Starting phenix.real_space_refine on Thu Mar 5 17:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z3a_14474/03_2026/7z3a_14474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z3a_14474/03_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_14474/03_2026/7z3a_14474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z3a_14474/03_2026/7z3a_14474.map" model { file = "/net/cci-nas-00/data/ceres_data/7z3a_14474/03_2026/7z3a_14474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z3a_14474/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.19, per 1000 atoms: 0.22 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: 2.56 Conformation dependent library (CDL) restraints added in 833.0 milliseconds 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: 0.72 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: 5.01 Time building geometry restraints manager: 3.11 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 - 21.47: 15571 21.47 - 42.93: 503 42.93 - 64.40: 115 64.40 - 85.87: 234 85.87 - 107.33: 152 Dihedral angle restraints: 16575 sinusoidal: 8537 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 16572 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: 1.770 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.560 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 19.121 107.331 11291 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 covalent geometry : bond 0.02446 (24493) covalent geometry : angle 1.91672 (33281) SS BOND : bond 0.00883 ( 40) SS BOND : angle 2.83338 ( 80) hydrogen bonds : bond 0.16602 ( 672) hydrogen bonds : angle 7.65716 ( 1704) link_ALPHA1-3 : bond 0.08752 ( 2) link_ALPHA1-3 : angle 5.81558 ( 6) link_ALPHA1-6 : bond 0.05507 ( 2) link_ALPHA1-6 : angle 2.69123 ( 6) link_BETA1-4 : bond 0.07998 ( 83) link_BETA1-4 : angle 6.32658 ( 249) link_BETA1-6 : bond 0.07985 ( 1) link_BETA1-6 : angle 5.32441 ( 3) link_NAG-ASN : bond 0.07803 ( 67) link_NAG-ASN : angle 2.47381 ( 201) link_NAG-THR : bond 0.07123 ( 1) link_NAG-THR : angle 8.48508 ( 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 : 0.716 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: 0.1869 time to fit residues: 201.9722 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 : 0.771 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061044 restraints weight = 100384.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062934 restraints weight = 56002.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064139 restraints weight = 39474.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064930 restraints weight = 31834.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065409 restraints weight = 27733.115| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3352 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= 0.190 Angle : 1.089 44.741 33828 Z= 0.480 Chirality : 0.058 0.439 4172 Planarity : 0.005 0.072 3994 Dihedral : 15.907 82.624 6207 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.22 % Allowed : 10.34 % Favored : 87.44 % 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: 0.04 (0.16), residues: 2731 helix: 0.58 (0.25), residues: 413 sheet: 0.41 (0.16), residues: 902 loop : -0.31 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.040 0.002 TYR L 30 PHE 0.028 0.002 PHE G 78 TRP 0.030 0.002 TRP K 100H HIS 0.011 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00411 (24493) covalent geometry : angle 0.98250 (33281) SS BOND : bond 0.00811 ( 40) SS BOND : angle 1.22429 ( 80) hydrogen bonds : bond 0.05501 ( 672) hydrogen bonds : angle 6.26696 ( 1704) link_ALPHA1-3 : bond 0.01402 ( 2) link_ALPHA1-3 : angle 4.01996 ( 6) link_ALPHA1-6 : bond 0.00643 ( 2) link_ALPHA1-6 : angle 1.69169 ( 6) link_BETA1-4 : bond 0.01234 ( 83) link_BETA1-4 : angle 4.84023 ( 249) link_BETA1-6 : bond 0.00983 ( 1) link_BETA1-6 : angle 3.20280 ( 3) link_NAG-ASN : bond 0.00827 ( 67) link_NAG-ASN : angle 3.05897 ( 201) link_NAG-THR : bond 0.00491 ( 1) link_NAG-THR : angle 1.64924 ( 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 504 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.7920 (t80) cc_final: 0.7602 (t80) REVERT: B 585 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8377 (mtp85) REVERT: B 633 ARG cc_start: 0.8725 (ptp-110) cc_final: 0.8464 (mtm110) REVERT: C 69 TRP cc_start: 0.8274 (m-90) cc_final: 0.7962 (m-90) REVERT: C 86 LEU cc_start: 0.9553 (mt) cc_final: 0.9352 (mp) REVERT: C 98 ASN cc_start: 0.8560 (t0) cc_final: 0.8065 (t0) REVERT: C 114 GLN cc_start: 0.9013 (tp40) cc_final: 0.8584 (tm-30) REVERT: C 449 ILE cc_start: 0.9321 (mt) cc_final: 0.9102 (tt) REVERT: E 577 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 601 LYS cc_start: 0.8957 (mttt) cc_final: 0.8569 (mmmm) REVERT: D 373 MET cc_start: 0.7783 (mmm) cc_final: 0.7468 (mpp) REVERT: D 381 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7132 (mt-10) REVERT: F 530 MET cc_start: 0.9141 (mtm) cc_final: 0.8682 (mtm) REVERT: F 635 ILE cc_start: 0.9419 (pt) cc_final: 0.9201 (pt) REVERT: F 648 GLU cc_start: 0.8901 (mm-30) cc_final: 0.7948 (mm-30) REVERT: G 59 TYR cc_start: 0.7722 (m-80) cc_final: 0.7149 (m-80) REVERT: G 100 ASP cc_start: 0.7296 (m-30) cc_final: 0.6887 (t0) REVERT: I 3 GLU cc_start: 0.7905 (pm20) cc_final: 0.7527 (pm20) REVERT: I 25 ASN cc_start: 0.8804 (t0) cc_final: 0.8322 (m-40) REVERT: I 41 GLN cc_start: 0.8525 (mp10) cc_final: 0.8311 (mp10) REVERT: I 68 ASN cc_start: 0.8488 (m-40) cc_final: 0.7920 (t0) REVERT: I 76 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8909 (mtm110) REVERT: I 82 GLU cc_start: 0.8568 (tt0) cc_final: 0.8366 (tp30) REVERT: I 105 VAL cc_start: 0.8417 (t) cc_final: 0.7587 (p) REVERT: H 10 GLU cc_start: 0.7647 (tp30) cc_final: 0.7326 (tp30) REVERT: H 29 PHE cc_start: 0.8395 (t80) cc_final: 0.8022 (t80) REVERT: H 30 THR cc_start: 0.9443 (p) cc_final: 0.9184 (t) REVERT: H 112 SER cc_start: 0.7762 (t) cc_final: 0.7409 (m) REVERT: L 2 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5325 (t80) REVERT: L 36 TYR cc_start: 0.8356 (m-80) cc_final: 0.8132 (m-80) REVERT: L 80 VAL cc_start: 0.7446 (t) cc_final: 0.7109 (p) REVERT: L 89 TYR cc_start: 0.8370 (t80) cc_final: 0.8132 (t80) REVERT: M 29 ILE cc_start: 0.8649 (pt) cc_final: 0.8363 (pt) REVERT: M 43 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8060 (ptpp) REVERT: M 53 PHE cc_start: 0.7761 (t80) cc_final: 0.6976 (t80) REVERT: O 72 LEU cc_start: 0.9546 (tp) cc_final: 0.8948 (tp) REVERT: O 76 ARG cc_start: 0.7522 (mmp80) cc_final: 0.7261 (mmp80) REVERT: O 78 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7711 (mp0) REVERT: O 94 ARG cc_start: 0.8807 (mmp80) cc_final: 0.8433 (mmp80) REVERT: O 95 ASP cc_start: 0.8593 (t0) cc_final: 0.7618 (t0) REVERT: J 12 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8602 (mmtm) REVERT: J 30 THR cc_start: 0.9330 (p) cc_final: 0.9057 (t) REVERT: J 52 ASN cc_start: 0.9112 (t0) cc_final: 0.8427 (t0) REVERT: J 86 ASP cc_start: 0.8839 (m-30) cc_final: 0.8591 (m-30) REVERT: N 36 TYR cc_start: 0.8494 (m-80) cc_final: 0.8147 (m-80) REVERT: K 72 ASP cc_start: 0.8182 (t0) cc_final: 0.7534 (t0) REVERT: K 78 VAL cc_start: 0.9559 (t) cc_final: 0.9225 (p) REVERT: K 100 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8201 (mp0) REVERT: P 91 TYR cc_start: 0.8907 (t80) cc_final: 0.8391 (t80) outliers start: 54 outliers final: 28 residues processed: 488 average time/residue: 0.1697 time to fit residues: 127.7315 Evaluate side-chains 362 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 105 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** J 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057150 restraints weight = 103883.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058865 restraints weight = 60548.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059950 restraints weight = 43968.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060648 restraints weight = 36234.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061065 restraints weight = 32079.465| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24689 Z= 0.235 Angle : 1.017 43.930 33828 Z= 0.447 Chirality : 0.056 0.418 4172 Planarity : 0.005 0.108 3994 Dihedral : 11.338 69.653 6202 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 2.59 % Allowed : 12.64 % Favored : 84.78 % 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: 1.31 (0.27), residues: 373 sheet: 0.29 (0.17), residues: 909 loop : -0.58 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 82A TYR 0.028 0.002 TYR O 86 PHE 0.021 0.002 PHE G 53 TRP 0.032 0.003 TRP D 69 HIS 0.014 0.002 HIS L 60 Details of bonding type rmsd covalent geometry : bond 0.00519 (24493) covalent geometry : angle 0.93356 (33281) SS BOND : bond 0.00369 ( 40) SS BOND : angle 0.98238 ( 80) hydrogen bonds : bond 0.05011 ( 672) hydrogen bonds : angle 5.85480 ( 1704) link_ALPHA1-3 : bond 0.01559 ( 2) link_ALPHA1-3 : angle 3.10350 ( 6) link_ALPHA1-6 : bond 0.00361 ( 2) link_ALPHA1-6 : angle 1.70559 ( 6) link_BETA1-4 : bond 0.01155 ( 83) link_BETA1-4 : angle 4.15178 ( 249) link_BETA1-6 : bond 0.00879 ( 1) link_BETA1-6 : angle 2.17888 ( 3) link_NAG-ASN : bond 0.00547 ( 67) link_NAG-ASN : angle 2.75588 ( 201) link_NAG-THR : bond 0.00649 ( 1) link_NAG-THR : angle 3.10776 ( 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 414 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 0.892 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: A 217 TYR cc_start: 0.8355 (m-10) cc_final: 0.8141 (m-80) REVERT: B 633 ARG cc_start: 0.8686 (ptp-110) cc_final: 0.8421 (mtp-110) REVERT: B 652 GLN cc_start: 0.7014 (mt0) cc_final: 0.6530 (mt0) REVERT: C 69 TRP cc_start: 0.8272 (m-90) cc_final: 0.8042 (m-90) REVERT: C 98 ASN cc_start: 0.8684 (t0) cc_final: 0.8188 (t0) REVERT: C 114 GLN cc_start: 0.9080 (tp40) cc_final: 0.8720 (tm-30) REVERT: E 538 THR cc_start: 0.6365 (p) cc_final: 0.5862 (p) REVERT: E 577 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 295 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7727 (p0) REVERT: F 530 MET cc_start: 0.9121 (mtm) cc_final: 0.8629 (mtm) REVERT: F 574 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8713 (UNCLASSIFIED) REVERT: F 621 MET cc_start: 0.8814 (tpt) cc_final: 0.8449 (tpt) REVERT: F 648 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8550 (mm-30) REVERT: I 3 GLU cc_start: 0.7952 (pm20) cc_final: 0.7557 (pm20) REVERT: I 25 ASN cc_start: 0.8731 (t0) cc_final: 0.8367 (m-40) REVERT: I 76 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8734 (mtm110) REVERT: H 29 PHE cc_start: 0.8854 (t80) cc_final: 0.8378 (t80) REVERT: H 30 THR cc_start: 0.9491 (p) cc_final: 0.9230 (t) REVERT: M 29 ILE cc_start: 0.9013 (pt) cc_final: 0.8769 (pt) REVERT: M 43 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8395 (mtmm) REVERT: O 59 GLU cc_start: 0.8443 (pm20) cc_final: 0.8186 (pm20) REVERT: O 94 ARG cc_start: 0.8954 (mmp80) cc_final: 0.8753 (mmp80) REVERT: O 95 ASP cc_start: 0.8952 (t0) cc_final: 0.8044 (t70) REVERT: J 12 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8556 (mmtm) REVERT: J 30 THR cc_start: 0.9565 (p) cc_final: 0.9224 (t) REVERT: J 31 LYS cc_start: 0.9164 (tppp) cc_final: 0.8914 (tppp) REVERT: J 52 ASN cc_start: 0.9098 (t0) cc_final: 0.8384 (t0) REVERT: J 76 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8828 (mt-10) REVERT: J 79 TYR cc_start: 0.8546 (m-80) cc_final: 0.8259 (m-10) REVERT: J 80 MET cc_start: 0.8092 (ttp) cc_final: 0.7855 (ptm) REVERT: J 86 ASP cc_start: 0.8906 (m-30) cc_final: 0.8630 (m-30) REVERT: N 89 TYR cc_start: 0.9160 (t80) cc_final: 0.8854 (t80) REVERT: N 94 MET cc_start: 0.8913 (ttt) cc_final: 0.8610 (ttp) REVERT: K 72 ASP cc_start: 0.8032 (t0) cc_final: 0.7359 (t0) REVERT: P 49 PHE cc_start: 0.8175 (t80) cc_final: 0.7973 (t80) outliers start: 63 outliers final: 47 residues processed: 398 average time/residue: 0.1680 time to fit residues: 104.3693 Evaluate side-chains 350 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS 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 36 VAL 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 F residue 620 ASP 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 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 30 LYS 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: 10.0000 chunk 265 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 344 GLN O 36 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 = 0.3483 r_free = 0.3483 target = 0.073195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057499 restraints weight = 102721.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059206 restraints weight = 59614.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060296 restraints weight = 43111.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060971 restraints weight = 35377.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061450 restraints weight = 31376.311| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4590 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= 0.169 Angle : 0.932 43.394 33828 Z= 0.404 Chirality : 0.053 0.401 4172 Planarity : 0.004 0.048 3994 Dihedral : 8.714 59.182 6200 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.79 % Allowed : 14.20 % Favored : 83.01 % 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: -0.11 (0.16), residues: 2731 helix: 1.51 (0.27), residues: 373 sheet: 0.25 (0.17), residues: 879 loop : -0.67 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 100F TYR 0.029 0.002 TYR G 50 PHE 0.017 0.002 PHE G 78 TRP 0.035 0.002 TRP O 34 HIS 0.010 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00371 (24493) covalent geometry : angle 0.85439 (33281) SS BOND : bond 0.00295 ( 40) SS BOND : angle 0.92796 ( 80) hydrogen bonds : bond 0.04388 ( 672) hydrogen bonds : angle 5.60330 ( 1704) link_ALPHA1-3 : bond 0.01247 ( 2) link_ALPHA1-3 : angle 3.17139 ( 6) link_ALPHA1-6 : bond 0.00348 ( 2) link_ALPHA1-6 : angle 1.70507 ( 6) link_BETA1-4 : bond 0.01010 ( 83) link_BETA1-4 : angle 3.79327 ( 249) link_BETA1-6 : bond 0.00706 ( 1) link_BETA1-6 : angle 1.96757 ( 3) link_NAG-ASN : bond 0.00478 ( 67) link_NAG-ASN : angle 2.56110 ( 201) link_NAG-THR : bond 0.00284 ( 1) link_NAG-THR : angle 1.74500 ( 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 405 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 337 time to evaluate : 0.906 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: B 633 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.8245 (mtm110) REVERT: B 636 ASP cc_start: 0.7954 (p0) cc_final: 0.7646 (p0) REVERT: C 69 TRP cc_start: 0.8264 (m-90) cc_final: 0.8050 (m-90) REVERT: C 98 ASN cc_start: 0.8588 (t0) cc_final: 0.8272 (t0) REVERT: E 530 MET cc_start: 0.8820 (mmm) cc_final: 0.8532 (mmm) REVERT: E 577 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7931 (tm-30) REVERT: E 584 GLU cc_start: 0.8729 (tt0) cc_final: 0.8430 (tm-30) REVERT: E 601 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8706 (mmmm) REVERT: E 633 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8622 (ttm110) REVERT: D 269 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: D 295 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7954 (p0) REVERT: F 530 MET cc_start: 0.9077 (mtm) cc_final: 0.8791 (ttm) REVERT: F 574 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8595 (mtmt) REVERT: F 621 MET cc_start: 0.8931 (tpt) cc_final: 0.8380 (tpt) REVERT: F 625 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7254 (t160) REVERT: F 648 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8679 (mm-30) REVERT: I 25 ASN cc_start: 0.8694 (t0) cc_final: 0.8309 (m110) REVERT: I 76 ARG cc_start: 0.9337 (ttm110) cc_final: 0.8994 (mtm110) REVERT: I 82 GLU cc_start: 0.8733 (tt0) cc_final: 0.8414 (tp30) REVERT: I 95 ASP cc_start: 0.8615 (t70) cc_final: 0.7953 (t70) REVERT: H 30 THR cc_start: 0.9529 (p) cc_final: 0.9247 (t) REVERT: L 2 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5186 (t80) REVERT: M 29 ILE cc_start: 0.9023 (pt) cc_final: 0.8765 (pt) REVERT: M 43 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8602 (mtmm) REVERT: M 100 MET cc_start: 0.7023 (mtt) cc_final: 0.6784 (ttm) REVERT: O 95 ASP cc_start: 0.8931 (t0) cc_final: 0.8313 (t0) REVERT: O 104 LYS cc_start: 0.8978 (tppt) cc_final: 0.8641 (tptp) REVERT: J 12 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8509 (mmtm) REVERT: J 28 THR cc_start: 0.8555 (m) cc_final: 0.8191 (p) REVERT: J 30 THR cc_start: 0.9662 (p) cc_final: 0.9204 (t) REVERT: J 52 ASN cc_start: 0.9061 (t0) cc_final: 0.8313 (t0) REVERT: N 89 TYR cc_start: 0.9140 (t80) cc_final: 0.8849 (t80) REVERT: N 93 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7321 (t0) REVERT: N 94 MET cc_start: 0.8935 (ttt) cc_final: 0.8584 (ttp) REVERT: K 72 ASP cc_start: 0.8035 (t0) cc_final: 0.7409 (t0) REVERT: K 100 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8349 (mp0) REVERT: P 49 PHE cc_start: 0.8072 (t80) cc_final: 0.7843 (t80) REVERT: P 91 TYR cc_start: 0.8877 (t80) cc_final: 0.8652 (t80) outliers start: 68 outliers final: 44 residues processed: 385 average time/residue: 0.1611 time to fit residues: 97.3576 Evaluate side-chains 344 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 430 VAL 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 625 ASN 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 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 21 SER 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 L residue 80 VAL 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 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 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 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 99 TYR 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: 2.9990 chunk 160 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 422 GLN C 330 HIS C 344 GLN C 374 HIS J 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055014 restraints weight = 104522.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056620 restraints weight = 61727.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057644 restraints weight = 45316.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058292 restraints weight = 37625.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058663 restraints weight = 33538.333| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24689 Z= 0.265 Angle : 0.975 43.472 33828 Z= 0.432 Chirality : 0.053 0.410 4172 Planarity : 0.005 0.093 3994 Dihedral : 8.012 58.917 6200 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 3.49 % Allowed : 14.85 % Favored : 81.66 % 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: -0.32 (0.16), residues: 2731 helix: 1.41 (0.28), residues: 376 sheet: 0.13 (0.17), residues: 859 loop : -0.82 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 192 TYR 0.028 0.002 TYR G 50 PHE 0.020 0.002 PHE M 53 TRP 0.038 0.002 TRP O 34 HIS 0.010 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00593 (24493) covalent geometry : angle 0.90797 (33281) SS BOND : bond 0.00350 ( 40) SS BOND : angle 0.89752 ( 80) hydrogen bonds : bond 0.04843 ( 672) hydrogen bonds : angle 5.68807 ( 1704) link_ALPHA1-3 : bond 0.01101 ( 2) link_ALPHA1-3 : angle 3.09893 ( 6) link_ALPHA1-6 : bond 0.00432 ( 2) link_ALPHA1-6 : angle 1.64991 ( 6) link_BETA1-4 : bond 0.00941 ( 83) link_BETA1-4 : angle 3.62680 ( 249) link_BETA1-6 : bond 0.00566 ( 1) link_BETA1-6 : angle 2.05486 ( 3) link_NAG-ASN : bond 0.00405 ( 67) link_NAG-ASN : angle 2.53172 ( 201) link_NAG-THR : bond 0.00818 ( 1) link_NAG-THR : angle 3.25566 ( 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 392 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 307 time to evaluate : 0.845 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: B 530 MET cc_start: 0.8399 (mmt) cc_final: 0.8186 (mmt) REVERT: B 633 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8354 (mtm110) REVERT: B 636 ASP cc_start: 0.8081 (p0) cc_final: 0.7832 (p0) REVERT: C 69 TRP cc_start: 0.8278 (m-90) cc_final: 0.7896 (m-90) REVERT: C 98 ASN cc_start: 0.8728 (t0) cc_final: 0.8410 (t0) REVERT: E 577 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8154 (tm-30) REVERT: E 601 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8767 (mmmm) REVERT: D 269 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: F 530 MET cc_start: 0.9144 (mtm) cc_final: 0.8684 (mtm) REVERT: F 574 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8769 (mtmt) REVERT: F 577 GLN cc_start: 0.9339 (tp40) cc_final: 0.8628 (tm-30) REVERT: F 621 MET cc_start: 0.8971 (tpt) cc_final: 0.8555 (tpt) REVERT: F 625 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7330 (t160) REVERT: F 648 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8754 (mm-30) REVERT: G 64 LYS cc_start: 0.8228 (tttt) cc_final: 0.7942 (mtpp) REVERT: G 78 PHE cc_start: 0.6253 (m-80) cc_final: 0.5414 (m-80) REVERT: I 95 ASP cc_start: 0.8758 (t70) cc_final: 0.8122 (t70) REVERT: H 30 THR cc_start: 0.9655 (p) cc_final: 0.9372 (t) REVERT: L 2 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.5458 (t80) REVERT: M 29 ILE cc_start: 0.9233 (pt) cc_final: 0.9022 (pt) REVERT: M 43 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8544 (ptmt) REVERT: O 41 GLN cc_start: 0.8845 (mt0) cc_final: 0.8476 (tt0) REVERT: O 60 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: O 82 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8227 (mm-30) REVERT: J 12 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8553 (mmtm) REVERT: J 28 THR cc_start: 0.8791 (m) cc_final: 0.8429 (p) REVERT: J 30 THR cc_start: 0.9680 (p) cc_final: 0.9258 (t) REVERT: J 52 ASN cc_start: 0.9075 (t0) cc_final: 0.8424 (t0) REVERT: N 45 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8259 (mmtt) REVERT: N 93 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7547 (t0) REVERT: N 94 MET cc_start: 0.8959 (ttt) cc_final: 0.8616 (ttp) REVERT: K 72 ASP cc_start: 0.8204 (t0) cc_final: 0.7640 (t0) outliers start: 85 outliers final: 56 residues processed: 366 average time/residue: 0.1522 time to fit residues: 89.4244 Evaluate side-chains 334 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 VAL 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 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 E residue 574 LYS 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 363 GLN Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL 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 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 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 L residue 80 VAL Chi-restraints excluded: chain L residue 95 ILE 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 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 7 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 109 VAL 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 48 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 99 TYR 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 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 14 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 195 ASN A 425 ASN C 302 ASN C 344 GLN D 170 GLN F 651 ASN O 36 GLN N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.073144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057405 restraints weight = 102744.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059092 restraints weight = 59782.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060179 restraints weight = 43331.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060875 restraints weight = 35613.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061270 restraints weight = 31499.388| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5297 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= 0.136 Angle : 0.886 43.637 33828 Z= 0.385 Chirality : 0.051 0.387 4172 Planarity : 0.004 0.052 3994 Dihedral : 7.199 55.936 6198 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.79 % Allowed : 16.33 % 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: -0.16 (0.16), residues: 2731 helix: 1.79 (0.28), residues: 369 sheet: 0.20 (0.17), residues: 887 loop : -0.77 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 76 TYR 0.031 0.002 TYR G 50 PHE 0.018 0.001 PHE G 100H TRP 0.025 0.002 TRP A 69 HIS 0.014 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00291 (24493) covalent geometry : angle 0.82002 (33281) SS BOND : bond 0.00270 ( 40) SS BOND : angle 0.81842 ( 80) hydrogen bonds : bond 0.04086 ( 672) hydrogen bonds : angle 5.44341 ( 1704) link_ALPHA1-3 : bond 0.01008 ( 2) link_ALPHA1-3 : angle 3.10236 ( 6) link_ALPHA1-6 : bond 0.00511 ( 2) link_ALPHA1-6 : angle 1.47546 ( 6) link_BETA1-4 : bond 0.00947 ( 83) link_BETA1-4 : angle 3.38281 ( 249) link_BETA1-6 : bond 0.00615 ( 1) link_BETA1-6 : angle 1.88521 ( 3) link_NAG-ASN : bond 0.00459 ( 67) link_NAG-ASN : angle 2.42377 ( 201) link_NAG-THR : bond 0.00117 ( 1) link_NAG-THR : angle 1.33414 ( 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 395 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 327 time to evaluate : 0.760 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 435 TYR cc_start: 0.8661 (t80) cc_final: 0.8410 (t80) REVERT: B 621 MET cc_start: 0.8724 (tpt) cc_final: 0.8394 (tpt) REVERT: B 633 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8403 (mtm110) REVERT: C 69 TRP cc_start: 0.8256 (m-90) cc_final: 0.8005 (m-10) REVERT: C 98 ASN cc_start: 0.8644 (t0) cc_final: 0.8416 (t0) REVERT: E 577 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 269 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: D 363 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: F 530 MET cc_start: 0.9091 (mtm) cc_final: 0.8665 (ttm) REVERT: F 535 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8501 (mmt) REVERT: F 574 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8758 (mtmt) REVERT: F 621 MET cc_start: 0.9033 (tpt) cc_final: 0.8601 (tpt) REVERT: F 625 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7307 (t160) REVERT: F 648 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8804 (mm-30) REVERT: G 73 MET cc_start: 0.8896 (mmm) cc_final: 0.8571 (mmm) REVERT: I 95 ASP cc_start: 0.8667 (t70) cc_final: 0.7986 (t70) REVERT: H 30 THR cc_start: 0.9603 (p) cc_final: 0.9286 (t) REVERT: L 2 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5691 (t80) REVERT: L 23 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7582 (p) REVERT: M 29 ILE cc_start: 0.9057 (pt) cc_final: 0.8830 (pt) REVERT: M 43 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8486 (ptmt) REVERT: M 91 TYR cc_start: 0.8940 (m-80) cc_final: 0.8632 (m-80) REVERT: O 41 GLN cc_start: 0.8747 (mt0) cc_final: 0.8361 (tt0) REVERT: O 82 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8254 (mm-30) REVERT: J 28 THR cc_start: 0.8527 (m) cc_final: 0.8309 (p) REVERT: J 52 ASN cc_start: 0.8974 (t0) cc_final: 0.8355 (t0) REVERT: N 93 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7374 (t0) REVERT: N 94 MET cc_start: 0.8889 (ttt) cc_final: 0.8544 (ttp) REVERT: K 72 ASP cc_start: 0.8095 (t0) cc_final: 0.7519 (t0) REVERT: P 49 PHE cc_start: 0.8004 (t80) cc_final: 0.7741 (t80) outliers start: 68 outliers final: 47 residues processed: 370 average time/residue: 0.1555 time to fit residues: 90.9993 Evaluate side-chains 333 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 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 278 THR Chi-restraints excluded: chain C residue 330 HIS 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 269 GLU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 363 GLN Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 539 VAL 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 105 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER 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 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 17 SER Chi-restraints excluded: chain J residue 34 ILE 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 N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 99 TYR 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 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: 0.7980 chunk 66 optimal weight: 0.0670 chunk 229 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 651 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.071422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.055685 restraints weight = 105541.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057330 restraints weight = 61803.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058385 restraints weight = 45010.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059000 restraints weight = 37082.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059438 restraints weight = 33117.718| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24689 Z= 0.215 Angle : 0.911 43.500 33828 Z= 0.399 Chirality : 0.052 0.386 4172 Planarity : 0.004 0.049 3994 Dihedral : 7.209 59.750 6198 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.71 % Allowed : 17.19 % Favored : 80.10 % 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: -0.23 (0.16), residues: 2731 helix: 1.80 (0.28), residues: 366 sheet: 0.13 (0.17), residues: 859 loop : -0.81 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 94 TYR 0.027 0.002 TYR G 50 PHE 0.032 0.002 PHE G 78 TRP 0.027 0.002 TRP G 34 HIS 0.007 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00483 (24493) covalent geometry : angle 0.84750 (33281) SS BOND : bond 0.00275 ( 40) SS BOND : angle 0.93273 ( 80) hydrogen bonds : bond 0.04369 ( 672) hydrogen bonds : angle 5.47248 ( 1704) link_ALPHA1-3 : bond 0.01056 ( 2) link_ALPHA1-3 : angle 3.13260 ( 6) link_ALPHA1-6 : bond 0.00590 ( 2) link_ALPHA1-6 : angle 1.47919 ( 6) link_BETA1-4 : bond 0.00900 ( 83) link_BETA1-4 : angle 3.37747 ( 249) link_BETA1-6 : bond 0.00570 ( 1) link_BETA1-6 : angle 1.98040 ( 3) link_NAG-ASN : bond 0.00370 ( 67) link_NAG-ASN : angle 2.38001 ( 201) link_NAG-THR : bond 0.00636 ( 1) link_NAG-THR : angle 2.63770 ( 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 357 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.713 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: B 621 MET cc_start: 0.8810 (tpt) cc_final: 0.8593 (tpt) REVERT: C 69 TRP cc_start: 0.8209 (m-90) cc_final: 0.7739 (m-90) REVERT: E 530 MET cc_start: 0.8439 (mmt) cc_final: 0.8019 (mmt) REVERT: E 577 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8060 (tm-30) REVERT: E 585 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8193 (mtp-110) REVERT: D 269 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: F 530 MET cc_start: 0.9184 (mtm) cc_final: 0.8674 (mtm) REVERT: F 574 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8709 (mtmt) REVERT: F 621 MET cc_start: 0.9061 (tpt) cc_final: 0.8645 (tpt) REVERT: F 625 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7319 (t160) REVERT: G 64 LYS cc_start: 0.8142 (tttt) cc_final: 0.7776 (mtpp) REVERT: I 95 ASP cc_start: 0.8758 (t70) cc_final: 0.8074 (t70) REVERT: L 2 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.5604 (t80) REVERT: L 23 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (p) REVERT: M 43 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8511 (ptmt) REVERT: M 91 TYR cc_start: 0.9028 (m-80) cc_final: 0.8722 (m-80) REVERT: O 41 GLN cc_start: 0.8768 (mt0) cc_final: 0.8406 (tt0) REVERT: J 12 LYS cc_start: 0.8840 (mptt) cc_final: 0.8542 (mmtm) REVERT: J 52 ASN cc_start: 0.9047 (t0) cc_final: 0.8391 (t0) REVERT: J 94 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5595 (tpp-160) REVERT: J 100 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8453 (mm-30) REVERT: N 93 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7622 (t0) REVERT: N 94 MET cc_start: 0.8956 (ttt) cc_final: 0.8615 (ttp) REVERT: K 72 ASP cc_start: 0.8160 (t0) cc_final: 0.7559 (t0) REVERT: K 100 TRP cc_start: 0.7805 (t60) cc_final: 0.7605 (t-100) REVERT: P 49 PHE cc_start: 0.8148 (t80) cc_final: 0.7858 (t80) outliers start: 66 outliers final: 53 residues processed: 335 average time/residue: 0.1538 time to fit residues: 82.1753 Evaluate side-chains 329 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 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 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 528 SER 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 45 LEU Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 VAL 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 27 VAL 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 J residue 7 SER Chi-restraints excluded: chain J residue 17 SER 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 N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 99 TYR 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 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 193 optimal weight: 0.9980 chunk 221 optimal weight: 0.0050 chunk 156 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056831 restraints weight = 102567.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058505 restraints weight = 59933.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059574 restraints weight = 43511.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060203 restraints weight = 35811.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060652 restraints weight = 31977.089| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24689 Z= 0.145 Angle : 0.884 43.544 33828 Z= 0.384 Chirality : 0.050 0.377 4172 Planarity : 0.004 0.052 3994 Dihedral : 6.963 58.377 6198 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 17.77 % Favored : 79.69 % 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: -0.19 (0.16), residues: 2731 helix: 1.80 (0.28), residues: 367 sheet: 0.17 (0.17), residues: 887 loop : -0.79 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 633 TYR 0.030 0.002 TYR G 50 PHE 0.037 0.002 PHE G 78 TRP 0.032 0.002 TRP O 34 HIS 0.007 0.001 HIS O 33 Details of bonding type rmsd covalent geometry : bond 0.00321 (24493) covalent geometry : angle 0.82330 (33281) SS BOND : bond 0.00280 ( 40) SS BOND : angle 0.80380 ( 80) hydrogen bonds : bond 0.04067 ( 672) hydrogen bonds : angle 5.37842 ( 1704) link_ALPHA1-3 : bond 0.01079 ( 2) link_ALPHA1-3 : angle 3.07944 ( 6) link_ALPHA1-6 : bond 0.00592 ( 2) link_ALPHA1-6 : angle 1.42878 ( 6) link_BETA1-4 : bond 0.00919 ( 83) link_BETA1-4 : angle 3.25944 ( 249) link_BETA1-6 : bond 0.00607 ( 1) link_BETA1-6 : angle 1.92316 ( 3) link_NAG-ASN : bond 0.00396 ( 67) link_NAG-ASN : angle 2.30543 ( 201) link_NAG-THR : bond 0.00275 ( 1) link_NAG-THR : angle 1.70712 ( 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: 62 poor density : 296 time to evaluate : 0.897 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: B 621 MET cc_start: 0.8728 (tpt) cc_final: 0.8388 (tpt) REVERT: B 633 ARG cc_start: 0.8945 (mtm110) cc_final: 0.8717 (mtm110) REVERT: B 636 ASP cc_start: 0.8001 (p0) cc_final: 0.7797 (p0) REVERT: C 69 TRP cc_start: 0.8192 (m-90) cc_final: 0.7767 (m-90) REVERT: C 98 ASN cc_start: 0.8675 (t0) cc_final: 0.8406 (t0) REVERT: C 492 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8110 (mm-30) REVERT: E 530 MET cc_start: 0.8421 (mmt) cc_final: 0.8141 (mmt) REVERT: E 577 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7939 (tm-30) REVERT: E 585 ARG cc_start: 0.8384 (mtp85) cc_final: 0.8174 (mtp-110) REVERT: D 269 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: D 363 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: F 530 MET cc_start: 0.9094 (mtm) cc_final: 0.8779 (ttm) REVERT: F 574 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8737 (mtmt) REVERT: F 621 MET cc_start: 0.9066 (tpt) cc_final: 0.8666 (tpt) REVERT: F 625 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7327 (t160) REVERT: G 105 GLN cc_start: 0.9221 (pt0) cc_final: 0.8724 (pp30) REVERT: I 95 ASP cc_start: 0.8685 (t70) cc_final: 0.7980 (t70) REVERT: L 2 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5880 (t80) REVERT: L 32 LEU cc_start: 0.6609 (tt) cc_final: 0.5933 (mt) REVERT: L 49 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7487 (t80) REVERT: M 43 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8637 (ptmt) REVERT: M 91 TYR cc_start: 0.8958 (m-80) cc_final: 0.8584 (m-80) REVERT: O 41 GLN cc_start: 0.8738 (mt0) cc_final: 0.8368 (tt0) REVERT: J 12 LYS cc_start: 0.8797 (mptt) cc_final: 0.8472 (mmtm) REVERT: J 31 LYS cc_start: 0.9062 (tppp) cc_final: 0.8555 (tttt) REVERT: J 52 ASN cc_start: 0.8911 (t0) cc_final: 0.8264 (t0) REVERT: J 94 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.5483 (tpp-160) REVERT: J 100 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8491 (mm-30) REVERT: N 93 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7473 (t0) REVERT: N 94 MET cc_start: 0.8921 (ttt) cc_final: 0.8578 (ttp) REVERT: K 72 ASP cc_start: 0.8101 (t0) cc_final: 0.7550 (t0) REVERT: K 100 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8651 (mp0) outliers start: 62 outliers final: 46 residues processed: 342 average time/residue: 0.1518 time to fit residues: 83.9751 Evaluate side-chains 334 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL 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 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 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 625 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain H residue 25 SER 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 80 VAL 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 100 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 86 TYR 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 N residue 10 VAL Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 99 TYR 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 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 226 optimal weight: 0.0070 chunk 171 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 203 optimal weight: 8.9990 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055069 restraints weight = 104428.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056682 restraints weight = 61144.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057707 restraints weight = 44631.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058288 restraints weight = 36888.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058740 restraints weight = 33020.291| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24689 Z= 0.223 Angle : 0.925 43.468 33828 Z= 0.409 Chirality : 0.051 0.397 4172 Planarity : 0.004 0.048 3994 Dihedral : 7.145 58.208 6198 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.67 % Allowed : 17.64 % Favored : 79.69 % 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: 1.59 (0.28), residues: 368 sheet: 0.04 (0.17), residues: 862 loop : -0.87 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 633 TYR 0.026 0.002 TYR O 49 PHE 0.019 0.002 PHE G 78 TRP 0.041 0.002 TRP O 34 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00503 (24493) covalent geometry : angle 0.86611 (33281) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.17990 ( 80) hydrogen bonds : bond 0.04461 ( 672) hydrogen bonds : angle 5.41948 ( 1704) link_ALPHA1-3 : bond 0.01053 ( 2) link_ALPHA1-3 : angle 3.06537 ( 6) link_ALPHA1-6 : bond 0.00685 ( 2) link_ALPHA1-6 : angle 1.44929 ( 6) link_BETA1-4 : bond 0.00894 ( 83) link_BETA1-4 : angle 3.27792 ( 249) link_BETA1-6 : bond 0.00577 ( 1) link_BETA1-6 : angle 2.00904 ( 3) link_NAG-ASN : bond 0.00381 ( 67) link_NAG-ASN : angle 2.34752 ( 201) link_NAG-THR : bond 0.00710 ( 1) link_NAG-THR : angle 2.77818 ( 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 354 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.491 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: B 633 ARG cc_start: 0.8994 (mtm110) cc_final: 0.8749 (mtm110) REVERT: C 69 TRP cc_start: 0.8229 (m-90) cc_final: 0.7676 (m-90) REVERT: C 98 ASN cc_start: 0.8613 (t0) cc_final: 0.8384 (t0) REVERT: E 530 MET cc_start: 0.8583 (mmt) cc_final: 0.8312 (mmt) REVERT: E 577 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 621 MET cc_start: 0.7606 (tpp) cc_final: 0.7367 (tpp) REVERT: D 269 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: F 530 MET cc_start: 0.9146 (mtm) cc_final: 0.8655 (mtm) REVERT: F 574 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8758 (mtmt) REVERT: F 621 MET cc_start: 0.9046 (tpt) cc_final: 0.8651 (tpt) REVERT: F 625 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7337 (t160) REVERT: G 105 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8765 (pp30) REVERT: I 95 ASP cc_start: 0.8770 (t70) cc_final: 0.8088 (t70) REVERT: L 2 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5999 (t80) REVERT: L 32 LEU cc_start: 0.7064 (tt) cc_final: 0.6405 (mt) REVERT: L 49 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7698 (t80) REVERT: M 43 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8649 (ptmt) REVERT: M 91 TYR cc_start: 0.9046 (m-80) cc_final: 0.8684 (m-80) REVERT: O 41 GLN cc_start: 0.8777 (mt0) cc_final: 0.8416 (tt0) REVERT: O 82 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8326 (mm-30) REVERT: J 31 LYS cc_start: 0.9059 (tppp) cc_final: 0.8627 (pttt) REVERT: J 52 ASN cc_start: 0.9003 (t0) cc_final: 0.8352 (t0) REVERT: J 94 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6751 (tpp80) REVERT: J 100 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8512 (mm-30) REVERT: N 93 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7730 (t0) REVERT: N 94 MET cc_start: 0.8975 (ttt) cc_final: 0.8630 (ttp) REVERT: K 72 ASP cc_start: 0.8263 (t0) cc_final: 0.7591 (t0) outliers start: 65 outliers final: 50 residues processed: 332 average time/residue: 0.1513 time to fit residues: 81.1601 Evaluate side-chains 329 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL 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 C residue 36 VAL Chi-restraints excluded: chain C residue 37 THR 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 574 LYS 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 G residue 45 LEU Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR 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 80 VAL 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 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 34 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 89 VAL 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 51 ILE Chi-restraints excluded: chain K residue 99 TYR 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 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 101 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 73 optimal weight: 0.0470 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 221 optimal weight: 0.0970 chunk 54 optimal weight: 0.2980 chunk 196 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS O 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057773 restraints weight = 105044.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059466 restraints weight = 61047.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060553 restraints weight = 44138.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061242 restraints weight = 36299.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061655 restraints weight = 32138.868| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5932 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= 0.134 Angle : 0.892 43.473 33828 Z= 0.391 Chirality : 0.050 0.364 4172 Planarity : 0.004 0.054 3994 Dihedral : 6.748 59.594 6198 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.01 % Allowed : 18.30 % Favored : 79.69 % 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: -0.28 (0.16), residues: 2731 helix: 1.86 (0.28), residues: 350 sheet: -0.02 (0.16), residues: 929 loop : -0.78 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 633 TYR 0.032 0.002 TYR G 50 PHE 0.026 0.001 PHE G 78 TRP 0.064 0.002 TRP O 34 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (24493) covalent geometry : angle 0.83603 (33281) SS BOND : bond 0.00293 ( 40) SS BOND : angle 1.09991 ( 80) hydrogen bonds : bond 0.03927 ( 672) hydrogen bonds : angle 5.36500 ( 1704) link_ALPHA1-3 : bond 0.01118 ( 2) link_ALPHA1-3 : angle 3.01765 ( 6) link_ALPHA1-6 : bond 0.00739 ( 2) link_ALPHA1-6 : angle 1.45986 ( 6) link_BETA1-4 : bond 0.00918 ( 83) link_BETA1-4 : angle 3.12495 ( 249) link_BETA1-6 : bond 0.00625 ( 1) link_BETA1-6 : angle 1.90431 ( 3) link_NAG-ASN : bond 0.00460 ( 67) link_NAG-ASN : angle 2.27806 ( 201) link_NAG-THR : bond 0.00058 ( 1) link_NAG-THR : angle 1.35951 ( 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 370 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8234 (m110) cc_final: 0.7998 (p0) REVERT: C 69 TRP cc_start: 0.8171 (m-90) cc_final: 0.7771 (m-90) REVERT: E 530 MET cc_start: 0.8198 (mmt) cc_final: 0.7959 (mmt) REVERT: E 577 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7897 (tm-30) REVERT: E 621 MET cc_start: 0.7696 (tpp) cc_final: 0.7431 (tpp) REVERT: D 269 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: D 363 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: D 426 MET cc_start: 0.7528 (ttm) cc_final: 0.6716 (ttm) REVERT: D 427 TRP cc_start: 0.8196 (m100) cc_final: 0.7889 (m100) REVERT: D 479 TRP cc_start: 0.8780 (m-10) cc_final: 0.8350 (m-10) REVERT: F 530 MET cc_start: 0.9074 (mtm) cc_final: 0.8668 (ttm) REVERT: F 574 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8744 (mtmt) REVERT: F 621 MET cc_start: 0.9068 (tpt) cc_final: 0.8666 (tpt) REVERT: F 625 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7214 (t160) REVERT: G 20 LEU cc_start: 0.9065 (mm) cc_final: 0.8724 (tp) REVERT: I 25 ASN cc_start: 0.9052 (m-40) cc_final: 0.8683 (m-40) REVERT: I 95 ASP cc_start: 0.8642 (t70) cc_final: 0.7910 (t70) REVERT: L 2 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6080 (t80) REVERT: M 43 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8749 (ptmt) REVERT: O 41 GLN cc_start: 0.8755 (mt0) cc_final: 0.8436 (tt0) REVERT: O 49 TYR cc_start: 0.6035 (m-80) cc_final: 0.4425 (m-10) REVERT: O 76 ARG cc_start: 0.8924 (ptp-110) cc_final: 0.8642 (ptp90) REVERT: J 3 GLN cc_start: 0.8094 (mp10) cc_final: 0.7744 (mp10) REVERT: J 6 GLU cc_start: 0.8164 (mp0) cc_final: 0.7326 (mp0) REVERT: J 31 LYS cc_start: 0.9010 (tppp) cc_final: 0.8603 (pttt) REVERT: J 52 ASN cc_start: 0.8832 (t0) cc_final: 0.8292 (t0) REVERT: J 76 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8642 (mm-30) REVERT: J 94 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6543 (ttp80) REVERT: J 99 TYR cc_start: 0.8742 (t80) cc_final: 0.8419 (t80) REVERT: J 100 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8524 (mm-30) REVERT: N 93 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7603 (t70) REVERT: N 94 MET cc_start: 0.8838 (ttt) cc_final: 0.8527 (ttp) REVERT: K 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7561 (t0) REVERT: K 100 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8318 (mp0) outliers start: 49 outliers final: 36 residues processed: 359 average time/residue: 0.1513 time to fit residues: 86.6122 Evaluate side-chains 334 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 84 VAL 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 430 VAL Chi-restraints excluded: chain C residue 491 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 625 ASN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 86 TYR 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 M residue 20 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 109 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 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 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 246 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 chunk 90 optimal weight: 0.0770 chunk 127 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 142 optimal weight: 0.3980 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 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 = 0.072357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056755 restraints weight = 105531.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058407 restraints weight = 61640.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059446 restraints weight = 44840.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060083 restraints weight = 36992.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060528 restraints weight = 32944.467| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24689 Z= 0.154 Angle : 0.894 43.404 33828 Z= 0.395 Chirality : 0.050 0.363 4172 Planarity : 0.004 0.053 3994 Dihedral : 6.720 59.514 6198 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.97 % Allowed : 18.63 % Favored : 79.40 % 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: -0.25 (0.16), residues: 2731 helix: 1.74 (0.28), residues: 367 sheet: 0.08 (0.17), residues: 887 loop : -0.79 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 633 TYR 0.075 0.002 TYR L 30 PHE 0.016 0.001 PHE M 78 TRP 0.091 0.002 TRP O 34 HIS 0.006 0.001 HIS O 33 Details of bonding type rmsd covalent geometry : bond 0.00344 (24493) covalent geometry : angle 0.83861 (33281) SS BOND : bond 0.00282 ( 40) SS BOND : angle 0.99974 ( 80) hydrogen bonds : bond 0.03987 ( 672) hydrogen bonds : angle 5.31807 ( 1704) link_ALPHA1-3 : bond 0.01055 ( 2) link_ALPHA1-3 : angle 3.05963 ( 6) link_ALPHA1-6 : bond 0.00709 ( 2) link_ALPHA1-6 : angle 1.38790 ( 6) link_BETA1-4 : bond 0.00898 ( 83) link_BETA1-4 : angle 3.11537 ( 249) link_BETA1-6 : bond 0.00591 ( 1) link_BETA1-6 : angle 1.96589 ( 3) link_NAG-ASN : bond 0.00362 ( 67) link_NAG-ASN : angle 2.28319 ( 201) link_NAG-THR : bond 0.00434 ( 1) link_NAG-THR : angle 2.09652 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.81 seconds wall clock time: 65 minutes 44.38 seconds (3944.38 seconds total)