 ( 18) link_ALPHA1-3 : angle 1.84983 ( 54) link_ALPHA1-6 : bond 0.00810 ( 21) link_ALPHA1-6 : angle 1.48862 ( 63) link_BETA1-4 : bond 0.00500 ( 72) link_BETA1-4 : angle 1.73284 ( 216) link_NAG-ASN : bond 0.00352 ( 60) link_NAG-ASN : angle 2.20835 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.7910 (m100) cc_final: 0.7570 (m100) REVERT: K 74 SER cc_start: 0.5264 (p) cc_final: 0.5046 (p) REVERT: K 96 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7944 (ttm110) REVERT: K 107 THR cc_start: 0.6415 (p) cc_final: 0.5981 (t) REVERT: Q 100 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7473 (mpt) REVERT: E 81 GLU cc_start: 0.7359 (pm20) cc_final: 0.6632 (pm20) REVERT: E 106 LYS cc_start: 0.4387 (pptt) cc_final: 0.3117 (pmtt) REVERT: O 10 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7999 (mm) REVERT: O 40 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: I 40 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7732 (ttm170) REVERT: D 33 ASP cc_start: 0.8379 (p0) cc_final: 0.8136 (p0) REVERT: L 70 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7496 (mtt-85) REVERT: N 35 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8944 (mmpt) REVERT: R 63 SER cc_start: 0.8673 (m) cc_final: 0.8411 (m) REVERT: R 66 ASP cc_start: 0.9084 (t0) cc_final: 0.8759 (t0) REVERT: C 542 ARG cc_start: 0.8486 (ptt180) cc_final: 0.8247 (ptt-90) REVERT: C 653 GLN cc_start: 0.7482 (mt0) cc_final: 0.7066 (tt0) REVERT: G 35 TRP cc_start: 0.8510 (m100) cc_final: 0.8241 (m100) REVERT: G 95 MET cc_start: 0.9462 (ptm) cc_final: 0.9247 (ptm) REVERT: G 271 MET cc_start: 0.9111 (mmm) cc_final: 0.8838 (mmp) REVERT: G 340 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8096 (mt-10) REVERT: G 347 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8857 (tttm) REVERT: M 621 GLU cc_start: 0.7339 (pt0) cc_final: 0.7089 (pt0) REVERT: J 35 TRP cc_start: 0.8469 (m-90) cc_final: 0.8141 (m100) REVERT: J 169 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8723 (mptp) REVERT: J 271 MET cc_start: 0.8958 (mmm) cc_final: 0.8728 (mmp) REVERT: J 275 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: F 652 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6417 (tp40) REVERT: F 655 LYS cc_start: 0.6937 (ttmm) cc_final: 0.6338 (mtpt) REVERT: F 658 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7412 (tp40) REVERT: F 660 LEU cc_start: 0.7736 (tt) cc_final: 0.7502 (tm) REVERT: P 340 GLU cc_start: 0.8594 (tt0) cc_final: 0.8165 (tm-30) REVERT: P 416 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8731 (mt) REVERT: P 430 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8963 (mm) outliers start: 78 outliers final: 59 residues processed: 455 average time/residue: 0.7343 time to fit residues: 382.3298 Evaluate side-chains 467 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 396 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 40 ARG Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain N residue 33 ASP Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 127 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 113 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 215 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 416 LEU Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 230 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN D 83 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN M 575 GLN M 607 ASN M 630 GLN J 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107354 restraints weight = 27338.764| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.10 r_work: 0.3011 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27324 Z= 0.142 Angle : 0.683 13.565 37407 Z= 0.329 Chirality : 0.046 0.234 4590 Planarity : 0.004 0.061 4434 Dihedral : 9.347 87.248 6936 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.78 % Allowed : 16.10 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.14 % 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: -0.00 (0.15), residues: 3018 helix: 0.92 (0.27), residues: 420 sheet: 0.27 (0.16), residues: 996 loop : -0.35 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 77 TYR 0.020 0.001 TYR F 638 PHE 0.015 0.001 PHE P 383 TRP 0.037 0.002 TRP P 479 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00314 (27099) covalent geometry : angle 0.64389 (36786) SS BOND : bond 0.00470 ( 45) SS BOND : angle 2.04598 ( 90) hydrogen bonds : bond 0.03771 ( 931) hydrogen bonds : angle 4.94610 ( 2844) Misc. bond : bond 0.00080 ( 3) link_ALPHA1-2 : bond 0.00290 ( 6) link_ALPHA1-2 : angle 1.84637 ( 18) link_ALPHA1-3 : bond 0.01001 ( 18) link_ALPHA1-3 : angle 1.83362 ( 54) link_ALPHA1-6 : bond 0.00797 ( 21) link_ALPHA1-6 : angle 1.49079 ( 63) link_BETA1-4 : bond 0.00489 ( 72) link_BETA1-4 : angle 1.67098 ( 216) link_NAG-ASN : bond 0.00315 ( 60) link_NAG-ASN : angle 2.13359 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13151.18 seconds wall clock time: 223 minutes 47.27 seconds (13427.27 seconds total)