Starting phenix.real_space_refine on Sat Jul 4 23:22:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z3a_14474/07_2026/7z3a_14474.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 134 5.16 5 C 15025 2.51 5 N 3913 2.21 5 O 4928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 24000 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3403 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 907 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "G" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "K" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 Time building chain proxies: 5.81, per 1000 atoms: 0.24 Number of scatterers: 24000 At special positions: 0 Unit cell: (135.7, 151.8, 162.15, 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 134 16.00 O 4928 8.00 N 3913 7.00 C 15025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 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 I 22 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " BETA1-6 " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG 0 1 " - " ASN D 262 " " NAG 1 1 " - " ASN D 276 " " NAG 2 1 " - " ASN D 289 " " NAG 3 1 " - " ASN D 301 " " NAG 4 1 " - " ASN D 362 " " NAG 5 1 " - " ASN D 386 " " NAG 6 1 " - " ASN D 392 " " NAG 7 1 " - " ASN D 448 " " NAG 8 1 " - " ASN D 295 " " NAG 9 1 " - " ASN F 611 " " NAG A 601 " - " ASN A 156 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 396 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 156 " " NAG C 602 " - " ASN C 396 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 160 " " NAG D 603 " - " ASN D 332 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 130 " " NAG D 606 " - " ASN D 396 " " NAG E 701 " - " ASN E 616 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 637 " " NAG Q 1 " - " ASN A 130 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 241 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 289 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 362 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN B 625 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 197 " " NAG i 1 " - " ASN C 241 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 289 " " NAG m 1 " - " ASN C 295 " " NAG n 1 " - " ASN C 301 " " NAG o 1 " - " ASN C 362 " " NAG p 1 " - " ASN C 386 " " NAG q 1 " - " ASN C 392 " " NAG r 1 " - " ASN C 448 " " NAG s 1 " - " ASN C 160 " " NAG t 1 " - " ASN C 234 " " NAG u 1 " - " ASN E 611 " " NAG v 1 " - " ASN E 625 " " NAG w 1 " - " ASN D 88 " " NAG x 1 " - " ASN D 197 " " NAG y 1 " - " ASN D 234 " " NAG z 1 " - " ASN D 241 " " NAGAA 1 " - " ASN F 625 " NAG-THR " NAG C 603 " - " THR C 415 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 44 sheets defined 19.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.585A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.526A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.215A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 651 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.619A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.515A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.752A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.548A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.111A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.673A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.624A pdb=" N ASN F 625 " --> pdb=" O MET F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.904A pdb=" N HIS G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.730A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.562A pdb=" N ASP M 86 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 30 Processing helix chain 'O' and resid 78 through 82 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.560A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 3.531A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.908A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.805A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 298 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.463A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.728A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.095A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 7.520A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 74 through 76 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AC3, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.926A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 298 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 329 through 333 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'D' and resid 302 through 307 removed outlier: 6.618A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.822A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.907A pdb=" N MET G 100D" --> pdb=" O ILE G 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 12 current: chain 'I' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 47 current: chain 'I' and resid 97 through 99 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.756A pdb=" N ALA H 16 " --> pdb=" O LEU H 82C" (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 18 " --> pdb=" O ARG H 82A" (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG H 82A" --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 20 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N CYS H 22 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA H 24 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR H 77 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.055A pdb=" N PHE H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95 through 97 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AD6, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.801A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 9 through 12 current: chain 'O' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 44 through 47 current: chain 'O' and resid 97 through 99 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.748A pdb=" N ALA J 16 " --> pdb=" O LEU J 82C" (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 18 " --> pdb=" O ARG J 82A" (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG J 82A" --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL J 20 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP J 81 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N CYS J 22 " --> pdb=" O TYR J 79 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA J 24 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR J 77 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.293A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU J 45 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 12 current: chain 'N' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 48 current: chain 'N' and resid 95 through 97 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'N' and resid 18 through 21 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 removed outlier: 5.537A pdb=" N ALA K 16 " --> pdb=" O ASN K 82B" (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.231A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 95 through 97 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'P' and resid 18 through 22 672 hydrogen bonds defined for protein. 1704 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: 4.58 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4857 1.32 - 1.46: 8072 1.46 - 1.60: 11295 1.60 - 1.73: 97 1.73 - 1.87: 172 Bond restraints: 24493 Sorted by residual: bond pdb=" CB TYR O 48 " pdb=" CG TYR O 48 " ideal model delta sigma weight residual 1.512 1.340 0.172 2.20e-02 2.07e+03 6.13e+01 bond pdb=" NE1 TRP M 103 " pdb=" CE2 TRP M 103 " ideal model delta sigma weight residual 1.370 1.293 0.077 1.10e-02 8.26e+03 4.92e+01 bond pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" NE ARG D 66 " pdb=" CZ ARG D 66 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.35e+01 bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.19e+01 ... (remaining 24488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.60: 33267 9.60 - 19.19: 10 19.19 - 28.79: 0 28.79 - 38.39: 2 38.39 - 47.98: 2 Bond angle restraints: 33281 Sorted by residual: angle pdb=" C8 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" N2 NAG V 2 " ideal model delta sigma weight residual 115.06 163.04 -47.98 3.00e+00 1.11e-01 2.56e+02 angle pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" O7 NAG V 2 " ideal model delta sigma weight residual 123.46 75.90 47.56 3.00e+00 1.11e-01 2.51e+02 angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.79 -36.23 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C8 NAG V 2 " pdb=" C7 NAG V 2 " pdb=" O7 NAG V 2 " ideal model delta sigma weight residual 121.48 87.14 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N LEU N 32 " pdb=" CA LEU N 32 " pdb=" C LEU N 32 " ideal model delta sigma weight residual 108.13 122.66 -14.53 1.72e+00 3.38e-01 7.14e+01 ... (remaining 33276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12827 17.78 - 35.55: 379 35.55 - 53.33: 120 53.33 - 71.10: 45 71.10 - 88.88: 10 Dihedral angle restraints: 13381 sinusoidal: 5343 harmonic: 8038 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 146.42 -53.42 1 1.00e+01 1.00e-02 3.88e+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 93.00 144.01 -51.01 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ASN D 396 " pdb=" C ASN D 396 " pdb=" N ASP D 397 " pdb=" CA ASP D 397 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 13378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2794 0.122 - 0.244: 799 0.244 - 0.365: 387 0.365 - 0.487: 171 0.487 - 0.609: 21 Chirality restraints: 4172 Sorted by residual: chirality pdb=" C1 NAG 8 2 " pdb=" O4 NAG 8 1 " pdb=" C2 NAG 8 2 " pdb=" O5 NAG 8 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.14e+02 chirality pdb=" C1 NAG 0 2 " pdb=" O4 NAG 0 1 " pdb=" C2 NAG 0 2 " pdb=" O5 NAG 0 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.18e+02 ... (remaining 4169 not shown) Planarity restraints: 4061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 8 1 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG 8 1 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG 8 1 " -0.092 2.00e-02 2.50e+03 pdb=" N2 NAG 8 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG 8 1 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 8 2 " -0.327 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG 8 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG 8 2 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG 8 2 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG 8 2 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 606 " -0.188 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG D 606 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 606 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG D 606 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG D 606 " 0.023 2.00e-02 2.50e+03 ... (remaining 4058 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 92 2.57 - 3.15: 20019 3.15 - 3.73: 36228 3.73 - 4.32: 55952 4.32 - 4.90: 84180 Nonbonded interactions: 196471 Sorted by model distance: nonbonded pdb=" OD1 ASP K 101 " pdb=" CG2 VAL P 46 " model vdw 1.982 3.460 nonbonded pdb=" NE1 TRP K 100H" pdb=" OD2 ASP K 101 " model vdw 2.123 3.120 nonbonded pdb=" OD2 ASP M 72 " pdb=" NZ LYS M 75 " model vdw 2.383 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.395 3.120 nonbonded pdb=" N TYR N 30 " pdb=" N ASP N 31 " model vdw 2.400 2.560 ... (remaining 196466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain '9' selection = chain 'AA' selection = chain 'Q' selection = chain 'W' selection = chain 'g' selection = chain 'l' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = (chain 'A' and resid 35 through 603) selection = chain 'C' selection = (chain 'D' and resid 35 through 603) } ncs_group { reference = (chain 'B' and (resid 523 through 653 or resid 702 through 703)) selection = chain 'E' selection = (chain 'F' and (resid 523 through 653 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.570 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.025 0.174 24689 Z= 1.323 Angle : 1.995 47.982 33828 Z= 1.206 Chirality : 0.160 0.609 4172 Planarity : 0.011 0.303 3994 Dihedral : 10.355 88.879 8097 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.41 % Allowed : 0.94 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.16), residues: 2731 helix: 0.29 (0.24), residues: 378 sheet: 0.40 (0.16), residues: 948 loop : 0.10 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 100F TYR 0.083 0.010 TYR L 30 PHE 0.056 0.007 PHE G 78 TRP 0.061 0.010 TRP A 479 HIS 0.018 0.003 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.02446 / 1.29 (24493) covalent geometry : angle 1.91672 / 1.20 (33281) SS BOND : bond 0.00883 / 0.51 ( 40) SS BOND : angle 2.83338 / 1.88 ( 80) hydrogen bonds : bond 0.16602 / 11.27 ( 672) hydrogen bonds : angle 7.65716 / 5.42 ( 1704) link_ALPHA1-3 : bond 0.08752 / 4.42 ( 2) link_ALPHA1-3 : angle 5.81558 / 3.93 ( 6) link_ALPHA1-6 : bond 0.05507 / 2.75 ( 2) link_ALPHA1-6 : angle 2.69123 / 1.66 ( 6) link_BETA1-4 : bond 0.07998 / 5.19 ( 83) link_BETA1-4 : angle 6.32658 / 4.40 ( 249) link_BETA1-6 : bond 0.07985 / 4.20 ( 1) link_BETA1-6 : angle 5.32441 / 2.81 ( 3) link_NAG-ASN : bond 0.07803 / 4.89 ( 67) link_NAG-ASN : angle 2.47381 / 1.70 ( 201) link_NAG-THR : bond 0.07123 / 3.75 ( 1) link_NAG-THR : angle 8.48508 / 4.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 720 time to evaluate : 0.686 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: 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 52 LEU cc_start: 0.9463 (mt) cc_final: 0.9243 (mm) REVERT: A 217 TYR cc_start: 0.7609 (m-80) cc_final: 0.6992 (m-10) REVERT: A 251 ILE cc_start: 0.9505 (mt) cc_final: 0.9298 (pt) REVERT: A 315 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7797 (mtp85) REVERT: C 69 TRP cc_start: 0.8516 (m-90) cc_final: 0.7925 (m-90) REVERT: C 86 LEU cc_start: 0.9584 (mt) cc_final: 0.9343 (mp) REVERT: C 373 MET cc_start: 0.8411 (mtm) cc_final: 0.8106 (mtp) REVERT: C 491 ILE cc_start: 0.9350 (mt) cc_final: 0.9099 (mm) REVERT: E 586 TYR cc_start: 0.9244 (t80) cc_final: 0.8746 (t80) REVERT: E 591 GLN cc_start: 0.8852 (tt0) cc_final: 0.8589 (tm-30) REVERT: E 595 ILE cc_start: 0.8913 (mt) cc_final: 0.8627 (mm) REVERT: E 601 LYS cc_start: 0.8861 (mttt) cc_final: 0.8547 (mmmt) REVERT: D 69 TRP cc_start: 0.7613 (m-90) cc_final: 0.7203 (m-90) REVERT: D 373 MET cc_start: 0.8178 (mmm) cc_final: 0.7944 (mmt) REVERT: D 381 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7243 (mt-10) REVERT: D 460 SER cc_start: 0.7710 (m) cc_final: 0.7332 (p) REVERT: F 523 LEU cc_start: 0.7482 (mt) cc_final: 0.7063 (mp) REVERT: F 530 MET cc_start: 0.9282 (mtm) cc_final: 0.8895 (mtm) REVERT: F 570 VAL cc_start: 0.7829 (p) cc_final: 0.7607 (t) REVERT: F 625 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7646 (t160) REVERT: F 630 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8494 (mt-10) REVERT: F 648 GLU cc_start: 0.8838 (mm-30) cc_final: 0.7973 (mm-30) REVERT: G 4 LEU cc_start: 0.8243 (mt) cc_final: 0.7983 (mp) REVERT: G 29 ILE cc_start: 0.9086 (pt) cc_final: 0.8106 (pt) REVERT: G 50 TYR cc_start: 0.7741 (p90) cc_final: 0.7221 (p90) REVERT: G 53 PHE cc_start: 0.7690 (t80) cc_final: 0.7058 (t80) REVERT: G 58 ASN cc_start: 0.7311 (t0) cc_final: 0.6710 (m-40) REVERT: G 59 TYR cc_start: 0.7633 (m-80) cc_final: 0.6988 (m-80) REVERT: I 25 ASN cc_start: 0.8950 (t0) cc_final: 0.8333 (m-40) REVERT: I 60 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: I 81 ASP cc_start: 0.8759 (m-30) cc_final: 0.8377 (m-30) REVERT: I 82 GLU cc_start: 0.8576 (tt0) cc_final: 0.8239 (tp30) REVERT: I 86 TYR cc_start: 0.8143 (m-80) cc_final: 0.7749 (m-80) REVERT: I 91 ASP cc_start: 0.7553 (t0) cc_final: 0.6508 (p0) REVERT: I 95 ASP cc_start: 0.8157 (t0) cc_final: 0.7118 (t70) REVERT: I 105 VAL cc_start: 0.8276 (t) cc_final: 0.7362 (p) REVERT: H 29 PHE cc_start: 0.8783 (t80) cc_final: 0.8133 (t80) REVERT: H 48 ILE cc_start: 0.9261 (mt) cc_final: 0.8966 (mp) REVERT: H 71 ARG cc_start: 0.8419 (ppt90) cc_final: 0.7987 (ptt90) REVERT: H 86 ASP cc_start: 0.8788 (m-30) cc_final: 0.8275 (m-30) REVERT: H 112 SER cc_start: 0.7932 (t) cc_final: 0.7414 (m) REVERT: L 36 TYR cc_start: 0.8645 (m-80) cc_final: 0.8434 (m-80) REVERT: L 62 PHE cc_start: 0.8540 (m-80) cc_final: 0.7918 (m-10) REVERT: L 80 VAL cc_start: 0.7954 (t) cc_final: 0.6676 (p) REVERT: L 89 TYR cc_start: 0.8762 (t80) cc_final: 0.8226 (t80) REVERT: M 11 LEU cc_start: 0.6985 (tp) cc_final: 0.6774 (mt) REVERT: M 29 ILE cc_start: 0.8842 (pt) cc_final: 0.8331 (pt) REVERT: M 53 PHE cc_start: 0.8070 (t80) cc_final: 0.7719 (t80) REVERT: M 64 LYS cc_start: 0.8325 (tttt) cc_final: 0.7972 (tptt) REVERT: M 100 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6373 (mtt180) REVERT: M 107 THR cc_start: 0.9265 (t) cc_final: 0.9035 (p) REVERT: O 16 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8799 (ttpt) REVERT: O 34 TRP cc_start: 0.8818 (m100) cc_final: 0.8544 (m100) REVERT: O 95 ASP cc_start: 0.8274 (t0) cc_final: 0.7382 (t0) REVERT: J 12 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8489 (mmtm) REVERT: J 27 TYR cc_start: 0.4984 (t80) cc_final: 0.4446 (t80) REVERT: J 29 PHE cc_start: 0.7757 (t80) cc_final: 0.7226 (t80) REVERT: J 31 LYS cc_start: 0.8820 (mttt) cc_final: 0.8474 (mtmt) REVERT: J 71 ARG cc_start: 0.8407 (ppt90) cc_final: 0.7859 (ptt90) REVERT: J 80 MET cc_start: 0.8688 (ttp) cc_final: 0.8333 (ttp) REVERT: J 86 ASP cc_start: 0.9148 (m-30) cc_final: 0.8646 (p0) REVERT: J 111 VAL cc_start: 0.8735 (t) cc_final: 0.7983 (t) REVERT: N 18 ILE cc_start: 0.8664 (pt) cc_final: 0.8394 (mp) REVERT: N 36 TYR cc_start: 0.8597 (m-80) cc_final: 0.7903 (m-80) REVERT: N 61 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: N 86 TYR cc_start: 0.7856 (m-80) cc_final: 0.7568 (m-10) REVERT: N 103 LEU cc_start: 0.8690 (tp) cc_final: 0.8407 (tt) REVERT: K 3 GLN cc_start: 0.8393 (tt0) cc_final: 0.7867 (tm-30) REVERT: K 5 LEU cc_start: 0.9298 (tp) cc_final: 0.9054 (tp) REVERT: K 6 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6507 (mt-10) REVERT: K 25 SER cc_start: 0.8384 (m) cc_final: 0.6898 (p) REVERT: K 51 ILE cc_start: 0.9051 (tt) cc_final: 0.8830 (tp) REVERT: K 72 ASP cc_start: 0.8199 (t0) cc_final: 0.7780 (t0) REVERT: K 89 VAL cc_start: 0.8631 (t) cc_final: 0.8372 (p) REVERT: P 80 VAL cc_start: 0.8656 (t) cc_final: 0.8430 (p) outliers start: 10 outliers final: 2 residues processed: 729 average time/residue: 0.1941 time to fit residues: 210.6807 Evaluate side-chains 351 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 425 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100CASN I 6 GLN L 60 HIS O 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.076779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061119 restraints weight = 101205.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062991 restraints weight = 56776.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064196 restraints weight = 40174.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064962 restraints weight = 32414.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065418 restraints weight = 28330.042| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24689 Z= 0.192 Angle : 1.055 44.577 33828 Z= 0.472 Chirality : 0.055 0.409 4172 Planarity : 0.005 0.068 3994 Dihedral : 5.562 48.413 3013 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.17 % Allowed : 10.42 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.16), residues: 2731 helix: 0.61 (0.25), residues: 413 sheet: 0.44 (0.17), residues: 896 loop : -0.31 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.041 0.002 TYR L 30 PHE 0.026 0.002 PHE G 78 TRP 0.031 0.002 TRP K 100H HIS 0.011 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (24493) covalent geometry : angle 0.95522 / 0.45 (33281) SS BOND : bond 0.00712 / 0.34 ( 40) SS BOND : angle 1.21822 / 0.76 ( 80) hydrogen bonds : bond 0.05703 / 3.84 ( 672) hydrogen bonds : angle 6.28362 / 4.37 ( 1704) link_ALPHA1-3 : bond 0.01294 / 0.67 ( 2) link_ALPHA1-3 : angle 3.17073 / 2.22 ( 6) link_ALPHA1-6 : bond 0.00920 / 0.45 ( 2) link_ALPHA1-6 : angle 1.25361 / 0.76 ( 6) link_BETA1-4 : bond 0.01252 / 0.79 ( 83) link_BETA1-4 : angle 4.54361 / 3.20 ( 249) link_BETA1-6 : bond 0.01069 / 0.56 ( 1) link_BETA1-6 : angle 3.07085 / 1.62 ( 3) link_NAG-ASN : bond 0.00811 / 0.55 ( 67) link_NAG-ASN : angle 3.09087 / 2.12 ( 201) link_NAG-THR : bond 0.00693 / 0.36 ( 1) link_NAG-THR : angle 1.87880 / 1.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 447 time to evaluate : 1.367 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 376 PHE cc_start: 0.7878 (t80) cc_final: 0.7580 (t80) REVERT: B 585 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8331 (mtp85) REVERT: C 69 TRP cc_start: 0.8307 (m-90) cc_final: 0.7975 (m-90) REVERT: C 86 LEU cc_start: 0.9564 (mt) cc_final: 0.9296 (mp) REVERT: C 98 ASN cc_start: 0.8653 (t0) cc_final: 0.8216 (t0) REVERT: C 114 GLN cc_start: 0.8998 (tp40) cc_final: 0.8563 (tm-30) REVERT: C 449 ILE cc_start: 0.9332 (mt) cc_final: 0.9110 (tt) REVERT: E 577 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7991 (tm-30) REVERT: E 601 LYS cc_start: 0.8957 (mttt) cc_final: 0.8573 (mmmm) REVERT: D 373 MET cc_start: 0.7815 (mmm) cc_final: 0.7490 (mpp) REVERT: D 381 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7124 (mt-10) REVERT: F 530 MET cc_start: 0.9142 (mtm) cc_final: 0.8692 (mtm) REVERT: F 635 ILE cc_start: 0.9429 (pt) cc_final: 0.9214 (pt) REVERT: F 648 GLU cc_start: 0.8864 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 59 TYR cc_start: 0.7737 (m-80) cc_final: 0.7160 (m-80) REVERT: G 100 ASP cc_start: 0.7249 (m-30) cc_final: 0.6840 (t0) REVERT: I 3 GLU cc_start: 0.7836 (pm20) cc_final: 0.7497 (pm20) REVERT: I 25 ASN cc_start: 0.8786 (t0) cc_final: 0.8293 (m-40) REVERT: I 68 ASN cc_start: 0.8496 (m-40) cc_final: 0.7927 (t0) REVERT: I 76 ARG cc_start: 0.9127 (ttm110) cc_final: 0.8900 (mtm110) REVERT: I 82 GLU cc_start: 0.8591 (tt0) cc_final: 0.8250 (tp30) REVERT: I 91 ASP cc_start: 0.7104 (t0) cc_final: 0.6809 (p0) REVERT: I 105 VAL cc_start: 0.8448 (t) cc_final: 0.7258 (p) REVERT: H 10 GLU cc_start: 0.7646 (tp30) cc_final: 0.7344 (tp30) REVERT: H 29 PHE cc_start: 0.8428 (t80) cc_final: 0.7962 (t80) REVERT: H 30 THR cc_start: 0.9448 (p) cc_final: 0.9180 (t) REVERT: H 112 SER cc_start: 0.7768 (t) cc_final: 0.7395 (m) REVERT: L 2 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5046 (t80) REVERT: L 36 TYR cc_start: 0.8372 (m-80) cc_final: 0.8105 (m-80) REVERT: L 80 VAL cc_start: 0.7411 (t) cc_final: 0.7066 (p) REVERT: L 89 TYR cc_start: 0.8367 (t80) cc_final: 0.8158 (t80) REVERT: M 29 ILE cc_start: 0.8658 (pt) cc_final: 0.8383 (pt) REVERT: M 43 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8056 (ptpp) REVERT: M 53 PHE cc_start: 0.7783 (t80) cc_final: 0.7127 (t80) REVERT: O 72 LEU cc_start: 0.9563 (tp) cc_final: 0.8949 (tp) REVERT: O 76 ARG cc_start: 0.7471 (mmp80) cc_final: 0.7204 (mmp80) REVERT: O 78 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7565 (mp0) REVERT: O 94 ARG cc_start: 0.8814 (mmp80) cc_final: 0.8432 (mmp80) REVERT: O 95 ASP cc_start: 0.8600 (t0) cc_final: 0.7649 (t0) REVERT: J 12 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8578 (mmtm) REVERT: J 30 THR cc_start: 0.9315 (p) cc_final: 0.9039 (t) REVERT: J 52 ASN cc_start: 0.9104 (t0) cc_final: 0.8407 (t0) REVERT: J 86 ASP cc_start: 0.8838 (m-30) cc_final: 0.8585 (m-30) REVERT: N 36 TYR cc_start: 0.8517 (m-80) cc_final: 0.8116 (m-80) REVERT: K 72 ASP cc_start: 0.8191 (t0) cc_final: 0.7532 (t0) REVERT: K 78 VAL cc_start: 0.9558 (t) cc_final: 0.9218 (p) REVERT: K 100 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8170 (mp0) REVERT: P 91 TYR cc_start: 0.8929 (t80) cc_final: 0.8443 (t80) outliers start: 53 outliers final: 29 residues processed: 484 average time/residue: 0.1715 time to fit residues: 128.5130 Evaluate side-chains 360 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 60 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain P residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 330 HIS C 422 GLN E 540 GLN D 302 ASN D 413 HIS G 100CASN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN J 35 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.073249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057642 restraints weight = 101728.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059387 restraints weight = 58554.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060502 restraints weight = 41914.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061217 restraints weight = 34271.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061624 restraints weight = 30174.897| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24689 Z= 0.214 Angle : 0.969 43.737 33828 Z= 0.431 Chirality : 0.052 0.381 4172 Planarity : 0.005 0.092 3994 Dihedral : 5.179 43.220 3008 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 2.59 % Allowed : 12.80 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.16), residues: 2731 helix: 1.30 (0.27), residues: 374 sheet: 0.24 (0.16), residues: 936 loop : -0.57 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 192 TYR 0.028 0.002 TYR O 86 PHE 0.022 0.002 PHE K 29 TRP 0.027 0.002 TRP D 69 HIS 0.013 0.001 HIS L 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (24493) covalent geometry : angle 0.89547 / 0.41 (33281) SS BOND : bond 0.00319 / 0.21 ( 40) SS BOND : angle 0.98344 / 0.64 ( 80) hydrogen bonds : bond 0.04949 / 3.35 ( 672) hydrogen bonds : angle 5.86095 / 4.13 ( 1704) link_ALPHA1-3 : bond 0.01127 / 0.57 ( 2) link_ALPHA1-3 : angle 2.55437 / 1.74 ( 6) link_ALPHA1-6 : bond 0.00600 / 0.29 ( 2) link_ALPHA1-6 : angle 1.36322 / 0.82 ( 6) link_BETA1-4 : bond 0.01084 / 0.69 ( 83) link_BETA1-4 : angle 3.73835 / 2.62 ( 249) link_BETA1-6 : bond 0.00886 / 0.47 ( 1) link_BETA1-6 : angle 2.06220 / 1.09 ( 3) link_NAG-ASN : bond 0.00676 / 0.36 ( 67) link_NAG-ASN : angle 2.67976 / 1.88 ( 201) link_NAG-THR : bond 0.00570 / 0.30 ( 1) link_NAG-THR : angle 2.68857 / 1.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 355 time to evaluate : 0.912 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: B 633 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8593 (mtp-110) REVERT: B 652 GLN cc_start: 0.7048 (mt0) cc_final: 0.6382 (mt0) REVERT: C 69 TRP cc_start: 0.8269 (m-90) cc_final: 0.8047 (m-90) REVERT: C 98 ASN cc_start: 0.8672 (t0) cc_final: 0.8145 (t0) REVERT: C 114 GLN cc_start: 0.9061 (tp40) cc_final: 0.8664 (tm-30) REVERT: E 538 THR cc_start: 0.6233 (p) cc_final: 0.5740 (p) REVERT: E 577 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8046 (tm-30) REVERT: E 601 LYS cc_start: 0.8941 (mttt) cc_final: 0.8556 (mmmm) REVERT: D 295 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7711 (p0) REVERT: F 530 MET cc_start: 0.9136 (mtm) cc_final: 0.8632 (mtm) REVERT: F 574 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8744 (UNCLASSIFIED) REVERT: F 621 MET cc_start: 0.8829 (tpt) cc_final: 0.8447 (tpt) REVERT: F 648 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8330 (mm-30) REVERT: I 3 GLU cc_start: 0.7975 (pm20) cc_final: 0.7584 (pm20) REVERT: I 25 ASN cc_start: 0.8702 (t0) cc_final: 0.8316 (m-40) REVERT: I 76 ARG cc_start: 0.9143 (ttm110) cc_final: 0.8757 (mtm110) REVERT: I 91 ASP cc_start: 0.7537 (t0) cc_final: 0.7283 (p0) REVERT: H 29 PHE cc_start: 0.8776 (t80) cc_final: 0.8218 (t80) REVERT: H 30 THR cc_start: 0.9473 (p) cc_final: 0.9197 (t) REVERT: L 36 TYR cc_start: 0.8422 (m-80) cc_final: 0.8206 (m-80) REVERT: M 29 ILE cc_start: 0.8952 (pt) cc_final: 0.8686 (pt) REVERT: M 43 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8483 (mtmm) REVERT: O 20 ILE cc_start: 0.8754 (mp) cc_final: 0.8486 (mp) REVERT: O 59 GLU cc_start: 0.8422 (pm20) cc_final: 0.8175 (pm20) REVERT: O 94 ARG cc_start: 0.8963 (mmp80) cc_final: 0.8664 (mmp80) REVERT: O 95 ASP cc_start: 0.8891 (t0) cc_final: 0.7852 (t70) REVERT: J 12 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8559 (mmtm) REVERT: J 30 THR cc_start: 0.9531 (p) cc_final: 0.9195 (t) REVERT: J 31 LYS cc_start: 0.9142 (tppp) cc_final: 0.8884 (tppp) REVERT: J 52 ASN cc_start: 0.9103 (t0) cc_final: 0.8386 (t0) REVERT: J 76 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8810 (mt-10) REVERT: J 79 TYR cc_start: 0.8464 (m-80) cc_final: 0.8201 (m-10) REVERT: J 86 ASP cc_start: 0.8902 (m-30) cc_final: 0.8627 (m-30) REVERT: N 89 TYR cc_start: 0.9122 (t80) cc_final: 0.8838 (t80) REVERT: N 94 MET cc_start: 0.8896 (ttt) cc_final: 0.8595 (ttp) REVERT: K 72 ASP cc_start: 0.7997 (t0) cc_final: 0.7316 (t0) REVERT: P 49 PHE cc_start: 0.8125 (t80) cc_final: 0.7908 (t80) outliers start: 63 outliers final: 46 residues processed: 402 average time/residue: 0.1588 time to fit residues: 100.8474 Evaluate side-chains 354 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 374 HIS ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 96 GLN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.072006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056366 restraints weight = 105453.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058024 restraints weight = 62024.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059061 restraints weight = 45280.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059738 restraints weight = 37535.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060177 restraints weight = 33257.094| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24689 Z= 0.219 Angle : 0.942 43.432 33828 Z= 0.416 Chirality : 0.051 0.364 4172 Planarity : 0.005 0.049 3994 Dihedral : 5.117 40.597 3006 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 2.87 % Allowed : 14.32 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.16), residues: 2731 helix: 1.39 (0.27), residues: 373 sheet: 0.26 (0.17), residues: 915 loop : -0.74 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 100F TYR 0.028 0.002 TYR G 50 PHE 0.018 0.002 PHE G 78 TRP 0.040 0.002 TRP O 34 HIS 0.009 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (24493) covalent geometry : angle 0.87777 / 0.40 (33281) SS BOND : bond 0.00325 / 0.23 ( 40) SS BOND : angle 0.96737 / 0.63 ( 80) hydrogen bonds : bond 0.04652 / 3.23 ( 672) hydrogen bonds : angle 5.66828 / 3.99 ( 1704) link_ALPHA1-3 : bond 0.01099 / 0.56 ( 2) link_ALPHA1-3 : angle 2.27590 / 1.54 ( 6) link_ALPHA1-6 : bond 0.00456 / 0.22 ( 2) link_ALPHA1-6 : angle 1.42553 / 0.85 ( 6) link_BETA1-4 : bond 0.00925 / 0.60 ( 83) link_BETA1-4 : angle 3.41983 / 2.40 ( 249) link_BETA1-6 : bond 0.00658 / 0.35 ( 1) link_BETA1-6 : angle 1.85705 / 0.98 ( 3) link_NAG-ASN : bond 0.00414 / 0.26 ( 67) link_NAG-ASN : angle 2.55603 / 1.78 ( 201) link_NAG-THR : bond 0.00528 / 0.28 ( 1) link_NAG-THR : angle 2.51957 / 1.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 0.766 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: B 636 ASP cc_start: 0.7974 (p0) cc_final: 0.7672 (p0) REVERT: C 69 TRP cc_start: 0.8324 (m-90) cc_final: 0.8019 (m-90) REVERT: C 98 ASN cc_start: 0.8664 (t0) cc_final: 0.8362 (t0) REVERT: C 114 GLN cc_start: 0.9073 (tp40) cc_final: 0.8845 (tm-30) REVERT: E 577 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8069 (tm-30) REVERT: E 601 LYS cc_start: 0.8928 (mttt) cc_final: 0.8664 (mmmm) REVERT: D 269 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: D 295 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7917 (p0) REVERT: F 530 MET cc_start: 0.9120 (mtm) cc_final: 0.8645 (mtm) REVERT: F 574 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8776 (mtmt) REVERT: F 621 MET cc_start: 0.8937 (tpt) cc_final: 0.8436 (tpt) REVERT: F 625 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7395 (t160) REVERT: F 648 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8862 (mm-30) REVERT: G 78 PHE cc_start: 0.6655 (m-80) cc_final: 0.6326 (m-80) REVERT: G 94 ARG cc_start: 0.5779 (mmm160) cc_final: 0.5258 (tmm-80) REVERT: I 25 ASN cc_start: 0.8696 (t0) cc_final: 0.8325 (m110) REVERT: I 76 ARG cc_start: 0.9348 (ttm110) cc_final: 0.9038 (mtm110) REVERT: I 91 ASP cc_start: 0.7845 (t0) cc_final: 0.7630 (p0) REVERT: I 95 ASP cc_start: 0.8535 (t70) cc_final: 0.8098 (t70) REVERT: H 30 THR cc_start: 0.9564 (p) cc_final: 0.9276 (t) REVERT: L 2 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.5135 (t80) REVERT: M 29 ILE cc_start: 0.9077 (pt) cc_final: 0.8828 (pt) REVERT: M 43 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8426 (ptmt) REVERT: M 91 TYR cc_start: 0.8886 (m-80) cc_final: 0.8650 (m-80) REVERT: M 100 MET cc_start: 0.7115 (ttm) cc_final: 0.6895 (ttm) REVERT: O 95 ASP cc_start: 0.8983 (t0) cc_final: 0.8359 (t0) REVERT: J 12 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8507 (mmtm) REVERT: J 28 THR cc_start: 0.8624 (m) cc_final: 0.8247 (p) REVERT: J 30 THR cc_start: 0.9662 (p) cc_final: 0.9194 (t) REVERT: J 52 ASN cc_start: 0.9137 (t0) cc_final: 0.8382 (t0) REVERT: J 79 TYR cc_start: 0.8570 (m-80) cc_final: 0.8367 (m-10) REVERT: J 80 MET cc_start: 0.8659 (ptm) cc_final: 0.8218 (ptm) REVERT: N 89 TYR cc_start: 0.9189 (t80) cc_final: 0.8867 (t80) REVERT: N 93 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7393 (t0) REVERT: N 94 MET cc_start: 0.8953 (ttt) cc_final: 0.8622 (ttp) REVERT: K 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7538 (t0) REVERT: P 91 TYR cc_start: 0.9024 (t80) cc_final: 0.8699 (t80) outliers start: 70 outliers final: 47 residues processed: 381 average time/residue: 0.1618 time to fit residues: 96.8101 Evaluate side-chains 341 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 165 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 422 GLN C 302 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.070477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054754 restraints weight = 104245.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056367 restraints weight = 61333.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057397 restraints weight = 44758.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058047 restraints weight = 37054.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058380 restraints weight = 32964.727| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24689 Z= 0.273 Angle : 0.970 43.429 33828 Z= 0.432 Chirality : 0.052 0.366 4172 Planarity : 0.005 0.082 3994 Dihedral : 5.235 36.963 3006 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 3.49 % Allowed : 15.55 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.16), residues: 2731 helix: 1.28 (0.28), residues: 374 sheet: 0.12 (0.17), residues: 874 loop : -0.86 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 94 TYR 0.028 0.002 TYR G 50 PHE 0.021 0.002 PHE M 53 TRP 0.043 0.002 TRP O 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (24493) covalent geometry : angle 0.91070 / 0.42 (33281) SS BOND : bond 0.00390 / 0.27 ( 40) SS BOND : angle 1.00343 / 0.69 ( 80) hydrogen bonds : bond 0.04863 / 3.38 ( 672) hydrogen bonds : angle 5.75202 / 4.06 ( 1704) link_ALPHA1-3 : bond 0.01165 / 0.60 ( 2) link_ALPHA1-3 : angle 2.14509 / 1.44 ( 6) link_ALPHA1-6 : bond 0.00346 / 0.16 ( 2) link_ALPHA1-6 : angle 1.48207 / 0.88 ( 6) link_BETA1-4 : bond 0.00915 / 0.59 ( 83) link_BETA1-4 : angle 3.32641 / 2.33 ( 249) link_BETA1-6 : bond 0.00607 / 0.32 ( 1) link_BETA1-6 : angle 1.88706 / 0.99 ( 3) link_NAG-ASN : bond 0.00415 / 0.26 ( 67) link_NAG-ASN : angle 2.52908 / 1.72 ( 201) link_NAG-THR : bond 0.00772 / 0.41 ( 1) link_NAG-THR : angle 3.30607 / 1.77 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 308 time to evaluate : 0.821 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: B 633 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8291 (mtm110) REVERT: B 636 ASP cc_start: 0.8075 (p0) cc_final: 0.7805 (p0) REVERT: C 69 TRP cc_start: 0.8247 (m-90) cc_final: 0.7893 (m-10) REVERT: C 98 ASN cc_start: 0.8755 (t0) cc_final: 0.8441 (t0) REVERT: E 530 MET cc_start: 0.8703 (mmt) cc_final: 0.8432 (mmm) REVERT: E 577 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8174 (tm-30) REVERT: E 601 LYS cc_start: 0.9029 (mttt) cc_final: 0.8776 (mmmm) REVERT: D 269 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: D 295 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8006 (p0) REVERT: F 530 MET cc_start: 0.9106 (mtm) cc_final: 0.8669 (mtm) REVERT: F 574 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8710 (mtmt) REVERT: F 577 GLN cc_start: 0.9340 (tp40) cc_final: 0.8618 (tm-30) REVERT: F 621 MET cc_start: 0.8979 (tpt) cc_final: 0.8586 (tpt) REVERT: F 625 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7438 (t160) REVERT: F 648 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8679 (mm-30) REVERT: G 64 LYS cc_start: 0.8162 (tttt) cc_final: 0.7899 (mtpp) REVERT: G 78 PHE cc_start: 0.6497 (m-80) cc_final: 0.6056 (m-80) REVERT: G 95 GLU cc_start: 0.8276 (tt0) cc_final: 0.7733 (tt0) REVERT: I 91 ASP cc_start: 0.7872 (t0) cc_final: 0.7642 (p0) REVERT: I 95 ASP cc_start: 0.8709 (t70) cc_final: 0.8397 (t70) REVERT: H 30 THR cc_start: 0.9659 (p) cc_final: 0.9382 (t) REVERT: L 2 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5316 (t80) REVERT: L 3 GLU cc_start: 0.7617 (mp0) cc_final: 0.6933 (mp0) REVERT: M 43 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8641 (mtmm) REVERT: M 91 TYR cc_start: 0.8983 (m-80) cc_final: 0.8777 (m-80) REVERT: O 60 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8312 (mtm-85) REVERT: J 12 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8538 (mmtm) REVERT: J 28 THR cc_start: 0.8824 (m) cc_final: 0.8549 (p) REVERT: J 30 THR cc_start: 0.9648 (p) cc_final: 0.9238 (t) REVERT: J 52 ASN cc_start: 0.9052 (t0) cc_final: 0.8404 (t0) REVERT: J 80 MET cc_start: 0.8885 (ptm) cc_final: 0.8434 (ptm) REVERT: N 39 TYR cc_start: 0.7613 (m-10) cc_final: 0.7405 (m-10) REVERT: N 45 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8053 (mmtt) REVERT: N 93 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7598 (t0) REVERT: N 94 MET cc_start: 0.8973 (ttt) cc_final: 0.8632 (ttp) REVERT: K 72 ASP cc_start: 0.8220 (t0) cc_final: 0.7657 (t0) REVERT: P 49 PHE cc_start: 0.8222 (t80) cc_final: 0.7756 (t80) REVERT: P 53 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8762 (ttpp) outliers start: 85 outliers final: 59 residues processed: 369 average time/residue: 0.1507 time to fit residues: 88.8790 Evaluate side-chains 340 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 14 optimal weight: 0.4980 chunk 210 optimal weight: 0.9990 chunk 168 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 170 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 195 ASN A 425 ASN C 344 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.072984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057348 restraints weight = 102105.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.059086 restraints weight = 57665.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060196 restraints weight = 41163.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060918 restraints weight = 33522.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061335 restraints weight = 29486.277| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24689 Z= 0.132 Angle : 0.879 43.646 33828 Z= 0.383 Chirality : 0.049 0.325 4172 Planarity : 0.004 0.052 3994 Dihedral : 4.839 36.325 3006 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.42 % Allowed : 16.70 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.16), residues: 2731 helix: 1.86 (0.28), residues: 350 sheet: 0.12 (0.17), residues: 866 loop : -0.80 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 76 TYR 0.035 0.002 TYR O 49 PHE 0.018 0.002 PHE G 100H TRP 0.045 0.002 TRP O 34 HIS 0.006 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (24493) covalent geometry : angle 0.82252 / 0.37 (33281) SS BOND : bond 0.00254 / 0.17 ( 40) SS BOND : angle 0.82564 / 0.55 ( 80) hydrogen bonds : bond 0.04092 / 2.77 ( 672) hydrogen bonds : angle 5.49831 / 3.89 ( 1704) link_ALPHA1-3 : bond 0.01090 / 0.55 ( 2) link_ALPHA1-3 : angle 2.18798 / 1.46 ( 6) link_ALPHA1-6 : bond 0.00378 / 0.18 ( 2) link_ALPHA1-6 : angle 1.38779 / 0.83 ( 6) link_BETA1-4 : bond 0.00908 / 0.60 ( 83) link_BETA1-4 : angle 3.09472 / 2.17 ( 249) link_BETA1-6 : bond 0.00684 / 0.36 ( 1) link_BETA1-6 : angle 1.76631 / 0.94 ( 3) link_NAG-ASN : bond 0.00450 / 0.30 ( 67) link_NAG-ASN : angle 2.37279 / 1.63 ( 201) link_NAG-THR : bond 0.00130 / 0.07 ( 1) link_NAG-THR : angle 1.66008 / 0.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 1.036 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: B 636 ASP cc_start: 0.7821 (p0) cc_final: 0.7598 (p0) REVERT: C 69 TRP cc_start: 0.8260 (m-90) cc_final: 0.7861 (m-90) REVERT: C 98 ASN cc_start: 0.8673 (t0) cc_final: 0.8410 (t0) REVERT: E 577 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 601 LYS cc_start: 0.9094 (mttt) cc_final: 0.8740 (mmmm) REVERT: D 47 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 269 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: D 295 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.8044 (p0) REVERT: D 363 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: D 426 MET cc_start: 0.7468 (ttp) cc_final: 0.6686 (ttp) REVERT: D 427 TRP cc_start: 0.8229 (m100) cc_final: 0.7996 (m100) REVERT: F 530 MET cc_start: 0.9102 (mtm) cc_final: 0.8683 (ttm) REVERT: F 574 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8759 (mtmt) REVERT: F 621 MET cc_start: 0.9073 (tpt) cc_final: 0.8668 (tpt) REVERT: F 625 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7351 (t160) REVERT: F 648 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8932 (mm-30) REVERT: G 103 TRP cc_start: 0.7301 (t-100) cc_final: 0.7023 (m-90) REVERT: I 95 ASP cc_start: 0.8527 (t70) cc_final: 0.8159 (t70) REVERT: H 30 THR cc_start: 0.9613 (p) cc_final: 0.9304 (t) REVERT: L 2 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5292 (t80) REVERT: L 3 GLU cc_start: 0.7515 (mp0) cc_final: 0.6866 (mp0) REVERT: L 23 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7759 (p) REVERT: M 4 LEU cc_start: 0.8808 (mp) cc_final: 0.8593 (tt) REVERT: M 43 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8558 (ptmt) REVERT: M 91 TYR cc_start: 0.8950 (m-80) cc_final: 0.8624 (m-80) REVERT: O 76 ARG cc_start: 0.8876 (ptp-110) cc_final: 0.8461 (ptp-170) REVERT: J 12 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8575 (mmtm) REVERT: J 52 ASN cc_start: 0.8935 (t0) cc_final: 0.8308 (t0) REVERT: J 80 MET cc_start: 0.8753 (ptm) cc_final: 0.8449 (ptm) REVERT: J 94 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6258 (ttm-80) REVERT: N 50 GLU cc_start: 0.8180 (tp30) cc_final: 0.7959 (tp30) REVERT: N 93 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7408 (t0) REVERT: N 94 MET cc_start: 0.8878 (ttt) cc_final: 0.8547 (ttp) REVERT: K 72 ASP cc_start: 0.8079 (t0) cc_final: 0.7512 (t0) REVERT: P 49 PHE cc_start: 0.7855 (t80) cc_final: 0.7507 (t80) outliers start: 59 outliers final: 38 residues processed: 381 average time/residue: 0.1634 time to fit residues: 99.8209 Evaluate side-chains 336 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 209 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 143 optimal weight: 0.0670 overall best weight: 2.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 330 HIS A 425 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 100CASN K 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.071378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055795 restraints weight = 103188.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057444 restraints weight = 60090.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058490 restraints weight = 43527.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059175 restraints weight = 35777.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059506 restraints weight = 31647.909| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24689 Z= 0.193 Angle : 0.891 43.431 33828 Z= 0.392 Chirality : 0.050 0.324 4172 Planarity : 0.004 0.049 3994 Dihedral : 4.878 34.610 3006 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.63 % Allowed : 17.36 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.16), residues: 2731 helix: 1.60 (0.28), residues: 368 sheet: 0.08 (0.17), residues: 883 loop : -0.91 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 94 TYR 0.048 0.002 TYR L 30 PHE 0.026 0.002 PHE M 78 TRP 0.029 0.002 TRP D 69 HIS 0.006 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (24493) covalent geometry : angle 0.83702 / 0.38 (33281) SS BOND : bond 0.00290 / 0.21 ( 40) SS BOND : angle 0.84519 / 0.58 ( 80) hydrogen bonds : bond 0.04247 / 2.91 ( 672) hydrogen bonds : angle 5.46345 / 3.87 ( 1704) link_ALPHA1-3 : bond 0.01144 / 0.58 ( 2) link_ALPHA1-3 : angle 2.12782 / 1.43 ( 6) link_ALPHA1-6 : bond 0.00355 / 0.17 ( 2) link_ALPHA1-6 : angle 1.43237 / 0.86 ( 6) link_BETA1-4 : bond 0.00877 / 0.57 ( 83) link_BETA1-4 : angle 3.06715 / 2.16 ( 249) link_BETA1-6 : bond 0.00628 / 0.33 ( 1) link_BETA1-6 : angle 1.81753 / 0.96 ( 3) link_NAG-ASN : bond 0.00357 / 0.23 ( 67) link_NAG-ASN : angle 2.33777 / 1.60 ( 201) link_NAG-THR : bond 0.00664 / 0.35 ( 1) link_NAG-THR : angle 2.74567 / 1.48 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.923 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 475 MET cc_start: 0.8449 (mmm) cc_final: 0.8242 (mmt) REVERT: B 636 ASP cc_start: 0.7924 (p0) cc_final: 0.7702 (p0) REVERT: C 69 TRP cc_start: 0.8184 (m-90) cc_final: 0.7756 (m-90) REVERT: E 577 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8043 (tm-30) REVERT: E 585 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8161 (mtp-110) REVERT: E 601 LYS cc_start: 0.9123 (mttt) cc_final: 0.8739 (mmmm) REVERT: D 269 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: F 530 MET cc_start: 0.9134 (mtm) cc_final: 0.8822 (ttm) REVERT: F 574 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8725 (mtmt) REVERT: F 621 MET cc_start: 0.9009 (tpt) cc_final: 0.8621 (tpt) REVERT: F 625 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7306 (t160) REVERT: G 64 LYS cc_start: 0.8054 (tttt) cc_final: 0.7723 (mtpp) REVERT: I 95 ASP cc_start: 0.8853 (t70) cc_final: 0.8017 (t70) REVERT: H 12 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8857 (mmmt) REVERT: H 30 THR cc_start: 0.9646 (p) cc_final: 0.9378 (t) REVERT: L 2 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5581 (t80) REVERT: L 23 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7805 (p) REVERT: M 43 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8522 (ptmt) REVERT: M 91 TYR cc_start: 0.9001 (m-80) cc_final: 0.8629 (m-80) REVERT: O 76 ARG cc_start: 0.8939 (ptp-110) cc_final: 0.8482 (ptp-170) REVERT: J 12 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8604 (mmtm) REVERT: J 52 ASN cc_start: 0.9005 (t0) cc_final: 0.8388 (t0) REVERT: J 94 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5610 (tpp-160) REVERT: J 100 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8459 (mm-30) REVERT: N 45 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8154 (mmtt) REVERT: N 93 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7578 (t0) REVERT: N 94 MET cc_start: 0.8967 (ttt) cc_final: 0.8634 (ttp) REVERT: K 62 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8269 (p0) REVERT: K 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7594 (t0) REVERT: K 100 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8533 (mp0) outliers start: 64 outliers final: 47 residues processed: 352 average time/residue: 0.1675 time to fit residues: 93.9101 Evaluate side-chains 332 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 193 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 252 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055777 restraints weight = 102755.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057449 restraints weight = 58632.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058530 restraints weight = 42158.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059204 restraints weight = 34440.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059647 restraints weight = 30461.184| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24689 Z= 0.183 Angle : 0.897 43.528 33828 Z= 0.395 Chirality : 0.049 0.314 4172 Planarity : 0.004 0.049 3994 Dihedral : 4.805 22.158 3004 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.75 % Allowed : 17.60 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.16), residues: 2731 helix: 1.56 (0.28), residues: 370 sheet: 0.08 (0.17), residues: 877 loop : -0.92 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 633 TYR 0.038 0.002 TYR O 49 PHE 0.029 0.002 PHE M 78 TRP 0.037 0.002 TRP G 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (24493) covalent geometry : angle 0.84417 / 0.38 (33281) SS BOND : bond 0.00264 / 0.18 ( 40) SS BOND : angle 0.80880 / 0.56 ( 80) hydrogen bonds : bond 0.04227 / 2.88 ( 672) hydrogen bonds : angle 5.43727 / 3.85 ( 1704) link_ALPHA1-3 : bond 0.01138 / 0.58 ( 2) link_ALPHA1-3 : angle 2.08446 / 1.40 ( 6) link_ALPHA1-6 : bond 0.00331 / 0.16 ( 2) link_ALPHA1-6 : angle 1.44897 / 0.87 ( 6) link_BETA1-4 : bond 0.00871 / 0.57 ( 83) link_BETA1-4 : angle 3.02864 / 2.12 ( 249) link_BETA1-6 : bond 0.00654 / 0.34 ( 1) link_BETA1-6 : angle 1.82555 / 0.96 ( 3) link_NAG-ASN : bond 0.00363 / 0.24 ( 67) link_NAG-ASN : angle 2.37161 / 1.60 ( 201) link_NAG-THR : bond 0.00521 / 0.27 ( 1) link_NAG-THR : angle 2.46187 / 1.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 291 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8523 (mmm) cc_final: 0.8269 (mmt) REVERT: B 636 ASP cc_start: 0.7939 (p0) cc_final: 0.7720 (p0) REVERT: C 69 TRP cc_start: 0.8215 (m-90) cc_final: 0.7713 (m-90) REVERT: C 98 ASN cc_start: 0.8722 (t0) cc_final: 0.8422 (t0) REVERT: E 577 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8054 (tm-30) REVERT: E 585 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8163 (mtp-110) REVERT: E 601 LYS cc_start: 0.9172 (mttt) cc_final: 0.8767 (mmmm) REVERT: E 621 MET cc_start: 0.7638 (tpp) cc_final: 0.7348 (tpp) REVERT: D 269 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: F 530 MET cc_start: 0.9166 (mtm) cc_final: 0.8838 (ttm) REVERT: F 574 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8729 (mtmt) REVERT: F 621 MET cc_start: 0.9055 (tpt) cc_final: 0.8669 (tpt) REVERT: F 625 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7354 (t160) REVERT: G 37 ILE cc_start: 0.9069 (mm) cc_final: 0.8843 (mm) REVERT: I 95 ASP cc_start: 0.8818 (t70) cc_final: 0.8009 (t70) REVERT: L 2 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.5530 (t80) REVERT: L 49 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7552 (t80) REVERT: M 43 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8577 (ptmt) REVERT: M 73 MET cc_start: 0.8303 (mtp) cc_final: 0.8070 (mmm) REVERT: M 91 TYR cc_start: 0.9062 (m-80) cc_final: 0.8698 (m-80) REVERT: O 49 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5120 (m-10) REVERT: O 76 ARG cc_start: 0.8970 (ptp-110) cc_final: 0.8517 (ptp-170) REVERT: J 12 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8532 (mmtm) REVERT: J 31 LYS cc_start: 0.9096 (tppp) cc_final: 0.8537 (tttt) REVERT: J 52 ASN cc_start: 0.8934 (t0) cc_final: 0.8278 (t0) REVERT: J 94 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.5472 (tpp-160) REVERT: J 100 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8491 (mm-30) REVERT: N 93 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7690 (t0) REVERT: N 94 MET cc_start: 0.8970 (ttt) cc_final: 0.8635 (ttp) REVERT: K 72 ASP cc_start: 0.8148 (t0) cc_final: 0.7556 (t0) outliers start: 67 outliers final: 48 residues processed: 340 average time/residue: 0.1651 time to fit residues: 90.3450 Evaluate side-chains 331 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 86 TYR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 187 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056226 restraints weight = 103332.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057888 restraints weight = 59688.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058954 restraints weight = 43194.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059580 restraints weight = 35440.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060040 restraints weight = 31498.230| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24689 Z= 0.161 Angle : 0.889 43.541 33828 Z= 0.392 Chirality : 0.049 0.311 4172 Planarity : 0.004 0.050 3994 Dihedral : 4.791 24.793 3004 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.75 % Allowed : 17.93 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.16), residues: 2731 helix: 1.57 (0.28), residues: 368 sheet: 0.05 (0.17), residues: 901 loop : -0.86 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 633 TYR 0.066 0.002 TYR L 30 PHE 0.035 0.002 PHE G 100H TRP 0.030 0.002 TRP G 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (24493) covalent geometry : angle 0.83801 / 0.38 (33281) SS BOND : bond 0.00269 / 0.18 ( 40) SS BOND : angle 1.09458 / 0.73 ( 80) hydrogen bonds : bond 0.04080 / 2.81 ( 672) hydrogen bonds : angle 5.39021 / 3.81 ( 1704) link_ALPHA1-3 : bond 0.01134 / 0.58 ( 2) link_ALPHA1-3 : angle 2.07615 / 1.39 ( 6) link_ALPHA1-6 : bond 0.00340 / 0.16 ( 2) link_ALPHA1-6 : angle 1.42544 / 0.86 ( 6) link_BETA1-4 : bond 0.00864 / 0.57 ( 83) link_BETA1-4 : angle 2.94851 / 2.07 ( 249) link_BETA1-6 : bond 0.00651 / 0.34 ( 1) link_BETA1-6 : angle 1.80835 / 0.96 ( 3) link_NAG-ASN : bond 0.00358 / 0.23 ( 67) link_NAG-ASN : angle 2.29799 / 1.56 ( 201) link_NAG-THR : bond 0.00449 / 0.24 ( 1) link_NAG-THR : angle 2.29275 / 1.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 TYR cc_start: 0.8829 (t80) cc_final: 0.8605 (t80) REVERT: A 475 MET cc_start: 0.8463 (mmm) cc_final: 0.8226 (mmt) REVERT: B 633 ARG cc_start: 0.8869 (mtm110) cc_final: 0.8581 (mtm110) REVERT: B 636 ASP cc_start: 0.7970 (p0) cc_final: 0.7759 (p0) REVERT: C 69 TRP cc_start: 0.8182 (m-90) cc_final: 0.7697 (m-90) REVERT: C 98 ASN cc_start: 0.8551 (t0) cc_final: 0.8329 (t0) REVERT: E 577 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8017 (tm-30) REVERT: E 601 LYS cc_start: 0.9142 (mttt) cc_final: 0.8730 (mmmm) REVERT: E 621 MET cc_start: 0.7825 (tpp) cc_final: 0.7233 (tpp) REVERT: D 269 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: F 530 MET cc_start: 0.9135 (mtm) cc_final: 0.8729 (ttm) REVERT: F 574 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8685 (mtmt) REVERT: F 621 MET cc_start: 0.9053 (tpt) cc_final: 0.8703 (tpt) REVERT: F 625 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7361 (t160) REVERT: I 41 GLN cc_start: 0.8619 (mp10) cc_final: 0.8339 (mp10) REVERT: I 95 ASP cc_start: 0.8808 (t70) cc_final: 0.7882 (t70) REVERT: L 2 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5720 (t80) REVERT: L 49 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7503 (t80) REVERT: M 43 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8665 (ptmt) REVERT: M 91 TYR cc_start: 0.9040 (m-80) cc_final: 0.8681 (m-80) REVERT: O 76 ARG cc_start: 0.8989 (ptp-110) cc_final: 0.8542 (ptp-170) REVERT: J 12 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8600 (mptt) REVERT: J 31 LYS cc_start: 0.9031 (tppp) cc_final: 0.8583 (pttt) REVERT: J 52 ASN cc_start: 0.8947 (t0) cc_final: 0.8304 (t0) REVERT: J 94 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6788 (tpp80) REVERT: J 100 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8526 (mm-30) REVERT: N 93 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7685 (t0) REVERT: N 94 MET cc_start: 0.8969 (ttt) cc_final: 0.8633 (ttp) REVERT: K 72 ASP cc_start: 0.8216 (t0) cc_final: 0.7607 (t0) outliers start: 67 outliers final: 50 residues processed: 336 average time/residue: 0.1615 time to fit residues: 87.4650 Evaluate side-chains 326 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 73 optimal weight: 0.0670 chunk 162 optimal weight: 6.9990 chunk 198 optimal weight: 0.0770 chunk 86 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 196 optimal weight: 0.0050 chunk 134 optimal weight: 8.9990 overall best weight: 1.0292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.072534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056866 restraints weight = 104909.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058573 restraints weight = 60102.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059657 restraints weight = 43186.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060325 restraints weight = 35387.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060702 restraints weight = 31392.288| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24689 Z= 0.137 Angle : 0.880 43.535 33828 Z= 0.388 Chirality : 0.049 0.290 4172 Planarity : 0.004 0.054 3994 Dihedral : 4.689 25.334 3004 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.17 % Allowed : 18.63 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.16), residues: 2731 helix: 1.57 (0.28), residues: 370 sheet: 0.01 (0.17), residues: 902 loop : -0.85 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 633 TYR 0.034 0.002 TYR G 50 PHE 0.022 0.001 PHE A 53 TRP 0.057 0.002 TRP O 34 HIS 0.005 0.001 HIS O 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24493) covalent geometry : angle 0.83218 / 0.38 (33281) SS BOND : bond 0.00279 / 0.19 ( 40) SS BOND : angle 1.02849 / 0.69 ( 80) hydrogen bonds : bond 0.03910 / 2.67 ( 672) hydrogen bonds : angle 5.33737 / 3.78 ( 1704) link_ALPHA1-3 : bond 0.01112 / 0.56 ( 2) link_ALPHA1-3 : angle 2.09422 / 1.41 ( 6) link_ALPHA1-6 : bond 0.00394 / 0.19 ( 2) link_ALPHA1-6 : angle 1.40880 / 0.85 ( 6) link_BETA1-4 : bond 0.00865 / 0.57 ( 83) link_BETA1-4 : angle 2.85435 / 2.00 ( 249) link_BETA1-6 : bond 0.00667 / 0.35 ( 1) link_BETA1-6 : angle 1.78356 / 0.95 ( 3) link_NAG-ASN : bond 0.00385 / 0.26 ( 67) link_NAG-ASN : angle 2.23533 / 1.52 ( 201) link_NAG-THR : bond 0.00308 / 0.16 ( 1) link_NAG-THR : angle 1.90746 / 1.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 TYR cc_start: 0.8801 (t80) cc_final: 0.8566 (t80) REVERT: A 475 MET cc_start: 0.8442 (mmm) cc_final: 0.8168 (mmt) REVERT: B 633 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8639 (mtm110) REVERT: B 636 ASP cc_start: 0.7919 (p0) cc_final: 0.7710 (p0) REVERT: C 69 TRP cc_start: 0.8118 (m-90) cc_final: 0.7685 (m-90) REVERT: E 577 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7959 (tm-30) REVERT: E 601 LYS cc_start: 0.9068 (mttt) cc_final: 0.8740 (mmmm) REVERT: E 621 MET cc_start: 0.7904 (tpp) cc_final: 0.7369 (tpp) REVERT: D 269 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: D 363 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: D 426 MET cc_start: 0.7628 (ttp) cc_final: 0.7093 (ttm) REVERT: D 427 TRP cc_start: 0.8320 (m100) cc_final: 0.7815 (m100) REVERT: F 530 MET cc_start: 0.9137 (mtm) cc_final: 0.8727 (ttm) REVERT: F 574 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8749 (mtmt) REVERT: F 621 MET cc_start: 0.9052 (tpt) cc_final: 0.8670 (tpt) REVERT: F 625 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7406 (t160) REVERT: G 20 LEU cc_start: 0.9048 (mm) cc_final: 0.8645 (tp) REVERT: G 94 ARG cc_start: 0.7041 (mmm-85) cc_final: 0.6788 (tmm-80) REVERT: G 95 GLU cc_start: 0.8169 (tt0) cc_final: 0.7216 (tm-30) REVERT: I 41 GLN cc_start: 0.8629 (mp10) cc_final: 0.8338 (mp10) REVERT: I 95 ASP cc_start: 0.8823 (t70) cc_final: 0.7852 (t70) REVERT: L 2 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5885 (t80) REVERT: M 17 THR cc_start: 0.8567 (m) cc_final: 0.8362 (p) REVERT: M 43 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8677 (ptmt) REVERT: M 91 TYR cc_start: 0.9025 (m-80) cc_final: 0.8665 (m-80) REVERT: O 76 ARG cc_start: 0.9049 (ptp-110) cc_final: 0.8643 (ptp-170) REVERT: J 3 GLN cc_start: 0.8114 (mp10) cc_final: 0.7760 (mp10) REVERT: J 6 GLU cc_start: 0.8199 (mp0) cc_final: 0.7465 (mp0) REVERT: J 12 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8500 (mmtm) REVERT: J 31 LYS cc_start: 0.9020 (tppp) cc_final: 0.8604 (pttt) REVERT: J 52 ASN cc_start: 0.8856 (t0) cc_final: 0.8310 (t0) REVERT: J 94 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6596 (ttp80) REVERT: J 99 TYR cc_start: 0.8761 (t80) cc_final: 0.8426 (t80) REVERT: J 100 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8545 (mm-30) REVERT: N 93 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7651 (t0) REVERT: N 94 MET cc_start: 0.8896 (ttt) cc_final: 0.8559 (ttp) REVERT: K 72 ASP cc_start: 0.8170 (t0) cc_final: 0.7548 (t0) outliers start: 53 outliers final: 41 residues processed: 340 average time/residue: 0.1643 time to fit residues: 89.1265 Evaluate side-chains 331 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain L residue 2 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 99 TYR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 246 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056666 restraints weight = 104363.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058337 restraints weight = 59960.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059417 restraints weight = 43309.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060100 restraints weight = 35534.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060534 restraints weight = 31444.947| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24689 Z= 0.145 Angle : 0.880 43.484 33828 Z= 0.388 Chirality : 0.048 0.298 4172 Planarity : 0.004 0.052 3994 Dihedral : 4.679 26.001 3004 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.13 % Allowed : 18.71 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.16), residues: 2731 helix: 1.73 (0.28), residues: 351 sheet: 0.10 (0.17), residues: 896 loop : -0.80 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 633 TYR 0.060 0.002 TYR L 30 PHE 0.025 0.001 PHE A 53 TRP 0.086 0.002 TRP O 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (24493) covalent geometry : angle 0.83365 / 0.38 (33281) SS BOND : bond 0.00238 / 0.16 ( 40) SS BOND : angle 0.95518 / 0.64 ( 80) hydrogen bonds : bond 0.03875 / 2.66 ( 672) hydrogen bonds : angle 5.34777 / 3.79 ( 1704) link_ALPHA1-3 : bond 0.01122 / 0.57 ( 2) link_ALPHA1-3 : angle 2.08863 / 1.41 ( 6) link_ALPHA1-6 : bond 0.00405 / 0.20 ( 2) link_ALPHA1-6 : angle 1.41840 / 0.86 ( 6) link_BETA1-4 : bond 0.00857 / 0.57 ( 83) link_BETA1-4 : angle 2.81897 / 1.98 ( 249) link_BETA1-6 : bond 0.00640 / 0.34 ( 1) link_BETA1-6 : angle 1.76725 / 0.94 ( 3) link_NAG-ASN : bond 0.00352 / 0.23 ( 67) link_NAG-ASN : angle 2.20836 / 1.51 ( 201) link_NAG-THR : bond 0.00413 / 0.22 ( 1) link_NAG-THR : angle 2.07547 / 1.13 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3989.51 seconds wall clock time: 70 minutes 20.58 seconds (4220.58 seconds total)