Starting phenix.real_space_refine on Sun Jul 5 23:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttw_41613/07_2026/8ttw_41613.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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 153 5.16 5 C 19545 2.51 5 N 5199 2.21 5 O 6378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31275 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "M" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "O" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "P" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "Q" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "R" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "b" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "c" 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 chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" 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 chiralities: 9 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 chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" 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 chiralities: 9 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "z" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "0" 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 chiralities: 5 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" 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 chiralities: 9 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 chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" C1 MAN b 4 " occ=0.93 ... (9 atoms not shown) pdb=" O6 MAN b 4 " occ=0.93 residue: pdb=" C1 MAN b 8 " occ=0.80 ... (9 atoms not shown) pdb=" O6 MAN b 8 " occ=0.80 residue: pdb=" C1 MAN b 9 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN b 9 " occ=0.85 residue: pdb=" C1 MAN n 4 " occ=0.77 ... (9 atoms not shown) pdb=" O6 MAN n 4 " occ=0.77 residue: pdb=" C1 MAN n 8 " occ=0.74 ... (9 atoms not shown) pdb=" O6 MAN n 8 " occ=0.74 residue: pdb=" C1 MAN n 9 " occ=0.82 ... (9 atoms not shown) pdb=" O6 MAN n 9 " occ=0.82 residue: pdb=" C1 MAN z 4 " occ=0.90 ... (9 atoms not shown) pdb=" O6 MAN z 4 " occ=0.90 residue: pdb=" C1 MAN z 8 " occ=0.87 ... (9 atoms not shown) pdb=" O6 MAN z 8 " occ=0.87 residue: pdb=" C1 MAN z 9 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN z 9 " occ=0.79 Time building chain proxies: 6.96, per 1000 atoms: 0.22 Number of scatterers: 31275 At special positions: 0 Unit cell: (196.248, 190.032, 149.184, 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 153 16.00 O 6378 8.00 N 5199 7.00 C 19545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.02 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN 3 5 " - " MAN 3 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN z 4 " - " MAN z 5 " " MAN z 5 " - " MAN z 6 " " MAN z 8 " - " MAN z 9 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 7 " - " MAN 3 8 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA o 3 " - " MAN o 4 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA z 3 " - " MAN z 4 " " MAN z 7 " - " MAN z 10 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 7 " - " MAN 3 9 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 7 " " MAN f 7 " - " MAN f 9 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA o 3 " - " MAN o 5 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 9 " " BMA z 3 " - " MAN z 7 " " MAN z 7 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 295 " " NAG 2 1 " - " ASN I 301 " " NAG 3 1 " - " ASN I 332 " " NAG 4 1 " - " ASN I 363 " " NAG 5 1 " - " ASN I 386 " " NAG 6 1 " - " ASN I 392 " " NAG 7 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 88 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 355 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 133 " " NAG I 602 " - " ASN I 355 " " NAG I 603 " - " ASN I 339 " " NAG I 604 " - " ASN I 88 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN B 637 " " NAG U 1 " - " ASN E 276 " " NAG V 1 " - " ASN F 637 " " NAG W 1 " - " ASN I 276 " " NAG X 1 " - " ASN J 637 " " NAG Y 1 " - " ASN A 156 " " NAG Z 1 " - " ASN A 160 " " NAG a 1 " - " ASN A 197 " " NAG b 1 " - " ASN A 234 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 295 " " NAG e 1 " - " ASN A 301 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 363 " " NAG h 1 " - " ASN A 386 " " NAG i 1 " - " ASN A 392 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 262 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 197 " " NAG z 1 " - " ASN I 234 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 80 sheets defined 11.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.793A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.501A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.612A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.781A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.703A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.871A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.025A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.681A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 596 removed outlier: 4.128A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.643A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.746A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 removed outlier: 3.550A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.636A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.965A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.601A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.575A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.918A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.027A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.673A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.660A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'H' and resid 121 through 127 removed outlier: 3.764A pdb=" N SER H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.546A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.777A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 117 removed outlier: 4.177A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.603A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.557A pdb=" N VAL I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.735A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 475 through 480' Processing helix chain 'J' and resid 523 through 527 removed outlier: 4.654A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 4.058A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 585 removed outlier: 3.610A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 596 removed outlier: 4.159A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 removed outlier: 3.633A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 661 Processing helix chain 'K' and resid 185 through 189 Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.784A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.545A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 5.217A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 removed outlier: 3.701A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.862A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.041A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 removed outlier: 3.611A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.847A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.942A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.434A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.713A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 35 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 136 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 181 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 136 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.615A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.340A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.837A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 175 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.597A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.202A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.473A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.822A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 170 through 177 removed outlier: 3.705A pdb=" N SER E 158 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.828A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.027A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.765A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.925A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.452A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.442A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.714A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD9, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.796A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 136 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 181 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.796A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 136 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 152 through 154 removed outlier: 4.604A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.366A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.815A pdb=" N PHE H 118 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU H 175 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.608A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 494 through 498 removed outlier: 5.177A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AF2, first strand: chain 'I' and resid 170 through 177 removed outlier: 3.684A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 200 through 203 removed outlier: 5.880A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.005A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 358 through 361 Processing sheet with id=AF5, first strand: chain 'I' and resid 271 through 274 removed outlier: 10.807A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 456 current: chain 'I' and resid 413 through 416 Processing sheet with id=AF6, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.941A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.485A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.417A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.717A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AG3, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.658A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 136 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 181 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.658A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 136 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 152 through 154 removed outlier: 4.619A pdb=" N TYR K 194 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.337A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.506A pdb=" N PHE L 118 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.599A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.606A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS M 22 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER M 70 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.531A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.531A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 20 through 22 Processing sheet with id=AH5, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.698A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 6 through 7 removed outlier: 3.647A pdb=" N THR O 21 " --> pdb=" O SER O 7 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.526A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.526A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 18 through 19 removed outlier: 3.621A pdb=" N SER O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER O 70 " --> pdb=" O SER O 79 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AI2, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.726A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 6 through 7 removed outlier: 3.656A pdb=" N THR Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.528A pdb=" N VAL Q 12 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.528A pdb=" N VAL Q 12 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 67 through 68 Processing sheet with id=AI7, first strand: chain 'R' and resid 20 through 22 Processing sheet with id=AI8, first strand: chain 'R' and resid 45 through 48 removed outlier: 6.729A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2367 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4866 1.31 - 1.45: 9602 1.45 - 1.59: 17266 1.59 - 1.72: 0 1.72 - 1.86: 204 Bond restraints: 31938 Sorted by residual: bond pdb=" C12 83J A 605 " pdb=" N02 83J A 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J I 605 " pdb=" N02 83J I 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J E 605 " pdb=" N02 83J E 605 " ideal model delta sigma weight residual 1.339 1.453 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C13 83J E 605 " pdb=" N05 83J E 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C13 83J I 605 " pdb=" N05 83J I 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 31933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 43039 3.75 - 7.50: 357 7.50 - 11.25: 17 11.25 - 15.00: 3 15.00 - 18.75: 12 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C13 83J A 605 " pdb=" C15 83J A 605 " pdb=" C20 83J A 605 " ideal model delta sigma weight residual 118.87 100.12 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C13 83J E 605 " pdb=" C15 83J E 605 " pdb=" C20 83J E 605 " ideal model delta sigma weight residual 118.87 100.18 18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" C13 83J I 605 " pdb=" C15 83J I 605 " pdb=" C20 83J I 605 " ideal model delta sigma weight residual 118.87 100.20 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C25 83J A 605 " pdb=" C22 83J A 605 " pdb=" O11 83J A 605 " ideal model delta sigma weight residual 124.45 105.98 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C25 83J E 605 " pdb=" C22 83J E 605 " pdb=" O11 83J E 605 " ideal model delta sigma weight residual 124.45 106.10 18.35 3.00e+00 1.11e-01 3.74e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 16423 29.88 - 59.76: 1319 59.76 - 89.64: 114 89.64 - 119.52: 0 119.52 - 149.39: 6 Dihedral angle restraints: 17862 sinusoidal: 7086 harmonic: 10776 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 1.69 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 179.17 -86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual 93.00 6.97 86.03 1 1.00e+01 1.00e-02 8.94e+01 ... (remaining 17859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5074 0.104 - 0.207: 235 0.207 - 0.311: 17 0.311 - 0.415: 6 0.415 - 0.518: 2 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA CYS E 196 " pdb=" N CYS E 196 " pdb=" C CYS E 196 " pdb=" CB CYS E 196 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C1 NAG 4 1 " pdb=" ND2 ASN I 363 " pdb=" C2 NAG 4 1 " pdb=" O5 NAG 4 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 5331 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 140 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C TYR L 140 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR L 140 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO L 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 205 " -0.020 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C CYS I 205 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS I 205 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO I 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 205 " 0.019 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C CYS A 205 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 206 " 0.021 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 383 2.54 - 3.13: 24507 3.13 - 3.72: 45146 3.72 - 4.31: 68814 4.31 - 4.90: 116490 Nonbonded interactions: 255340 Sorted by model distance: nonbonded pdb=" O3 NAG I 604 " pdb=" O7 NAG I 604 " model vdw 1.953 3.040 nonbonded pdb=" O3 NAG E 604 " pdb=" O7 NAG E 604 " model vdw 1.960 3.040 nonbonded pdb=" O3 NAG X 2 " pdb=" O7 NAG X 2 " model vdw 1.963 3.040 nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.966 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 1.976 3.040 ... (remaining 255335 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'c' selection = chain 'o' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain '3' and (resid 1 or resid 4 through 9)) selection = (chain 'b' and (resid 2 or resid 5 through 10)) selection = (chain 'f' and (resid 1 or resid 4 through 9)) selection = (chain 'n' and (resid 2 or resid 5 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 9)) selection = (chain 'z' and (resid 2 or resid 5 through 10)) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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=0.74 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: 3.400 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: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.910 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 32148 Z= 0.259 Angle : 0.890 18.748 44007 Z= 0.399 Chirality : 0.050 0.518 5334 Planarity : 0.004 0.084 5301 Dihedral : 19.640 149.394 10785 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.52 % Favored : 91.80 % Rotamer: Outliers : 10.42 % Allowed : 30.06 % Favored : 59.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.13), residues: 3684 helix: -3.64 (0.18), residues: 426 sheet: -0.95 (0.16), residues: 1152 loop : -1.63 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 588 TYR 0.017 0.001 TYR H 91 PHE 0.009 0.001 PHE E 391 TRP 0.018 0.001 TRP I 69 HIS 0.003 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.26 (31938) covalent geometry : angle 0.85523 / 0.39 (43428) SS BOND : bond 0.00555 / 0.33 ( 51) SS BOND : angle 2.64816 / 1.74 ( 102) hydrogen bonds : bond 0.27746 / 18.32 ( 844) hydrogen bonds : angle 11.24124 / 7.76 ( 2367) link_ALPHA1-2 : bond 0.00248 / 0.15 ( 15) link_ALPHA1-2 : angle 2.03471 / 1.29 ( 45) link_ALPHA1-3 : bond 0.00306 / 0.19 ( 15) link_ALPHA1-3 : angle 2.17157 / 1.35 ( 45) link_ALPHA1-6 : bond 0.00379 / 0.23 ( 15) link_ALPHA1-6 : angle 2.12960 / 1.31 ( 45) link_BETA1-4 : bond 0.00390 / 0.23 ( 51) link_BETA1-4 : angle 1.94887 / 1.23 ( 153) link_NAG-ASN : bond 0.00423 / 0.25 ( 63) link_NAG-ASN : angle 2.55383 / 1.62 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 322 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8086 (mpt) REVERT: E 189 LYS cc_start: 0.7253 (tptt) cc_final: 0.6962 (tmtt) REVERT: E 360 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (ptt-90) REVERT: F 616 ASN cc_start: 0.8235 (p0) cc_final: 0.7988 (p0) REVERT: G 105 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: H 61 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7159 (ptp-170) REVERT: K 100 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: L 61 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6974 (mtm110) REVERT: L 79 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: L 107 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6198 (mmtt) outliers start: 338 outliers final: 305 residues processed: 644 average time/residue: 0.4906 time to fit residues: 391.5391 Evaluate side-chains 634 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 321 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 368 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 630 GLN C 105 GLN D 3 GLN D 124 GLN E 195 ASN F 630 GLN H 3 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN J 630 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 37 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 51 ASN Q 77 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.222947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167390 restraints weight = 33124.933| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.77 r_work: 0.3325 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32148 Z= 0.232 Angle : 0.822 15.240 44007 Z= 0.398 Chirality : 0.051 0.297 5334 Planarity : 0.006 0.151 5301 Dihedral : 14.087 155.296 4617 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.22 % Favored : 92.29 % Rotamer: Outliers : 13.20 % Allowed : 26.03 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3684 helix: -2.66 (0.21), residues: 435 sheet: -0.87 (0.14), residues: 1272 loop : -1.59 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 476 TYR 0.043 0.002 TYR H 140 PHE 0.014 0.002 PHE G 91 TRP 0.018 0.002 TRP J 610 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (31938) covalent geometry : angle 0.78609 / 0.39 (43428) SS BOND : bond 0.00675 / 0.39 ( 51) SS BOND : angle 1.97643 / 1.39 ( 102) hydrogen bonds : bond 0.05748 / 3.85 ( 844) hydrogen bonds : angle 7.18225 / 4.96 ( 2367) link_ALPHA1-2 : bond 0.00495 / 0.29 ( 15) link_ALPHA1-2 : angle 1.73143 / 1.13 ( 45) link_ALPHA1-3 : bond 0.00411 / 0.25 ( 15) link_ALPHA1-3 : angle 1.83066 / 1.19 ( 45) link_ALPHA1-6 : bond 0.00388 / 0.23 ( 15) link_ALPHA1-6 : angle 1.84822 / 1.13 ( 45) link_BETA1-4 : bond 0.00479 / 0.31 ( 51) link_BETA1-4 : angle 2.04931 / 1.27 ( 153) link_NAG-ASN : bond 0.00536 / 0.33 ( 63) link_NAG-ASN : angle 2.71014 / 1.85 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 428 poor density : 331 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8307 (mt) REVERT: A 358 ILE cc_start: 0.8176 (pt) cc_final: 0.7959 (pp) REVERT: A 419 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7738 (ptm160) REVERT: A 456 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7594 (ttp-170) REVERT: C 30 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: D 11 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7103 (tp) REVERT: D 166 GLN cc_start: 0.7802 (mt0) cc_final: 0.7548 (tp40) REVERT: E 153 GLU cc_start: 0.6902 (tt0) cc_final: 0.6619 (tt0) REVERT: F 535 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: F 624 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7996 (p0) REVERT: G 30 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: G 80 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8457 (tp) REVERT: G 100 ASP cc_start: 0.7632 (t0) cc_final: 0.7426 (m-30) REVERT: H 61 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6492 (ptt-90) REVERT: H 79 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.5723 (mp10) REVERT: I 100 MET cc_start: 0.8866 (mtp) cc_final: 0.8657 (mtp) REVERT: I 189 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6392 (tmtt) REVERT: I 268 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7417 (mt-10) REVERT: I 360 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8136 (ptt-90) REVERT: I 456 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7527 (ttp-170) REVERT: J 575 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8064 (tp-100) REVERT: J 640 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: J 654 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: K 13 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7798 (mmtt) REVERT: L 61 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6603 (ptt-90) REVERT: L 65 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7247 (m) REVERT: L 79 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: M 77 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: M 100 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.5939 (mmm) REVERT: N 11 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6801 (mm) REVERT: O 29 MET cc_start: 0.3632 (OUTLIER) cc_final: 0.3377 (pmt) REVERT: O 77 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: P 28 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6648 (mp) REVERT: P 50 ASN cc_start: 0.8092 (t0) cc_final: 0.7551 (t0) REVERT: Q 77 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6219 (pm20) outliers start: 428 outliers final: 252 residues processed: 693 average time/residue: 0.4967 time to fit residues: 422.7376 Evaluate side-chains 587 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 308 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 456 ARG Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 29 MET Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 333 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 290 optimal weight: 30.0000 chunk 317 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 chunk 246 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 overall best weight: 3.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 137 ASN I 183 GLN K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN N 37 GLN N 51 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN P 37 GLN P 51 ASN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.220801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166663 restraints weight = 33056.355| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.55 r_work: 0.3315 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 32148 Z= 0.308 Angle : 0.866 11.358 44007 Z= 0.416 Chirality : 0.053 0.291 5334 Planarity : 0.006 0.138 5301 Dihedral : 12.921 155.126 4420 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.17 % Favored : 92.37 % Rotamer: Outliers : 12.74 % Allowed : 27.47 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 3684 helix: -2.47 (0.22), residues: 435 sheet: -0.97 (0.14), residues: 1290 loop : -1.67 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 476 TYR 0.033 0.002 TYR H 140 PHE 0.014 0.002 PHE G 91 TRP 0.021 0.002 TRP J 610 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.31 (31938) covalent geometry : angle 0.82609 / 0.41 (43428) SS BOND : bond 0.00915 / 0.55 ( 51) SS BOND : angle 2.45774 / 1.73 ( 102) hydrogen bonds : bond 0.05666 / 3.80 ( 844) hydrogen bonds : angle 6.66905 / 4.61 ( 2367) link_ALPHA1-2 : bond 0.00367 / 0.22 ( 15) link_ALPHA1-2 : angle 1.90529 / 1.25 ( 45) link_ALPHA1-3 : bond 0.00483 / 0.29 ( 15) link_ALPHA1-3 : angle 1.83222 / 1.19 ( 45) link_ALPHA1-6 : bond 0.00477 / 0.29 ( 15) link_ALPHA1-6 : angle 1.87438 / 1.16 ( 45) link_BETA1-4 : bond 0.00477 / 0.31 ( 51) link_BETA1-4 : angle 2.24235 / 1.39 ( 153) link_NAG-ASN : bond 0.00582 / 0.36 ( 63) link_NAG-ASN : angle 2.85396 / 1.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 413 poor density : 321 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 358 ILE cc_start: 0.8056 (pt) cc_final: 0.7818 (pp) REVERT: A 456 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7671 (ttp-170) REVERT: B 658 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: C 30 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8329 (m-10) REVERT: D 11 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7321 (tp) REVERT: E 153 GLU cc_start: 0.6857 (tt0) cc_final: 0.6391 (pt0) REVERT: F 535 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7482 (mmt) REVERT: F 616 ASN cc_start: 0.8364 (p0) cc_final: 0.8030 (p0) REVERT: F 624 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7952 (p0) REVERT: G 30 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: G 100 ASP cc_start: 0.7645 (t0) cc_final: 0.7422 (m-30) REVERT: G 105 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: G 179 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.6504 (p) REVERT: H 61 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6302 (ptt-90) REVERT: H 79 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.5641 (mp10) REVERT: H 131 SER cc_start: 0.6136 (OUTLIER) cc_final: 0.5926 (p) REVERT: I 84 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8446 (mp) REVERT: I 189 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6342 (tmtt) REVERT: I 265 LEU cc_start: 0.8312 (mt) cc_final: 0.8104 (OUTLIER) REVERT: I 360 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (ptt-90) REVERT: J 568 LEU cc_start: 0.7447 (tp) cc_final: 0.7180 (tp) REVERT: J 575 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7974 (tp-100) REVERT: J 640 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: J 654 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: K 30 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8379 (m-10) REVERT: K 69 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7826 (mm) REVERT: L 61 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6373 (ptt-90) REVERT: L 79 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.5975 (mp10) REVERT: N 11 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6701 (mm) REVERT: N 50 ASN cc_start: 0.7896 (t0) cc_final: 0.7372 (t0) REVERT: O 29 MET cc_start: 0.3521 (OUTLIER) cc_final: 0.3256 (pmt) REVERT: P 50 ASN cc_start: 0.8167 (t0) cc_final: 0.7570 (t0) outliers start: 413 outliers final: 260 residues processed: 663 average time/residue: 0.5214 time to fit residues: 424.7096 Evaluate side-chains 591 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 307 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 29 MET Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 224 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 331 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 358 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 105 GLN H 3 GLN H 100 GLN K 6 GLN K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 77 GLN N 37 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 77 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 77 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.224283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.168829 restraints weight = 32951.959| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.67 r_work: 0.3371 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32148 Z= 0.163 Angle : 0.742 12.990 44007 Z= 0.355 Chirality : 0.047 0.300 5334 Planarity : 0.005 0.146 5301 Dihedral : 12.041 155.945 4378 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.03 % Favored : 93.57 % Rotamer: Outliers : 10.76 % Allowed : 29.39 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.13), residues: 3684 helix: -2.05 (0.23), residues: 435 sheet: -0.89 (0.14), residues: 1293 loop : -1.55 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 500 TYR 0.026 0.001 TYR H 140 PHE 0.013 0.001 PHE L 118 TRP 0.017 0.001 TRP F 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (31938) covalent geometry : angle 0.70482 / 0.35 (43428) SS BOND : bond 0.00775 / 0.49 ( 51) SS BOND : angle 2.17968 / 1.53 ( 102) hydrogen bonds : bond 0.04310 / 2.90 ( 844) hydrogen bonds : angle 6.16615 / 4.25 ( 2367) link_ALPHA1-2 : bond 0.00519 / 0.32 ( 15) link_ALPHA1-2 : angle 1.69204 / 1.12 ( 45) link_ALPHA1-3 : bond 0.00482 / 0.29 ( 15) link_ALPHA1-3 : angle 1.67187 / 1.10 ( 45) link_ALPHA1-6 : bond 0.00362 / 0.23 ( 15) link_ALPHA1-6 : angle 1.70610 / 1.07 ( 45) link_BETA1-4 : bond 0.00372 / 0.24 ( 51) link_BETA1-4 : angle 1.94936 / 1.22 ( 153) link_NAG-ASN : bond 0.00476 / 0.31 ( 63) link_NAG-ASN : angle 2.53813 / 1.78 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 349 poor density : 316 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8225 (mt) REVERT: A 419 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: A 456 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7464 (ttp-110) REVERT: C 179 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.6813 (p) REVERT: D 11 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7314 (tp) REVERT: D 166 GLN cc_start: 0.8058 (mt0) cc_final: 0.7805 (tp40) REVERT: E 153 GLU cc_start: 0.6801 (tt0) cc_final: 0.6458 (tt0) REVERT: F 535 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: G 30 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: G 100 ASP cc_start: 0.7611 (t0) cc_final: 0.7382 (m-30) REVERT: G 105 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: H 20 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7240 (mtm180) REVERT: H 47 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8393 (mt) REVERT: H 61 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6477 (ptt-90) REVERT: H 79 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.5690 (mp10) REVERT: I 84 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8402 (mp) REVERT: I 189 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7431 (tptp) REVERT: I 360 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8127 (ptt-90) REVERT: J 575 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7988 (tp-100) REVERT: J 616 ASN cc_start: 0.8257 (p0) cc_final: 0.7943 (p0) REVERT: J 640 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: J 654 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5447 (tt0) REVERT: K 6 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: K 66 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8072 (ttt90) REVERT: L 61 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6603 (ptt-90) REVERT: L 79 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6013 (mp10) REVERT: M 100 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: N 11 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6822 (mm) REVERT: N 50 ASN cc_start: 0.8042 (t0) cc_final: 0.7644 (t0) REVERT: O 97 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.8101 (ttp-170) REVERT: P 28 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6552 (mp) REVERT: P 50 ASN cc_start: 0.8322 (t0) cc_final: 0.7681 (t0) REVERT: P 79 GLU cc_start: 0.5320 (OUTLIER) cc_final: 0.5056 (pp20) outliers start: 349 outliers final: 212 residues processed: 606 average time/residue: 0.5492 time to fit residues: 406.9267 Evaluate side-chains 537 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 299 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 53 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 274 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.222914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169309 restraints weight = 33215.347| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.56 r_work: 0.3323 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32148 Z= 0.222 Angle : 0.775 12.593 44007 Z= 0.369 Chirality : 0.049 0.299 5334 Planarity : 0.006 0.142 5301 Dihedral : 11.856 155.709 4330 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.98 % Favored : 92.64 % Rotamer: Outliers : 11.13 % Allowed : 28.68 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.13), residues: 3684 helix: -1.97 (0.23), residues: 435 sheet: -0.87 (0.14), residues: 1299 loop : -1.59 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 500 TYR 0.035 0.002 TYR D 140 PHE 0.015 0.002 PHE G 91 TRP 0.019 0.002 TRP J 610 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (31938) covalent geometry : angle 0.73631 / 0.36 (43428) SS BOND : bond 0.00652 / 0.39 ( 51) SS BOND : angle 2.21317 / 1.58 ( 102) hydrogen bonds : bond 0.04582 / 3.09 ( 844) hydrogen bonds : angle 6.03558 / 4.16 ( 2367) link_ALPHA1-2 : bond 0.00412 / 0.25 ( 15) link_ALPHA1-2 : angle 1.77862 / 1.17 ( 45) link_ALPHA1-3 : bond 0.00461 / 0.28 ( 15) link_ALPHA1-3 : angle 1.74929 / 1.14 ( 45) link_ALPHA1-6 : bond 0.00405 / 0.25 ( 15) link_ALPHA1-6 : angle 1.75695 / 1.11 ( 45) link_BETA1-4 : bond 0.00415 / 0.27 ( 51) link_BETA1-4 : angle 2.08288 / 1.30 ( 153) link_NAG-ASN : bond 0.00506 / 0.32 ( 63) link_NAG-ASN : angle 2.64023 / 1.85 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 361 poor density : 299 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 125 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 419 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7760 (ptm160) REVERT: A 456 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7693 (ttp-170) REVERT: B 658 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: C 30 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: C 69 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7935 (mm) REVERT: C 179 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.6871 (p) REVERT: D 11 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (tp) REVERT: D 166 GLN cc_start: 0.8091 (mt0) cc_final: 0.7881 (tp40) REVERT: E 153 GLU cc_start: 0.6870 (tt0) cc_final: 0.6376 (pt0) REVERT: F 535 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7793 (mpt) REVERT: F 658 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: G 30 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: G 80 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8470 (tp) REVERT: G 100 ASP cc_start: 0.7659 (t0) cc_final: 0.7445 (m-30) REVERT: G 105 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: H 20 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7309 (mtm180) REVERT: H 47 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8532 (mt) REVERT: H 61 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6353 (ptt-90) REVERT: H 79 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.5686 (mp10) REVERT: I 75 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8397 (m) REVERT: I 84 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8466 (mp) REVERT: I 205 CYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6551 (m) REVERT: I 360 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8156 (ptt-90) REVERT: J 568 LEU cc_start: 0.7512 (tp) cc_final: 0.7309 (tp) REVERT: J 575 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7999 (tp-100) REVERT: J 616 ASN cc_start: 0.8304 (p0) cc_final: 0.7973 (p0) REVERT: J 640 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: J 654 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5502 (tt0) REVERT: K 66 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8122 (ttt90) REVERT: L 79 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6022 (mp10) REVERT: M 58 THR cc_start: 0.7878 (m) cc_final: 0.7537 (p) REVERT: M 100 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: M 100 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.5902 (mmm) REVERT: N 11 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6784 (mm) REVERT: N 50 ASN cc_start: 0.8196 (t0) cc_final: 0.7445 (t0) REVERT: O 97 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8123 (ttp-170) REVERT: O 100 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: P 37 GLN cc_start: 0.7044 (tt0) cc_final: 0.6736 (tp-100) REVERT: P 50 ASN cc_start: 0.8352 (t0) cc_final: 0.7701 (t0) REVERT: R 90 MET cc_start: 0.8771 (tpp) cc_final: 0.8209 (mmt) outliers start: 361 outliers final: 237 residues processed: 599 average time/residue: 0.5270 time to fit residues: 388.1196 Evaluate side-chains 564 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 296 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 340 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 196 optimal weight: 40.0000 chunk 274 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 346 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 183 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 283 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN D 124 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.222619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.168938 restraints weight = 32866.736| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.48 r_work: 0.3328 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 32148 Z= 0.234 Angle : 0.784 11.617 44007 Z= 0.373 Chirality : 0.050 0.300 5334 Planarity : 0.006 0.138 5301 Dihedral : 11.723 155.523 4310 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.00 % Favored : 92.67 % Rotamer: Outliers : 10.76 % Allowed : 28.99 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3684 helix: -1.94 (0.23), residues: 435 sheet: -0.83 (0.14), residues: 1290 loop : -1.60 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 500 TYR 0.032 0.002 TYR D 140 PHE 0.014 0.002 PHE G 91 TRP 0.019 0.002 TRP J 610 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.23 (31938) covalent geometry : angle 0.74369 / 0.36 (43428) SS BOND : bond 0.00790 / 0.48 ( 51) SS BOND : angle 2.35393 / 1.67 ( 102) hydrogen bonds : bond 0.04570 / 3.08 ( 844) hydrogen bonds : angle 5.95795 / 4.10 ( 2367) link_ALPHA1-2 : bond 0.00395 / 0.24 ( 15) link_ALPHA1-2 : angle 1.80242 / 1.19 ( 45) link_ALPHA1-3 : bond 0.00452 / 0.27 ( 15) link_ALPHA1-3 : angle 1.75415 / 1.14 ( 45) link_ALPHA1-6 : bond 0.00404 / 0.25 ( 15) link_ALPHA1-6 : angle 1.78568 / 1.12 ( 45) link_BETA1-4 : bond 0.00429 / 0.27 ( 51) link_BETA1-4 : angle 2.11147 / 1.32 ( 153) link_NAG-ASN : bond 0.00525 / 0.33 ( 63) link_NAG-ASN : angle 2.64769 / 1.85 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 349 poor density : 303 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 125 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 168 LYS cc_start: 0.7090 (mmmm) cc_final: 0.6513 (pptt) REVERT: A 419 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7743 (ptm160) REVERT: A 456 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7696 (ttp-170) REVERT: B 658 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: C 30 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: C 69 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7956 (mm) REVERT: C 105 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: C 179 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.6914 (p) REVERT: D 11 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (tp) REVERT: D 79 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6431 (mp10) REVERT: D 166 GLN cc_start: 0.8066 (mt0) cc_final: 0.7845 (tp40) REVERT: E 153 GLU cc_start: 0.6870 (tt0) cc_final: 0.6378 (pt0) REVERT: F 535 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7802 (mpt) REVERT: F 658 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: G 30 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: G 80 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8484 (tp) REVERT: G 105 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: H 20 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7355 (mtm180) REVERT: H 47 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (mt) REVERT: H 79 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.5799 (mp10) REVERT: I 75 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (m) REVERT: I 84 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8501 (mp) REVERT: I 168 LYS cc_start: 0.7194 (mmmm) cc_final: 0.6609 (pptt) REVERT: I 205 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6551 (m) REVERT: I 360 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8126 (ptt-90) REVERT: J 575 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7996 (tp-100) REVERT: J 616 ASN cc_start: 0.8254 (p0) cc_final: 0.7926 (p0) REVERT: J 640 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: J 654 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5497 (tt0) REVERT: K 66 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8132 (ttt90) REVERT: K 69 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7889 (mm) REVERT: L 79 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: L 143 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5530 (pp20) REVERT: M 29 MET cc_start: 0.3802 (OUTLIER) cc_final: 0.3346 (pmm) REVERT: M 100 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: M 100 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6664 (mpm) REVERT: N 11 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6840 (mm) REVERT: N 50 ASN cc_start: 0.8275 (t0) cc_final: 0.7351 (t0) REVERT: O 97 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8136 (ttp-170) REVERT: O 100 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: P 37 GLN cc_start: 0.6933 (tt0) cc_final: 0.6709 (tp-100) REVERT: P 50 ASN cc_start: 0.8389 (t0) cc_final: 0.7717 (t0) REVERT: P 79 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.5160 (pp20) REVERT: Q 29 MET cc_start: 0.3356 (pmm) cc_final: 0.3002 (pmm) REVERT: R 90 MET cc_start: 0.8676 (tpp) cc_final: 0.8328 (mmt) outliers start: 349 outliers final: 242 residues processed: 590 average time/residue: 0.5050 time to fit residues: 367.5879 Evaluate side-chains 575 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 297 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 94 optimal weight: 30.0000 chunk 108 optimal weight: 0.0050 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 362 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN D 124 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN G 171 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.224269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.170918 restraints weight = 33267.033| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.60 r_work: 0.3333 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32148 Z= 0.191 Angle : 0.746 10.747 44007 Z= 0.355 Chirality : 0.048 0.303 5334 Planarity : 0.005 0.135 5301 Dihedral : 11.442 155.685 4291 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.65 % Favored : 93.02 % Rotamer: Outliers : 10.14 % Allowed : 29.85 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3684 helix: -1.78 (0.24), residues: 435 sheet: -0.78 (0.14), residues: 1290 loop : -1.57 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.020 0.002 TYR H 140 PHE 0.013 0.002 PHE G 91 TRP 0.018 0.002 TRP F 610 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (31938) covalent geometry : angle 0.70693 / 0.35 (43428) SS BOND : bond 0.00664 / 0.40 ( 51) SS BOND : angle 2.19002 / 1.49 ( 102) hydrogen bonds : bond 0.04265 / 2.87 ( 844) hydrogen bonds : angle 5.81482 / 4.00 ( 2367) link_ALPHA1-2 : bond 0.00428 / 0.25 ( 15) link_ALPHA1-2 : angle 1.75420 / 1.15 ( 45) link_ALPHA1-3 : bond 0.00466 / 0.28 ( 15) link_ALPHA1-3 : angle 1.71611 / 1.12 ( 45) link_ALPHA1-6 : bond 0.00375 / 0.23 ( 15) link_ALPHA1-6 : angle 1.73347 / 1.10 ( 45) link_BETA1-4 : bond 0.00406 / 0.26 ( 51) link_BETA1-4 : angle 2.02970 / 1.27 ( 153) link_NAG-ASN : bond 0.00478 / 0.30 ( 63) link_NAG-ASN : angle 2.56033 / 1.79 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 329 poor density : 302 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 125 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 168 LYS cc_start: 0.7042 (mmmm) cc_final: 0.6524 (pptt) REVERT: A 419 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7767 (ptm160) REVERT: A 456 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7686 (ttp-170) REVERT: B 658 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: C 30 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8417 (m-10) REVERT: C 69 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 105 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: C 179 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.6956 (p) REVERT: D 11 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (tp) REVERT: E 153 GLU cc_start: 0.6827 (tt0) cc_final: 0.6456 (tt0) REVERT: E 228 CYS cc_start: 0.8369 (t) cc_final: 0.8129 (t) REVERT: F 535 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7785 (mpt) REVERT: F 658 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: G 30 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: G 80 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8476 (tp) REVERT: G 105 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: G 179 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.6841 (p) REVERT: H 47 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8450 (mt) REVERT: H 79 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.5780 (mp10) REVERT: I 75 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8423 (m) REVERT: I 84 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8463 (mp) REVERT: I 167 ASP cc_start: 0.8226 (m-30) cc_final: 0.7916 (m-30) REVERT: I 205 CYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6542 (m) REVERT: I 308 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8710 (mtm-85) REVERT: I 360 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8037 (ptt-90) REVERT: J 568 LEU cc_start: 0.7488 (tp) cc_final: 0.7281 (tp) REVERT: J 575 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7987 (tp-100) REVERT: J 616 ASN cc_start: 0.8247 (p0) cc_final: 0.7915 (p0) REVERT: J 640 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: J 654 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5469 (tt0) REVERT: K 66 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8084 (ttt90) REVERT: L 79 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6125 (mp10) REVERT: M 100 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: M 100 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6675 (mpm) REVERT: N 11 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6803 (mm) REVERT: N 50 ASN cc_start: 0.8286 (t0) cc_final: 0.7285 (t0) REVERT: N 85 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: O 97 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.8113 (ttp-170) REVERT: O 100 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: P 37 GLN cc_start: 0.7140 (tt0) cc_final: 0.6754 (tp-100) REVERT: P 50 ASN cc_start: 0.8353 (t0) cc_final: 0.7756 (t0) REVERT: P 79 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.5195 (pp20) REVERT: P 85 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: Q 29 MET cc_start: 0.3244 (pmm) cc_final: 0.2884 (pmm) REVERT: R 90 MET cc_start: 0.8595 (tpp) cc_final: 0.8277 (mmt) outliers start: 329 outliers final: 227 residues processed: 582 average time/residue: 0.4807 time to fit residues: 345.9611 Evaluate side-chains 554 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 293 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 229 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN C 6 GLN D 3 GLN D 124 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.226650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.173537 restraints weight = 33242.321| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.51 r_work: 0.3387 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32148 Z= 0.135 Angle : 0.695 9.860 44007 Z= 0.332 Chirality : 0.046 0.305 5334 Planarity : 0.005 0.131 5301 Dihedral : 11.087 156.731 4286 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.86 % Favored : 93.81 % Rotamer: Outliers : 8.39 % Allowed : 31.73 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % 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: -1.83 (0.13), residues: 3684 helix: -1.46 (0.24), residues: 435 sheet: -0.75 (0.14), residues: 1299 loop : -1.45 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 20 TYR 0.019 0.001 TYR H 140 PHE 0.012 0.001 PHE I 383 TRP 0.016 0.001 TRP F 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (31938) covalent geometry : angle 0.65736 / 0.32 (43428) SS BOND : bond 0.00587 / 0.37 ( 51) SS BOND : angle 1.96220 / 1.43 ( 102) hydrogen bonds : bond 0.03740 / 2.52 ( 844) hydrogen bonds : angle 5.60170 / 3.85 ( 2367) link_ALPHA1-2 : bond 0.00505 / 0.30 ( 15) link_ALPHA1-2 : angle 1.64780 / 1.08 ( 45) link_ALPHA1-3 : bond 0.00500 / 0.30 ( 15) link_ALPHA1-3 : angle 1.65642 / 1.09 ( 45) link_ALPHA1-6 : bond 0.00345 / 0.22 ( 15) link_ALPHA1-6 : angle 1.63879 / 1.04 ( 45) link_BETA1-4 : bond 0.00371 / 0.24 ( 51) link_BETA1-4 : angle 1.88952 / 1.19 ( 153) link_NAG-ASN : bond 0.00498 / 0.32 ( 63) link_NAG-ASN : angle 2.48507 / 1.72 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 314 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7073 (mmmm) cc_final: 0.6522 (pptt) REVERT: A 419 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7696 (ptm160) REVERT: A 456 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7567 (ttp-170) REVERT: B 658 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: C 6 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: D 11 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7244 (tp) REVERT: D 79 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: D 143 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5264 (pp20) REVERT: E 153 GLU cc_start: 0.6714 (tt0) cc_final: 0.6442 (tt0) REVERT: E 168 LYS cc_start: 0.7089 (mmmm) cc_final: 0.6537 (pptt) REVERT: F 535 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7726 (mpt) REVERT: F 658 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: G 30 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: G 80 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8487 (tp) REVERT: G 105 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: G 117 LYS cc_start: 0.7929 (tttm) cc_final: 0.7622 (ttpt) REVERT: G 179 SER cc_start: 0.7546 (OUTLIER) cc_final: 0.6773 (p) REVERT: H 47 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8271 (mt) REVERT: H 79 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.5835 (mp10) REVERT: I 84 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8422 (mp) REVERT: I 167 ASP cc_start: 0.8120 (m-30) cc_final: 0.7815 (m-30) REVERT: I 168 LYS cc_start: 0.7088 (mmmm) cc_final: 0.6475 (pptt) REVERT: I 205 CYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6414 (m) REVERT: I 360 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: J 575 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: J 616 ASN cc_start: 0.8215 (p0) cc_final: 0.7892 (p0) REVERT: J 640 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: K 66 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (ttt90) REVERT: L 20 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7522 (mmm160) REVERT: L 79 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6242 (mp10) REVERT: L 143 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5485 (pp20) REVERT: M 100 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: N 11 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6792 (mm) REVERT: N 50 ASN cc_start: 0.8152 (t0) cc_final: 0.7339 (t0) REVERT: N 85 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: O 97 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.8062 (ttp-170) REVERT: O 100 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: P 28 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6585 (mp) REVERT: P 37 GLN cc_start: 0.7084 (tt0) cc_final: 0.6781 (tp-100) REVERT: P 50 ASN cc_start: 0.8313 (t0) cc_final: 0.7739 (t0) REVERT: P 79 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5286 (pp20) REVERT: P 85 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: Q 29 MET cc_start: 0.3312 (pmm) cc_final: 0.2960 (pmm) REVERT: R 90 MET cc_start: 0.8534 (tpp) cc_final: 0.8268 (mmt) outliers start: 272 outliers final: 175 residues processed: 542 average time/residue: 0.4945 time to fit residues: 328.3622 Evaluate side-chains 498 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 293 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 284 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 275 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 193 optimal weight: 10.0000 chunk 323 optimal weight: 0.4980 chunk 334 optimal weight: 6.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 124 GLN E 103 GLN F 575 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 100 GLN I 130 GLN J 575 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN M 3 GLN M 99 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.227167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174248 restraints weight = 33322.543| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.49 r_work: 0.3401 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32148 Z= 0.133 Angle : 0.690 9.410 44007 Z= 0.331 Chirality : 0.046 0.307 5334 Planarity : 0.005 0.129 5301 Dihedral : 10.895 157.371 4269 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.70 % Favored : 93.97 % Rotamer: Outliers : 7.46 % Allowed : 32.75 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 3684 helix: -1.25 (0.25), residues: 435 sheet: -0.68 (0.14), residues: 1299 loop : -1.39 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 71 TYR 0.018 0.001 TYR H 140 PHE 0.019 0.001 PHE D 139 TRP 0.017 0.001 TRP B 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (31938) covalent geometry : angle 0.65369 / 0.32 (43428) SS BOND : bond 0.00689 / 0.42 ( 51) SS BOND : angle 1.96057 / 1.39 ( 102) hydrogen bonds : bond 0.03612 / 2.44 ( 844) hydrogen bonds : angle 5.46634 / 3.76 ( 2367) link_ALPHA1-2 : bond 0.00491 / 0.29 ( 15) link_ALPHA1-2 : angle 1.63100 / 1.07 ( 45) link_ALPHA1-3 : bond 0.00505 / 0.30 ( 15) link_ALPHA1-3 : angle 1.64922 / 1.09 ( 45) link_ALPHA1-6 : bond 0.00346 / 0.22 ( 15) link_ALPHA1-6 : angle 1.60646 / 1.02 ( 45) link_BETA1-4 : bond 0.00378 / 0.25 ( 51) link_BETA1-4 : angle 1.84131 / 1.16 ( 153) link_NAG-ASN : bond 0.00527 / 0.32 ( 63) link_NAG-ASN : angle 2.46621 / 1.72 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 296 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 130 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7819 (mp10) REVERT: A 456 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7466 (ttp-170) REVERT: B 640 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (mm-40) REVERT: B 658 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7461 (tp40) REVERT: C 94 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7296 (t) REVERT: C 193 THR cc_start: 0.4804 (OUTLIER) cc_final: 0.4541 (p) REVERT: D 11 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7271 (tp) REVERT: D 79 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: D 143 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5077 (pp20) REVERT: E 153 GLU cc_start: 0.6765 (tt0) cc_final: 0.6539 (tt0) REVERT: F 535 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7757 (mpt) REVERT: F 658 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: G 30 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: G 80 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (tp) REVERT: G 94 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7153 (t) REVERT: G 105 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: G 117 LYS cc_start: 0.8026 (tttm) cc_final: 0.7649 (tmtt) REVERT: G 193 THR cc_start: 0.4662 (OUTLIER) cc_final: 0.4429 (p) REVERT: H 47 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8269 (mt) REVERT: H 79 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.5932 (mp10) REVERT: I 84 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8404 (mp) REVERT: I 168 LYS cc_start: 0.7103 (mmmm) cc_final: 0.6484 (pptt) REVERT: I 205 CYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6396 (m) REVERT: J 575 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: J 616 ASN cc_start: 0.8194 (p0) cc_final: 0.7863 (p0) REVERT: J 640 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8301 (mp10) REVERT: K 38 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7201 (ttm-80) REVERT: K 66 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8126 (ttt90) REVERT: L 20 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7546 (mmm160) REVERT: L 79 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6335 (mp10) REVERT: L 103 LYS cc_start: 0.7537 (mptp) cc_final: 0.7319 (mptp) REVERT: L 143 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5464 (pp20) REVERT: M 100 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: N 11 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6812 (mm) REVERT: N 50 ASN cc_start: 0.8131 (t0) cc_final: 0.7408 (t0) REVERT: N 85 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6499 (m-30) REVERT: O 97 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.8111 (ttp-170) REVERT: O 100 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: P 28 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6631 (mp) REVERT: P 37 GLN cc_start: 0.7104 (tt0) cc_final: 0.6798 (tp-100) REVERT: P 50 ASN cc_start: 0.8284 (t0) cc_final: 0.7614 (t0) REVERT: P 79 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5381 (pp20) REVERT: P 85 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: Q 29 MET cc_start: 0.3282 (pmm) cc_final: 0.2919 (pmm) REVERT: R 52 GLN cc_start: 0.7663 (pt0) cc_final: 0.7385 (mt0) REVERT: R 90 MET cc_start: 0.8485 (tpp) cc_final: 0.8260 (mmt) outliers start: 242 outliers final: 171 residues processed: 504 average time/residue: 0.5283 time to fit residues: 325.8184 Evaluate side-chains 496 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 292 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 356 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 208 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 235 optimal weight: 0.0060 chunk 277 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN C 6 GLN D 3 GLN D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 100 GLN J 575 GLN J 651 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN M 3 GLN M 99 GLN N 37 GLN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.228095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173120 restraints weight = 33139.484| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.64 r_work: 0.3426 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32148 Z= 0.125 Angle : 0.675 10.437 44007 Z= 0.324 Chirality : 0.045 0.307 5334 Planarity : 0.005 0.127 5301 Dihedral : 10.682 157.623 4260 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.03 % Rotamer: Outliers : 6.72 % Allowed : 33.46 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3684 helix: -1.15 (0.25), residues: 435 sheet: -0.62 (0.14), residues: 1299 loop : -1.34 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 20 TYR 0.025 0.001 TYR P 87 PHE 0.018 0.001 PHE D 139 TRP 0.016 0.001 TRP J 610 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (31938) covalent geometry : angle 0.63981 / 0.32 (43428) SS BOND : bond 0.00573 / 0.36 ( 51) SS BOND : angle 1.87464 / 1.32 ( 102) hydrogen bonds : bond 0.03499 / 2.36 ( 844) hydrogen bonds : angle 5.34813 / 3.68 ( 2367) link_ALPHA1-2 : bond 0.00496 / 0.29 ( 15) link_ALPHA1-2 : angle 1.61486 / 1.06 ( 45) link_ALPHA1-3 : bond 0.00517 / 0.31 ( 15) link_ALPHA1-3 : angle 1.62891 / 1.08 ( 45) link_ALPHA1-6 : bond 0.00339 / 0.21 ( 15) link_ALPHA1-6 : angle 1.58816 / 1.01 ( 45) link_BETA1-4 : bond 0.00378 / 0.25 ( 51) link_BETA1-4 : angle 1.79615 / 1.13 ( 153) link_NAG-ASN : bond 0.00458 / 0.29 ( 63) link_NAG-ASN : angle 2.37859 / 1.67 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 308 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 130 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7792 (mp10) REVERT: A 168 LYS cc_start: 0.7136 (mmmm) cc_final: 0.6692 (pptt) REVERT: B 640 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: B 658 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7441 (tp40) REVERT: C 94 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7272 (t) REVERT: D 11 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7316 (tp) REVERT: D 79 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: D 143 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5040 (pp20) REVERT: F 535 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7758 (mpt) REVERT: F 658 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: G 30 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: G 80 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8457 (tp) REVERT: G 94 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7076 (t) REVERT: G 105 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: G 117 LYS cc_start: 0.7993 (tttm) cc_final: 0.7613 (tmtt) REVERT: G 179 SER cc_start: 0.7296 (OUTLIER) cc_final: 0.6615 (p) REVERT: H 47 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8228 (mt) REVERT: H 79 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.5912 (mp10) REVERT: I 84 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8398 (mp) REVERT: I 168 LYS cc_start: 0.7090 (mmmm) cc_final: 0.6529 (pptt) REVERT: I 205 CYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6406 (m) REVERT: J 575 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: J 616 ASN cc_start: 0.8169 (p0) cc_final: 0.7834 (p0) REVERT: J 640 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: K 38 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7133 (ttm-80) REVERT: L 20 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7558 (mmm160) REVERT: L 79 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6357 (mp10) REVERT: L 103 LYS cc_start: 0.7453 (mptp) cc_final: 0.7212 (mptp) REVERT: L 143 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5421 (pp20) REVERT: M 100 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: N 11 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6726 (mm) REVERT: N 50 ASN cc_start: 0.7999 (t0) cc_final: 0.7306 (t0) REVERT: N 85 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: O 97 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7955 (ttp-170) REVERT: O 100 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: P 28 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6529 (mp) REVERT: P 37 GLN cc_start: 0.7041 (tt0) cc_final: 0.6792 (tp-100) REVERT: P 50 ASN cc_start: 0.8204 (t0) cc_final: 0.7515 (t0) REVERT: P 79 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5312 (pp20) REVERT: P 85 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: Q 29 MET cc_start: 0.3302 (pmm) cc_final: 0.2980 (pmm) REVERT: R 52 GLN cc_start: 0.7655 (pt0) cc_final: 0.7379 (mt0) outliers start: 218 outliers final: 157 residues processed: 491 average time/residue: 0.5238 time to fit residues: 314.1255 Evaluate side-chains 483 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 296 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 30 optimal weight: 0.8980 chunk 334 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 208 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 100 GLN J 575 GLN J 651 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 166 GLN M 3 GLN M 99 GLN N 37 GLN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.228691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.176157 restraints weight = 33307.085| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.49 r_work: 0.3421 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32148 Z= 0.122 Angle : 0.668 9.422 44007 Z= 0.322 Chirality : 0.045 0.308 5334 Planarity : 0.005 0.125 5301 Dihedral : 10.521 157.884 4246 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.86 % Favored : 93.81 % Rotamer: Outliers : 6.48 % Allowed : 33.64 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3684 helix: -1.04 (0.25), residues: 435 sheet: -0.58 (0.14), residues: 1308 loop : -1.30 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 71 TYR 0.034 0.001 TYR N 87 PHE 0.017 0.001 PHE D 139 TRP 0.016 0.001 TRP J 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (31938) covalent geometry : angle 0.63419 / 0.31 (43428) SS BOND : bond 0.00528 / 0.33 ( 51) SS BOND : angle 1.80026 / 1.27 ( 102) hydrogen bonds : bond 0.03425 / 2.31 ( 844) hydrogen bonds : angle 5.24335 / 3.61 ( 2367) link_ALPHA1-2 : bond 0.00497 / 0.29 ( 15) link_ALPHA1-2 : angle 1.59682 / 1.05 ( 45) link_ALPHA1-3 : bond 0.00530 / 0.32 ( 15) link_ALPHA1-3 : angle 1.62129 / 1.07 ( 45) link_ALPHA1-6 : bond 0.00340 / 0.21 ( 15) link_ALPHA1-6 : angle 1.56949 / 1.00 ( 45) link_BETA1-4 : bond 0.00385 / 0.25 ( 51) link_BETA1-4 : angle 1.76201 / 1.11 ( 153) link_NAG-ASN : bond 0.00449 / 0.29 ( 63) link_NAG-ASN : angle 2.31658 / 1.64 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11739.22 seconds wall clock time: 200 minutes 40.58 seconds (12040.58 seconds total)