Starting phenix.real_space_refine on Sun Aug 24 17:48:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vy2_21456/08_2025/6vy2_21456.map" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 132 5.16 5 C 13296 2.51 5 N 3456 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3601 Classifications: {'peptide': 458} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 433} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "N" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "Q" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "0" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 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: 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: "D" 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: 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.88, per 1000 atoms: 0.23 Number of scatterers: 21426 At special positions: 0 Unit cell: (151.96, 148.48, 131.08, 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 132 16.00 O 4542 8.00 N 3456 7.00 C 13296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 C 501 " - pdb=" SG CYS D 605 " distance=1.84 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.12 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 Atom "HETATM20874 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 4 3 " - " MAN 4 4 " " MAN 4 4 " - " MAN 4 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 4 " " MAN o 4 " - " MAN o 5 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA 4 3 " - " MAN 4 6 " " MAN 4 6 " - " MAN 4 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 6 " - " MAN Y 7 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 6 " " MAN o 6 " - " MAN o 7 " " BMA w 3 " - " MAN w 4 " " MAN w 4 " - " MAN w 5 " " BMA z 3 " - " MAN z 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 G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " 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 " NAG-ASN " NAG 0 1 " - " ASN E 276 " " NAG 1 1 " - " ASN E 289 " " NAG 2 1 " - " ASN E 334 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 386 " " NAG 5 1 " - " ASN E 392 " " NAG 6 1 " - " ASN E 448 " " NAG 7 1 " - " ASN E 461 " " NAG A 608 " - " ASN A 156 " " NAG A 611 " - " ASN A 187 " " NAG A 635 " - " ASN A 301 " " NAG A 641 " - " ASN A 358 " " NAG A 652 " - " ASN A 442 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 608 " - " ASN C 156 " " NAG C 611 " - " ASN C 187 " " NAG C 635 " - " ASN C 301 " " NAG C 641 " - " ASN C 358 " " NAG C 652 " - " ASN C 442 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 608 " - " ASN E 156 " " NAG E 611 " - " ASN E 187 " " NAG E 635 " - " ASN E 301 " " NAG E 641 " - " ASN E 358 " " NAG E 652 " - " ASN E 442 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 136 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 230 " " NAG S 1 " - " ASN A 241 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 289 " " NAG W 1 " - " ASN A 334 " " NAG X 1 " - " ASN A 339 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 461 " " NAG c 1 " - " ASN C 88 " " NAG d 1 " - " ASN C 130 " " NAG e 1 " - " ASN C 136 " " NAG f 1 " - " ASN C 160 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 230 " " 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 334 " " NAG n 1 " - " ASN C 339 " " NAG o 1 " - " ASN C 386 " " NAG p 1 " - " ASN C 392 " " NAG q 1 " - " ASN C 448 " " NAG r 1 " - " ASN C 461 " " NAG s 1 " - " ASN E 88 " " NAG t 1 " - " ASN E 130 " " NAG u 1 " - " ASN E 136 " " NAG v 1 " - " ASN E 160 " " NAG w 1 " - " ASN E 197 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN E 262 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 593.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 22.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.007A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.212A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.822A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.943A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.518A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.833A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 649 removed outlier: 5.127A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'C' and resid 100 through 116 removed outlier: 4.006A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.211A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.822A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.945A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 removed outlier: 3.518A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.832A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 649 removed outlier: 5.127A pdb=" N ASN D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TYR D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 663 Processing helix chain 'E' and resid 100 through 116 removed outlier: 4.007A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.212A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.823A pdb=" N ASN E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.944A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 544 removed outlier: 3.519A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 597 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.833A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 649 removed outlier: 5.129A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 663 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.629A pdb=" N THR J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'L' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR L 27B" --> pdb=" O ILE L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 26 through 27B' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR M 27B" --> pdb=" O ILE M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 26 through 27B' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 26 through 27B removed outlier: 4.454A pdb=" N TYR N 27B" --> pdb=" O ILE N 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 26 through 27B' Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.331A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.850A 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 92 removed outlier: 3.521A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.344A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.349A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 7.010A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.077A pdb=" N ASN A 301 " --> pdb=" O VAL A 322A" (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.321A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.520A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.343A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.347A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL C 292 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS C 293 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 334 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 7.011A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N VAL C 292 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ILE C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 359 " --> pdb=" O TYR C 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.078A pdb=" N ASN C 301 " --> pdb=" O VAL C 322A" (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.217A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.792A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.520A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.344A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.348A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS E 293 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 7.010A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 359 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 312 removed outlier: 7.078A pdb=" N ASN E 301 " --> pdb=" O VAL E 322A" (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 322A" --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.504A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR H 33 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.504A pdb=" N GLY H 10 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG H 94 " --> pdb=" O LEU H 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H 100J" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU H 96 " --> pdb=" O SER H 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP H 100 " --> pdb=" O LEU H 100D" (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU H 100D" --> pdb=" O TRP H 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.234A pdb=" N TYR I 33 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.979A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG I 94 " --> pdb=" O LEU I 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU I 100J" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU I 96 " --> pdb=" O SER I 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP I 100 " --> pdb=" O LEU I 100D" (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU I 100D" --> pdb=" O TRP I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.233A pdb=" N TYR J 33 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.979A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG J 94 " --> pdb=" O LEU J 100J" (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU J 100J" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU J 96 " --> pdb=" O SER J 100H" (cutoff:3.500A) removed outlier: 5.762A pdb=" N TRP J 100 " --> pdb=" O LEU J 100D" (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU J 100D" --> pdb=" O TRP J 100 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.493A pdb=" N VAL L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.495A pdb=" N VAL M 33 " --> pdb=" O LYS M 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.496A pdb=" N VAL N 33 " --> pdb=" O LYS N 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 13 Processing sheet with id=AE9, first strand: chain 'N' and resid 19 through 24 780 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6477 1.34 - 1.46: 5754 1.46 - 1.59: 9414 1.59 - 1.71: 0 1.71 - 1.83: 186 Bond restraints: 21831 Sorted by residual: bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 NAG A 611 " pdb=" O5 NAG A 611 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C1 NAG E 611 " pdb=" O5 NAG E 611 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 21826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 27674 2.02 - 4.04: 1469 4.04 - 6.06: 389 6.06 - 8.08: 87 8.08 - 10.09: 12 Bond angle restraints: 29631 Sorted by residual: angle pdb=" N MET A 154 " pdb=" CA MET A 154 " pdb=" C MET A 154 " ideal model delta sigma weight residual 110.97 117.08 -6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N MET C 154 " pdb=" CA MET C 154 " pdb=" C MET C 154 " ideal model delta sigma weight residual 110.97 117.04 -6.07 1.09e+00 8.42e-01 3.10e+01 angle pdb=" N MET E 154 " pdb=" CA MET E 154 " pdb=" C MET E 154 " ideal model delta sigma weight residual 110.97 117.00 -6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" C ASN E 195 " pdb=" N CYS E 196 " pdb=" CA CYS E 196 " ideal model delta sigma weight residual 121.66 112.67 8.99 1.76e+00 3.23e-01 2.61e+01 angle pdb=" C ASN A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta sigma weight residual 121.66 112.69 8.97 1.76e+00 3.23e-01 2.60e+01 ... (remaining 29626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.77: 13888 23.77 - 47.55: 896 47.55 - 71.32: 204 71.32 - 95.09: 225 95.09 - 118.86: 147 Dihedral angle restraints: 15360 sinusoidal: 8337 harmonic: 7023 Sorted by residual: dihedral pdb=" CA THR E 406 " pdb=" C THR E 406 " pdb=" N GLU E 407 " pdb=" CA GLU E 407 " ideal model delta harmonic sigma weight residual 180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA THR A 406 " pdb=" C THR A 406 " pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta harmonic sigma weight residual -180.00 -125.66 -54.34 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA THR C 406 " pdb=" C THR C 406 " pdb=" N GLU C 407 " pdb=" CA GLU C 407 " ideal model delta harmonic sigma weight residual -180.00 -125.70 -54.30 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 15357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 3757 0.193 - 0.386: 54 0.386 - 0.579: 13 0.579 - 0.772: 4 0.772 - 0.965: 9 Chirality restraints: 3837 Sorted by residual: chirality pdb=" C1 NAG w 1 " pdb=" ND2 ASN E 197 " pdb=" C2 NAG w 1 " pdb=" O5 NAG w 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 618 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 3834 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 618 " -0.016 2.00e-02 2.50e+03 1.06e-01 1.40e+02 pdb=" CG ASN F 618 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN F 618 " 0.110 2.00e-02 2.50e+03 pdb=" ND2 ASN F 618 " -0.170 2.00e-02 2.50e+03 pdb=" C1 NAG F 702 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 160 " 0.077 2.00e-02 2.50e+03 8.47e-02 8.96e+01 pdb=" CG ASN E 160 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 160 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN E 160 " -0.134 2.00e-02 2.50e+03 pdb=" C1 NAG v 1 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 156 " 0.074 2.00e-02 2.50e+03 7.86e-02 7.73e+01 pdb=" CG ASN E 156 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 156 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN E 156 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG E 608 " 0.097 2.00e-02 2.50e+03 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 546 2.63 - 3.19: 20229 3.19 - 3.76: 32967 3.76 - 4.33: 44578 4.33 - 4.90: 69159 Nonbonded interactions: 167479 Sorted by model distance: nonbonded pdb=" N ASP C 185 " pdb=" OD1 ASP C 185 " model vdw 2.056 3.120 nonbonded pdb=" N ASP E 185 " pdb=" OD1 ASP E 185 " model vdw 2.058 3.120 nonbonded pdb=" N ASP A 185 " pdb=" OD1 ASP A 185 " model vdw 2.059 3.120 nonbonded pdb=" OH TYR C 384 " pdb=" OH TYR I 100A" model vdw 2.082 3.040 nonbonded pdb=" NE ARG E 393 " pdb=" O7 NAG 3 1 " model vdw 2.116 3.120 ... (remaining 167474 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: 0.03 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '5' selection = chain '6' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '7' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain '4' selection = chain 'Y' selection = chain 'o' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'S' selection = chain 'i' selection = chain 'y' } Set up NCS constraints Number of NCS constrained groups: 9 pdb_interpretation.ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '5' selection = chain '6' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'u' selection = chain 'x' } pdb_interpretation.ncs_group { reference = chain '2' selection = chain '7' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain '4' selection = chain 'Y' selection = chain 'o' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'g' selection = chain 'j' selection = chain 'w' selection = chain 'z' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 'i' selection = chain 'y' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.009 0.315 22044 Z= 0.455 Angle : 1.364 27.806 30237 Z= 0.602 Chirality : 0.081 0.965 3837 Planarity : 0.004 0.071 3516 Dihedral : 22.298 118.862 10755 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.68 % Favored : 93.82 % Rotamer: Outliers : 4.96 % Allowed : 6.89 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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 aren not related in a simple way. whole: -2.41 (0.15), residues: 2412 helix: -2.12 (0.20), residues: 393 sheet: -0.70 (0.19), residues: 672 loop : -1.94 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 469 TYR 0.015 0.002 TYR E 217 PHE 0.011 0.002 PHE E 383 TRP 0.019 0.002 TRP H 100 HIS 0.003 0.001 HIS E 355 Details of bonding type rmsd covalent geometry : bond 0.00691 (21831) covalent geometry : angle 1.11211 (29631) SS BOND : bond 0.03671 ( 33) SS BOND : angle 3.08246 ( 66) hydrogen bonds : bond 0.15341 ( 726) hydrogen bonds : angle 7.46453 ( 1977) link_ALPHA1-3 : bond 0.00783 ( 12) link_ALPHA1-3 : angle 1.98995 ( 36) link_ALPHA1-6 : bond 0.00527 ( 15) link_ALPHA1-6 : angle 1.87302 ( 45) link_BETA1-4 : bond 0.00952 ( 81) link_BETA1-4 : angle 3.63101 ( 243) link_NAG-ASN : bond 0.09895 ( 72) link_NAG-ASN : angle 8.45718 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9328 (m-30) cc_final: 0.9094 (p0) REVERT: A 108 VAL cc_start: 0.9768 (t) cc_final: 0.9326 (p) REVERT: A 193 LEU cc_start: 0.9727 (tp) cc_final: 0.9381 (tp) REVERT: A 259 LEU cc_start: 0.9363 (mt) cc_final: 0.8921 (mt) REVERT: A 368 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 426 MET cc_start: 0.8774 (mtp) cc_final: 0.8396 (ttm) REVERT: A 434 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8810 (ptp) outliers start: 21 outliers final: 3 residues processed: 79 average time/residue: 0.0572 time to fit residues: 5.5867 Evaluate side-chains 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.144 Evaluate side-chains 49 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.024 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: B 580 VAL cc_start: 0.9814 (t) cc_final: 0.9609 (m) REVERT: B 581 LEU cc_start: 0.9806 (tp) cc_final: 0.9483 (tp) REVERT: B 584 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8522 (mt-10) REVERT: B 587 LEU cc_start: 0.9680 (mm) cc_final: 0.9410 (pp) REVERT: B 639 THR cc_start: 0.8418 (p) cc_final: 0.7704 (p) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.0695 time to fit residues: 3.4508 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.042 Evaluate side-chains 43 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8903 (mmm) cc_final: 0.8682 (mmm) REVERT: H 37 LEU cc_start: 0.8421 (mp) cc_final: 0.7780 (tt) REVERT: H 51 MET cc_start: 0.9507 (ttp) cc_final: 0.9092 (tmm) REVERT: H 58 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8795 (p) REVERT: H 72 ASP cc_start: 0.9401 (t0) cc_final: 0.8782 (p0) outliers start: 7 outliers final: 1 residues processed: 40 average time/residue: 0.0457 time to fit residues: 2.0220 Evaluate side-chains 20 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.034 Evaluate side-chains 32 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 MET cc_start: 0.8184 (mmm) cc_final: 0.7761 (mmm) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.0651 time to fit residues: 2.1539 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.055502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.049723 restraints weight = 532.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.050939 restraints weight = 403.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.051981 restraints weight = 327.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.052194 restraints weight = 267.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.052202 restraints weight = 255.055| |-----------------------------------------------------------------------------| r_work (final): 0.2584 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.039248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.037599 restraints weight = 550.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.037948 restraints weight = 207.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.038215 restraints weight = 131.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.038367 restraints weight = 91.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.038371 restraints weight = 73.177| |-----------------------------------------------------------------------------| r_work (final): 0.2357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.058327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052189 restraints weight = 813.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.052972 restraints weight = 589.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.053797 restraints weight = 481.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054319 restraints weight = 384.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.054870 restraints weight = 324.306| |-----------------------------------------------------------------------------| r_work (final): 0.2851 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.035761 restraints weight = 24623.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.037257 restraints weight = 15979.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038402 restraints weight = 11530.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.039267 restraints weight = 8971.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039958 restraints weight = 7348.327| |-----------------------------------------------------------------------------| r_work (final): 0.2848 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.034840 restraints weight = 8023.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036139 restraints weight = 4718.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.037013 restraints weight = 3273.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037669 restraints weight = 2508.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038189 restraints weight = 2040.576| |-----------------------------------------------------------------------------| r_work (final): 0.2685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.031884 restraints weight = 7494.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.033247 restraints weight = 4589.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.034258 restraints weight = 3289.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.035064 restraints weight = 2563.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.035649 restraints weight = 2107.698| |-----------------------------------------------------------------------------| r_work (final): 0.2643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.038663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.030040 restraints weight = 4866.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.031542 restraints weight = 2833.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.032688 restraints weight = 1947.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.033551 restraints weight = 1449.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034095 restraints weight = 1132.947| |-----------------------------------------------------------------------------| r_work (final): 0.2586 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.050736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.048030 restraints weight = 715.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.048955 restraints weight = 276.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.049519 restraints weight = 149.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.049837 restraints weight = 92.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.050061 restraints weight = 64.332| |-----------------------------------------------------------------------------| r_work (final): 0.2662 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.046918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.040312 restraints weight = 777.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.040507 restraints weight = 572.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.040675 restraints weight = 520.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041002 restraints weight = 492.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.041037 restraints weight = 448.283| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.715 22044 Z= 0.933 Angle : 2.570 60.546 30237 Z= 0.969 Chirality : 0.116 1.681 3837 Planarity : 0.007 0.100 3516 Dihedral : 24.842 170.318 6294 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 29.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Rotamer: Outliers : 1.27 % Allowed : 4.96 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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 aren not related in a simple way. whole: -2.17 (0.15), residues: 2412 helix: -1.56 (0.23), residues: 396 sheet: -0.53 (0.19), residues: 654 loop : -1.90 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 393 TYR 0.078 0.004 TYR I 100G PHE 0.054 0.004 PHE M 32 TRP 0.050 0.003 TRP B 571 HIS 0.005 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.01239 (21831) covalent geometry : angle 2.19323 (29631) SS BOND : bond 0.08255 ( 33) SS BOND : angle 3.32564 ( 66) hydrogen bonds : bond 0.07429 ( 726) hydrogen bonds : angle 6.99642 ( 1977) link_ALPHA1-3 : bond 0.23384 ( 12) link_ALPHA1-3 : angle 9.79000 ( 36) link_ALPHA1-6 : bond 0.49657 ( 15) link_ALPHA1-6 : angle 22.97557 ( 45) link_BETA1-4 : bond 0.02862 ( 81) link_BETA1-4 : angle 4.02418 ( 243) link_NAG-ASN : bond 0.05543 ( 72) link_NAG-ASN : angle 10.82619 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4820 Ramachandran restraints generated. 2410 Oldfield, 0 Emsley, 2410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4820 Ramachandran restraints generated. 2410 Oldfield, 0 Emsley, 2410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 47 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9483 (ppp) cc_final: 0.9264 (ppp) REVERT: A 107 ASP cc_start: 0.9326 (m-30) cc_final: 0.9104 (m-30) REVERT: A 176 PHE cc_start: 0.9439 (m-80) cc_final: 0.9215 (m-80) REVERT: A 193 LEU cc_start: 0.9713 (tp) cc_final: 0.9365 (tp) REVERT: A 381 GLU cc_start: 0.9562 (mm-30) cc_final: 0.9114 (mp0) REVERT: A 383 PHE cc_start: 0.9794 (m-80) cc_final: 0.9270 (m-80) REVERT: A 421 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (ttmt) REVERT: A 434 MET cc_start: 0.9674 (ttp) cc_final: 0.9399 (ppp) REVERT: A 453 LEU cc_start: 0.9556 (tp) cc_final: 0.9207 (tp) REVERT: A 475 MET cc_start: 0.7766 (tpt) cc_final: 0.7298 (tpp) outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 0.0806 time to fit residues: 4.5649 Evaluate side-chains 34 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.086 Evaluate side-chains 33 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8923 (mtp) cc_final: 0.8347 (mmt) REVERT: B 584 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8692 (mt-10) REVERT: B 639 THR cc_start: 0.8804 (p) cc_final: 0.8398 (p) REVERT: B 643 TYR cc_start: 0.9372 (m-80) cc_final: 0.9154 (m-80) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0867 time to fit residues: 3.0196 Evaluate side-chains 24 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.023 Evaluate side-chains 28 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.024 Fit side-chains revert: symmetry clash REVERT: J 51 MET cc_start: 0.9296 (ttp) cc_final: 0.8558 (tmm) REVERT: J 80 LEU cc_start: 0.9546 (tp) cc_final: 0.9306 (tp) outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.0186 time to fit residues: 0.5903 Evaluate side-chains 19 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 Evaluate side-chains 22 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0457 time to fit residues: 1.1193 Evaluate side-chains 12 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 0.4980 chunk 172 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 176 optimal weight: 0.5980 chunk 89 optimal weight: 0.0020 chunk 22 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 374 HIS A 404 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 HIS N 60 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.044544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.038808 restraints weight = 599.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.040134 restraints weight = 428.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.041055 restraints weight = 311.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.041593 restraints weight = 234.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.042000 restraints weight = 189.613| |-----------------------------------------------------------------------------| r_work (final): 0.2575 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.044012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.041033 restraints weight = 311.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.041680 restraints weight = 187.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.042376 restraints weight = 129.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.042810 restraints weight = 80.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.043139 restraints weight = 59.283| |-----------------------------------------------------------------------------| r_work (final): 0.2237 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.059552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.056655 restraints weight = 707.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057213 restraints weight = 415.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057653 restraints weight = 293.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057868 restraints weight = 220.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058053 restraints weight = 187.377| |-----------------------------------------------------------------------------| r_work (final): 0.2978 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.047856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035121 restraints weight = 24119.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036677 restraints weight = 15540.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.037861 restraints weight = 11196.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038729 restraints weight = 8661.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039472 restraints weight = 7090.663| |-----------------------------------------------------------------------------| r_work (final): 0.2834 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.043469 restraints weight = 7856.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045009 restraints weight = 4604.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046166 restraints weight = 3138.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046988 restraints weight = 2335.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047633 restraints weight = 1849.255| |-----------------------------------------------------------------------------| r_work (final): 0.2722 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.031096 restraints weight = 6687.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.032372 restraints weight = 4284.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.033319 restraints weight = 3101.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.034109 restraints weight = 2433.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.034589 restraints weight = 2011.992| |-----------------------------------------------------------------------------| r_work (final): 0.2623 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.029641 restraints weight = 5556.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.031145 restraints weight = 3111.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.032220 restraints weight = 2104.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.033093 restraints weight = 1560.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.033714 restraints weight = 1226.737| |-----------------------------------------------------------------------------| r_work (final): 0.2530 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.051681 restraints weight = 770.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.052525 restraints weight = 311.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053015 restraints weight = 148.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.053272 restraints weight = 80.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.053413 restraints weight = 48.134| |-----------------------------------------------------------------------------| r_work (final): 0.2779 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.047765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.041075 restraints weight = 712.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.041404 restraints weight = 540.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041582 restraints weight = 484.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.041729 restraints weight = 459.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.041799 restraints weight = 438.737| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.662 22044 Z= 0.852 Angle : 2.285 49.056 30237 Z= 0.901 Chirality : 0.132 1.756 3837 Planarity : 0.009 0.110 3516 Dihedral : 23.562 169.331 6294 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.47 % Favored : 93.28 % Rotamer: Outliers : 1.13 % Allowed : 4.67 % Favored : 94.19 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 aren not related in a simple way. whole: -2.27 (0.15), residues: 2412 helix: -1.71 (0.22), residues: 393 sheet: -0.41 (0.19), residues: 621 loop : -2.03 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 61 TYR 0.064 0.006 TYR H 100A PHE 0.038 0.004 PHE L 95B TRP 0.050 0.006 TRP J 47 HIS 0.136 0.011 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.01096 (21831) covalent geometry : angle 1.85678 (29631) SS BOND : bond 0.06670 ( 33) SS BOND : angle 2.91469 ( 66) hydrogen bonds : bond 0.06833 ( 726) hydrogen bonds : angle 7.07740 ( 1977) link_ALPHA1-3 : bond 0.23818 ( 12) link_ALPHA1-3 : angle 12.20083 ( 36) link_ALPHA1-6 : bond 0.46227 ( 15) link_ALPHA1-6 : angle 21.17883 ( 45) link_BETA1-4 : bond 0.01802 ( 81) link_BETA1-4 : angle 3.57153 ( 243) link_NAG-ASN : bond 0.05886 ( 72) link_NAG-ASN : angle 11.08648 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0007 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9516 (ppp) cc_final: 0.9209 (ppp) REVERT: A 107 ASP cc_start: 0.9315 (m-30) cc_final: 0.9113 (m-30) REVERT: A 154 MET cc_start: 0.7475 (mpp) cc_final: 0.7194 (mpp) REVERT: A 176 PHE cc_start: 0.9419 (m-80) cc_final: 0.9178 (m-80) REVERT: A 193 LEU cc_start: 0.9712 (tp) cc_final: 0.9491 (tp) REVERT: A 383 PHE cc_start: 0.9786 (m-80) cc_final: 0.9350 (m-80) REVERT: A 434 MET cc_start: 0.9593 (ttp) cc_final: 0.9392 (ppp) REVERT: A 453 LEU cc_start: 0.9563 (tp) cc_final: 0.9226 (tp) REVERT: A 475 MET cc_start: 0.7802 (tpt) cc_final: 0.7241 (tpp) outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 0.0586 time to fit residues: 3.2570 Evaluate side-chains 31 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.138 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9863 (m) cc_final: 0.9646 (p) REVERT: B 584 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 639 THR cc_start: 0.8736 (p) cc_final: 0.8299 (p) REVERT: B 643 TYR cc_start: 0.9394 (m-80) cc_final: 0.9076 (m-80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0709 time to fit residues: 2.2266 Evaluate side-chains 25 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 Evaluate side-chains 28 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.041 Fit side-chains REVERT: I 37 LEU cc_start: 0.8725 (mp) cc_final: 0.8335 (tp) REVERT: I 51 MET cc_start: 0.9524 (ttp) cc_final: 0.9021 (tmm) REVERT: I 72 ASP cc_start: 0.9248 (t70) cc_final: 0.8831 (p0) REVERT: I 80 LEU cc_start: 0.9467 (tp) cc_final: 0.8987 (tp) REVERT: I 82 MET cc_start: 0.9335 (mpp) cc_final: 0.8831 (mpp) REVERT: I 100 ASP cc_start: 0.9431 (t0) cc_final: 0.9159 (m-30) REVERT: I 101 ASP cc_start: 0.7038 (t0) cc_final: 0.6793 (t0) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.0397 time to fit residues: 1.2480 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.022 Evaluate side-chains 22 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.033 Fit side-chains REVERT: N 48 MET cc_start: 0.7198 (tpt) cc_final: 0.6300 (tpp) REVERT: N 95 PHE cc_start: 0.7792 (t80) cc_final: 0.7576 (p90) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0325 time to fit residues: 0.8086 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 186 optimal weight: 50.0000 chunk 53 optimal weight: 0.0670 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 83 optimal weight: 0.4980 chunk 202 optimal weight: 6.9990 chunk 31 optimal weight: 0.0770 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.039649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.036806 restraints weight = 540.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.037893 restraints weight = 236.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.038616 restraints weight = 150.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.039406 restraints weight = 100.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.039491 restraints weight = 33.359| |-----------------------------------------------------------------------------| r_work (final): 0.2603 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.045257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.041928 restraints weight = 311.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.042656 restraints weight = 179.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2262 r_free = 0.2262 target = 0.043269 restraints weight = 121.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.043644 restraints weight = 87.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.044018 restraints weight = 63.390| |-----------------------------------------------------------------------------| r_work (final): 0.2254 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056555 restraints weight = 855.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.057272 restraints weight = 495.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057707 restraints weight = 329.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058116 restraints weight = 256.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058332 restraints weight = 196.015| |-----------------------------------------------------------------------------| r_work (final): 0.2984 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035410 restraints weight = 23972.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036936 restraints weight = 15498.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038115 restraints weight = 11222.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.039069 restraints weight = 8698.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039804 restraints weight = 7061.769| |-----------------------------------------------------------------------------| r_work (final): 0.2855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.036586 restraints weight = 9481.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.037870 restraints weight = 5542.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.038762 restraints weight = 3845.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.039409 restraints weight = 2944.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039885 restraints weight = 2399.643| |-----------------------------------------------------------------------------| r_work (final): 0.2720 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032701 restraints weight = 7013.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033903 restraints weight = 4537.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.034723 restraints weight = 3349.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.035465 restraints weight = 2667.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.036015 restraints weight = 2236.796| |-----------------------------------------------------------------------------| r_work (final): 0.2667 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.029085 restraints weight = 5666.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.030546 restraints weight = 3387.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.031699 restraints weight = 2367.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.032607 restraints weight = 1783.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.033235 restraints weight = 1393.147| |-----------------------------------------------------------------------------| r_work (final): 0.2538 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052965 restraints weight = 761.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.053618 restraints weight = 229.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.053885 restraints weight = 87.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.054021 restraints weight = 36.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.054095 restraints weight = 17.700| |-----------------------------------------------------------------------------| r_work (final): 0.2732 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.047227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.040507 restraints weight = 717.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040938 restraints weight = 552.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040971 restraints weight = 483.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040972 restraints weight = 477.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040972 restraints weight = 477.209| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.636 22044 Z= 0.849 Angle : 2.352 48.330 30237 Z= 0.933 Chirality : 0.144 2.507 3837 Planarity : 0.010 0.189 3516 Dihedral : 23.412 168.275 6294 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 30.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.42 % Allowed : 2.41 % Favored : 97.17 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 aren not related in a simple way. whole: -2.30 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 393 sheet: -0.33 (0.19), residues: 621 loop : -2.13 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG I 66 TYR 0.056 0.005 TYR L 30 PHE 0.037 0.004 PHE N 62 TRP 0.057 0.005 TRP E 96 HIS 0.022 0.004 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01140 (21831) covalent geometry : angle 1.88424 (29631) SS BOND : bond 0.07916 ( 33) SS BOND : angle 4.48395 ( 66) hydrogen bonds : bond 0.06576 ( 726) hydrogen bonds : angle 7.04215 ( 1977) link_ALPHA1-3 : bond 0.24430 ( 12) link_ALPHA1-3 : angle 11.75590 ( 36) link_ALPHA1-6 : bond 0.44832 ( 15) link_ALPHA1-6 : angle 21.19048 ( 45) link_BETA1-4 : bond 0.01731 ( 81) link_BETA1-4 : angle 3.50775 ( 243) link_NAG-ASN : bond 0.05851 ( 72) link_NAG-ASN : angle 12.28192 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 40 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9528 (ppp) cc_final: 0.9282 (ppp) REVERT: A 98 ASN cc_start: 0.8311 (p0) cc_final: 0.8105 (p0) REVERT: A 154 MET cc_start: 0.7262 (mpp) cc_final: 0.6935 (mpp) REVERT: A 193 LEU cc_start: 0.9488 (tp) cc_final: 0.9250 (tp) REVERT: A 383 PHE cc_start: 0.9776 (m-80) cc_final: 0.9342 (m-80) REVERT: A 453 LEU cc_start: 0.9564 (tp) cc_final: 0.9219 (tp) REVERT: A 475 MET cc_start: 0.7776 (tpt) cc_final: 0.7191 (tpt) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.0604 time to fit residues: 3.0842 Evaluate side-chains 27 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.089 Evaluate side-chains 28 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9837 (m) cc_final: 0.9546 (p) REVERT: B 584 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 639 THR cc_start: 0.8715 (p) cc_final: 0.8179 (p) REVERT: B 643 TYR cc_start: 0.9321 (m-80) cc_final: 0.9117 (m-80) REVERT: B 648 GLU cc_start: 0.9009 (pm20) cc_final: 0.8590 (pm20) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0562 time to fit residues: 1.6890 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.023 Evaluate side-chains 24 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.022 Fit side-chains REVERT: I 37 LEU cc_start: 0.8770 (mp) cc_final: 0.7996 (tt) REVERT: I 51 MET cc_start: 0.9560 (ttp) cc_final: 0.9000 (tmm) REVERT: I 72 ASP cc_start: 0.9254 (t70) cc_final: 0.8854 (p0) REVERT: I 80 LEU cc_start: 0.9419 (tp) cc_final: 0.8850 (tp) REVERT: I 82 MET cc_start: 0.9280 (mpp) cc_final: 0.8795 (mpp) REVERT: I 96 LEU cc_start: 0.9372 (mp) cc_final: 0.8761 (mt) REVERT: I 100 ASP cc_start: 0.9388 (t0) cc_final: 0.9165 (m-30) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.0243 time to fit residues: 0.6772 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 Evaluate side-chains 18 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.019 Fit side-chains REVERT: N 32 PHE cc_start: 0.9040 (m-10) cc_final: 0.8828 (m-10) REVERT: N 48 MET cc_start: 0.7348 (tpt) cc_final: 0.6916 (tpt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0214 time to fit residues: 0.4772 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 0.0980 chunk 63 optimal weight: 0.0570 chunk 127 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 38 optimal weight: 0.0060 chunk 227 optimal weight: 10.0000 overall best weight: 0.1328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.039650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.036875 restraints weight = 498.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.037948 restraints weight = 228.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.038655 restraints weight = 147.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.039409 restraints weight = 98.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.039493 restraints weight = 32.909| |-----------------------------------------------------------------------------| r_work (final): 0.2603 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.045257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.042012 restraints weight = 293.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.042704 restraints weight = 172.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.043441 restraints weight = 118.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.043882 restraints weight = 72.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.044216 restraints weight = 54.582| |-----------------------------------------------------------------------------| r_work (final): 0.2258 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056819 restraints weight = 723.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057490 restraints weight = 428.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057915 restraints weight = 294.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058260 restraints weight = 222.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058406 restraints weight = 178.377| |-----------------------------------------------------------------------------| r_work (final): 0.2989 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035728 restraints weight = 26666.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.037316 restraints weight = 17036.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038476 restraints weight = 12192.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.039347 restraints weight = 9477.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040007 restraints weight = 7749.856| |-----------------------------------------------------------------------------| r_work (final): 0.2837 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.036789 restraints weight = 9236.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.038025 restraints weight = 5410.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.038922 restraints weight = 3761.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.039587 restraints weight = 2876.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.040047 restraints weight = 2327.358| |-----------------------------------------------------------------------------| r_work (final): 0.2719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.042029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.032013 restraints weight = 7142.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033256 restraints weight = 4632.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.034101 restraints weight = 3427.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.034927 restraints weight = 2703.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035414 restraints weight = 2264.286| |-----------------------------------------------------------------------------| r_work (final): 0.2665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.028843 restraints weight = 5546.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.030345 restraints weight = 3349.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.031445 restraints weight = 2351.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.032369 restraints weight = 1761.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.032989 restraints weight = 1374.386| |-----------------------------------------------------------------------------| r_work (final): 0.2599 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.052976 restraints weight = 704.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.053634 restraints weight = 219.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.053887 restraints weight = 85.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.054032 restraints weight = 36.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054094 restraints weight = 17.968| |-----------------------------------------------------------------------------| r_work (final): 0.2733 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.047227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.040524 restraints weight = 706.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040850 restraints weight = 549.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.041018 restraints weight = 496.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.041281 restraints weight = 464.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.041369 restraints weight = 439.507| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.658 22044 Z= 1.584 Angle : 2.487 48.330 30237 Z= 0.997 Chirality : 0.144 2.507 3837 Planarity : 0.010 0.189 3516 Dihedral : 23.412 168.275 6294 Min Nonbonded Distance : 0.531 Molprobity Statistics. All-atom Clashscore : 39.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 aren not related in a simple way. whole: -2.30 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 393 sheet: -0.33 (0.19), residues: 621 loop : -2.13 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG J 66 TYR 0.056 0.005 TYR M 30 PHE 0.037 0.004 PHE L 62 TRP 0.057 0.005 TRP A 96 HIS 0.022 0.004 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01140 (21831) covalent geometry : angle 1.88424 (29631) SS BOND : bond 0.60368 ( 33) SS BOND : angle 14.91891 ( 66) hydrogen bonds : bond 0.06575 ( 726) hydrogen bonds : angle 7.04215 ( 1977) link_ALPHA1-3 : bond 0.24430 ( 12) link_ALPHA1-3 : angle 11.75588 ( 36) link_ALPHA1-6 : bond 0.44832 ( 15) link_ALPHA1-6 : angle 21.19046 ( 45) link_BETA1-4 : bond 0.01731 ( 81) link_BETA1-4 : angle 3.50771 ( 243) link_NAG-ASN : bond 0.24142 ( 72) link_NAG-ASN : angle 13.41949 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 35 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9527 (ppp) cc_final: 0.9281 (ppp) REVERT: A 98 ASN cc_start: 0.8235 (p0) cc_final: 0.8006 (p0) REVERT: A 193 LEU cc_start: 0.9422 (tp) cc_final: 0.9199 (tp) REVERT: A 383 PHE cc_start: 0.9772 (m-80) cc_final: 0.9333 (m-80) REVERT: A 453 LEU cc_start: 0.9544 (tp) cc_final: 0.9198 (tp) REVERT: A 475 MET cc_start: 0.7751 (tpt) cc_final: 0.7175 (tpt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0461 time to fit residues: 2.3063 Evaluate side-chains 28 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.098 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9839 (m) cc_final: 0.9579 (p) REVERT: B 584 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8751 (mt-10) REVERT: B 639 THR cc_start: 0.8718 (p) cc_final: 0.8192 (p) REVERT: B 648 GLU cc_start: 0.9011 (pm20) cc_final: 0.8594 (pm20) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0652 time to fit residues: 2.0948 Evaluate side-chains 25 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.040 Evaluate side-chains 22 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.037 Fit side-chains REVERT: I 37 LEU cc_start: 0.8765 (mp) cc_final: 0.7992 (tt) REVERT: I 51 MET cc_start: 0.9562 (ttp) cc_final: 0.8997 (tmm) REVERT: I 72 ASP cc_start: 0.9237 (t70) cc_final: 0.8837 (p0) REVERT: I 80 LEU cc_start: 0.9431 (tp) cc_final: 0.8868 (tp) REVERT: I 82 MET cc_start: 0.9300 (mpp) cc_final: 0.8801 (mpp) REVERT: I 100 ASP cc_start: 0.9399 (t0) cc_final: 0.9169 (m-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0265 time to fit residues: 0.7281 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.041 Evaluate side-chains 17 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains REVERT: N 48 MET cc_start: 0.7371 (tpt) cc_final: 0.6943 (tpt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0218 time to fit residues: 0.4733 Evaluate side-chains 10 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 129 optimal weight: 0.0370 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.039650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.037016 restraints weight = 450.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.037937 restraints weight = 217.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.038692 restraints weight = 147.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.039407 restraints weight = 95.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.039490 restraints weight = 33.461| |-----------------------------------------------------------------------------| r_work (final): 0.2603 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.045257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.042025 restraints weight = 289.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.042718 restraints weight = 171.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.043442 restraints weight = 118.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.043913 restraints weight = 72.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.044214 restraints weight = 52.541| |-----------------------------------------------------------------------------| r_work (final): 0.2258 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056672 restraints weight = 745.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.057371 restraints weight = 456.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057812 restraints weight = 314.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058187 restraints weight = 240.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058415 restraints weight = 188.230| |-----------------------------------------------------------------------------| r_work (final): 0.2991 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.035275 restraints weight = 26231.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036729 restraints weight = 17010.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037853 restraints weight = 12376.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.038707 restraints weight = 9646.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039381 restraints weight = 7912.860| |-----------------------------------------------------------------------------| r_work (final): 0.2823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.036487 restraints weight = 9556.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.037775 restraints weight = 5523.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038672 restraints weight = 3797.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.039306 restraints weight = 2888.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.039774 restraints weight = 2347.672| |-----------------------------------------------------------------------------| r_work (final): 0.2716 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.041721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032557 restraints weight = 7600.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.033802 restraints weight = 4734.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.034657 restraints weight = 3398.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.035400 restraints weight = 2679.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035905 restraints weight = 2190.805| |-----------------------------------------------------------------------------| r_work (final): 0.2660 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.038177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.029229 restraints weight = 5358.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.030786 restraints weight = 3114.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.031980 restraints weight = 2110.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.032873 restraints weight = 1538.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.033528 restraints weight = 1180.443| |-----------------------------------------------------------------------------| r_work (final): 0.2609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.053059 restraints weight = 660.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053671 restraints weight = 204.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053910 restraints weight = 78.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054040 restraints weight = 34.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.054100 restraints weight = 17.363| |-----------------------------------------------------------------------------| r_work (final): 0.2732 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.047227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.040471 restraints weight = 728.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.040890 restraints weight = 557.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040950 restraints weight = 491.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040950 restraints weight = 479.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040950 restraints weight = 479.084| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.658 22044 Z= 1.584 Angle : 2.487 48.330 30237 Z= 0.997 Chirality : 0.144 2.507 3837 Planarity : 0.010 0.189 3516 Dihedral : 23.412 168.275 6294 Min Nonbonded Distance : 0.531 Molprobity Statistics. All-atom Clashscore : 39.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 aren not related in a simple way. whole: -2.30 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 393 sheet: -0.33 (0.19), residues: 621 loop : -2.13 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG H 66 TYR 0.056 0.005 TYR M 30 PHE 0.037 0.004 PHE N 62 TRP 0.057 0.005 TRP C 96 HIS 0.022 0.004 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01140 (21831) covalent geometry : angle 1.88424 (29631) SS BOND : bond 0.60368 ( 33) SS BOND : angle 14.91890 ( 66) hydrogen bonds : bond 0.06575 ( 726) hydrogen bonds : angle 7.04215 ( 1977) link_ALPHA1-3 : bond 0.24430 ( 12) link_ALPHA1-3 : angle 11.75588 ( 36) link_ALPHA1-6 : bond 0.44832 ( 15) link_ALPHA1-6 : angle 21.19046 ( 45) link_BETA1-4 : bond 0.01731 ( 81) link_BETA1-4 : angle 3.50771 ( 243) link_NAG-ASN : bond 0.24142 ( 72) link_NAG-ASN : angle 13.41948 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 34 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9526 (ppp) cc_final: 0.9280 (ppp) REVERT: A 98 ASN cc_start: 0.8280 (p0) cc_final: 0.7998 (p0) REVERT: A 193 LEU cc_start: 0.9426 (tp) cc_final: 0.9204 (tp) REVERT: A 383 PHE cc_start: 0.9772 (m-80) cc_final: 0.9336 (m-80) REVERT: A 453 LEU cc_start: 0.9545 (tp) cc_final: 0.9198 (tp) REVERT: A 475 MET cc_start: 0.7767 (tpt) cc_final: 0.7179 (tpt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0386 time to fit residues: 1.8277 Evaluate side-chains 27 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.090 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9852 (m) cc_final: 0.9548 (p) REVERT: B 584 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 639 THR cc_start: 0.8711 (p) cc_final: 0.8191 (p) REVERT: B 648 GLU cc_start: 0.9009 (pm20) cc_final: 0.8592 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0624 time to fit residues: 1.9375 Evaluate side-chains 25 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.024 Evaluate side-chains 22 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.027 Fit side-chains REVERT: I 37 LEU cc_start: 0.8755 (mp) cc_final: 0.7983 (tt) REVERT: I 51 MET cc_start: 0.9553 (ttp) cc_final: 0.8992 (tmm) REVERT: I 72 ASP cc_start: 0.9226 (t70) cc_final: 0.8829 (p0) REVERT: I 80 LEU cc_start: 0.9432 (tp) cc_final: 0.8854 (tp) REVERT: I 82 MET cc_start: 0.9302 (mpp) cc_final: 0.8796 (mpp) REVERT: I 100 ASP cc_start: 0.9404 (t0) cc_final: 0.9162 (m-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0168 time to fit residues: 0.4649 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 Evaluate side-chains 16 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.019 Fit side-chains REVERT: N 48 MET cc_start: 0.7357 (tpt) cc_final: 0.6922 (tpt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0204 time to fit residues: 0.4085 Evaluate side-chains 10 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 115 optimal weight: 0.0570 chunk 21 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 158 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 overall best weight: 0.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.039650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.036846 restraints weight = 517.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.037929 restraints weight = 232.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.038649 restraints weight = 148.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.039405 restraints weight = 98.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.039493 restraints weight = 33.220| |-----------------------------------------------------------------------------| r_work (final): 0.2603 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.045257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.042201 restraints weight = 265.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.042893 restraints weight = 157.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2262 r_free = 0.2262 target = 0.043556 restraints weight = 107.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.044062 restraints weight = 67.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.044347 restraints weight = 45.657| |-----------------------------------------------------------------------------| r_work (final): 0.2260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.056672 restraints weight = 745.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.057371 restraints weight = 456.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057812 restraints weight = 314.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058185 restraints weight = 240.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058412 restraints weight = 188.279| |-----------------------------------------------------------------------------| r_work (final): 0.2991 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035105 restraints weight = 25582.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036575 restraints weight = 16792.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037661 restraints weight = 12234.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038515 restraints weight = 9617.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.039208 restraints weight = 7895.139| |-----------------------------------------------------------------------------| r_work (final): 0.2821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.036469 restraints weight = 9647.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.037764 restraints weight = 5551.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038669 restraints weight = 3812.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.039300 restraints weight = 2894.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.039763 restraints weight = 2351.676| |-----------------------------------------------------------------------------| r_work (final): 0.2716 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.041721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.032707 restraints weight = 7155.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.033914 restraints weight = 4541.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034820 restraints weight = 3294.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.035511 restraints weight = 2577.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.036005 restraints weight = 2121.057| |-----------------------------------------------------------------------------| r_work (final): 0.2664 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.038566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.028897 restraints weight = 5522.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.030426 restraints weight = 3453.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.031546 restraints weight = 2445.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.032497 restraints weight = 1882.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.033193 restraints weight = 1464.916| |-----------------------------------------------------------------------------| r_work (final): 0.2589 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.053066 restraints weight = 629.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.053663 restraints weight = 202.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053909 restraints weight = 79.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054043 restraints weight = 34.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054109 restraints weight = 17.322| |-----------------------------------------------------------------------------| r_work (final): 0.2732 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.047227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.040485 restraints weight = 700.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040946 restraints weight = 550.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040946 restraints weight = 482.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040946 restraints weight = 482.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040946 restraints weight = 482.269| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.658 22044 Z= 1.584 Angle : 2.487 48.330 30237 Z= 0.997 Chirality : 0.144 2.507 3837 Planarity : 0.010 0.189 3516 Dihedral : 23.412 168.275 6294 Min Nonbonded Distance : 0.531 Molprobity Statistics. All-atom Clashscore : 40.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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 aren not related in a simple way. whole: -2.30 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 393 sheet: -0.33 (0.19), residues: 621 loop : -2.13 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG J 66 TYR 0.056 0.005 TYR M 30 PHE 0.037 0.004 PHE M 62 TRP 0.057 0.005 TRP C 96 HIS 0.022 0.004 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01140 (21831) covalent geometry : angle 1.88424 (29631) SS BOND : bond 0.60368 ( 33) SS BOND : angle 14.91890 ( 66) hydrogen bonds : bond 0.06575 ( 726) hydrogen bonds : angle 7.04215 ( 1977) link_ALPHA1-3 : bond 0.24430 ( 12) link_ALPHA1-3 : angle 11.75588 ( 36) link_ALPHA1-6 : bond 0.44832 ( 15) link_ALPHA1-6 : angle 21.19046 ( 45) link_BETA1-4 : bond 0.01731 ( 81) link_BETA1-4 : angle 3.50771 ( 243) link_NAG-ASN : bond 0.24142 ( 72) link_NAG-ASN : angle 13.41948 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 33 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9527 (ppp) cc_final: 0.9271 (ppp) REVERT: A 98 ASN cc_start: 0.8232 (p0) cc_final: 0.8007 (p0) REVERT: A 193 LEU cc_start: 0.9428 (tp) cc_final: 0.9206 (tp) REVERT: A 383 PHE cc_start: 0.9774 (m-80) cc_final: 0.9335 (m-80) REVERT: A 453 LEU cc_start: 0.9550 (tp) cc_final: 0.9203 (tp) REVERT: A 475 MET cc_start: 0.7772 (tpt) cc_final: 0.7187 (tpt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0299 time to fit residues: 1.4596 Evaluate side-chains 27 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.101 Evaluate side-chains 29 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9852 (m) cc_final: 0.9548 (p) REVERT: B 584 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 639 THR cc_start: 0.8713 (p) cc_final: 0.8191 (p) REVERT: B 648 GLU cc_start: 0.9008 (pm20) cc_final: 0.8591 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0550 time to fit residues: 1.7353 Evaluate side-chains 25 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.023 Evaluate side-chains 22 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.025 Fit side-chains REVERT: I 37 LEU cc_start: 0.8753 (mp) cc_final: 0.7981 (tt) REVERT: I 51 MET cc_start: 0.9551 (ttp) cc_final: 0.8992 (tmm) REVERT: I 72 ASP cc_start: 0.9223 (t70) cc_final: 0.8826 (p0) REVERT: I 80 LEU cc_start: 0.9432 (tp) cc_final: 0.8854 (tp) REVERT: I 82 MET cc_start: 0.9302 (mpp) cc_final: 0.8797 (mpp) REVERT: I 100 ASP cc_start: 0.9406 (t0) cc_final: 0.9163 (m-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0252 time to fit residues: 0.6945 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.023 Evaluate side-chains 16 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.020 Fit side-chains REVERT: N 48 MET cc_start: 0.7327 (tpt) cc_final: 0.6898 (tpt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0180 time to fit residues: 0.3651 Evaluate side-chains 9 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 0.1980 chunk 196 optimal weight: 0.3980 chunk 7 optimal weight: 0.0070 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 137 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 204 optimal weight: 0.0980 chunk 149 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.039013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.036578 restraints weight = 647.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.037667 restraints weight = 242.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.038765 restraints weight = 147.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.038927 restraints weight = 48.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.038980 restraints weight = 11.274| |-----------------------------------------------------------------------------| r_work (final): 0.2565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.044593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.041831 restraints weight = 252.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.042434 restraints weight = 158.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.043052 restraints weight = 109.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.043400 restraints weight = 69.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.043723 restraints weight = 51.956| |-----------------------------------------------------------------------------| r_work (final): 0.2239 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057199 restraints weight = 705.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057837 restraints weight = 467.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058307 restraints weight = 331.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058612 restraints weight = 250.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058797 restraints weight = 205.232| |-----------------------------------------------------------------------------| r_work (final): 0.2989 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.047417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.034784 restraints weight = 24633.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.036263 restraints weight = 16197.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037401 restraints weight = 11800.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.038267 restraints weight = 9199.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.038866 restraints weight = 7553.548| |-----------------------------------------------------------------------------| r_work (final): 0.2825 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.036480 restraints weight = 9164.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037631 restraints weight = 5410.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.038499 restraints weight = 3876.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.039126 restraints weight = 3005.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039570 restraints weight = 2465.125| |-----------------------------------------------------------------------------| r_work (final): 0.2710 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.032112 restraints weight = 6893.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033381 restraints weight = 4340.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.034344 restraints weight = 3143.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.035082 restraints weight = 2454.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035759 restraints weight = 1986.108| |-----------------------------------------------------------------------------| r_work (final): 0.2655 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.038692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.029483 restraints weight = 5391.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.031068 restraints weight = 3117.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.032326 restraints weight = 2099.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.033231 restraints weight = 1530.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.033822 restraints weight = 1189.137| |-----------------------------------------------------------------------------| r_work (final): 0.2582 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.052112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.051066 restraints weight = 627.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.051582 restraints weight = 201.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.051816 restraints weight = 90.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.051962 restraints weight = 40.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.052047 restraints weight = 18.555| |-----------------------------------------------------------------------------| r_work (final): 0.2673 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040560 restraints weight = 782.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.040933 restraints weight = 524.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.041359 restraints weight = 465.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.041459 restraints weight = 414.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041607 restraints weight = 393.328| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.619 22044 Z= 0.851 Angle : 2.280 46.468 30237 Z= 0.916 Chirality : 0.145 2.710 3837 Planarity : 0.010 0.134 3516 Dihedral : 23.075 167.461 6294 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 30.85 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.21 % Favored : 92.29 % Rotamer: Outliers : 0.28 % Allowed : 1.84 % Favored : 97.88 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 3.12 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.15), residues: 2412 helix: -1.88 (0.22), residues: 393 sheet: -0.23 (0.19), residues: 615 loop : -2.19 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 308 TYR 0.060 0.005 TYR J 100A PHE 0.036 0.004 PHE L 32 TRP 0.055 0.005 TRP A 96 HIS 0.021 0.003 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.01202 (21831) covalent geometry : angle 1.82464 (29631) SS BOND : bond 0.06611 ( 33) SS BOND : angle 5.10624 ( 66) hydrogen bonds : bond 0.06452 ( 726) hydrogen bonds : angle 7.05119 ( 1977) link_ALPHA1-3 : bond 0.23984 ( 12) link_ALPHA1-3 : angle 11.58406 ( 36) link_ALPHA1-6 : bond 0.44010 ( 15) link_ALPHA1-6 : angle 21.06204 ( 45) link_BETA1-4 : bond 0.01591 ( 81) link_BETA1-4 : angle 3.26517 ( 243) link_NAG-ASN : bond 0.05619 ( 72) link_NAG-ASN : angle 11.68164 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 37 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9557 (ppp) cc_final: 0.9281 (ppp) REVERT: A 98 ASN cc_start: 0.8238 (p0) cc_final: 0.7920 (p0) REVERT: A 193 LEU cc_start: 0.9444 (tp) cc_final: 0.9179 (tp) REVERT: A 383 PHE cc_start: 0.9782 (m-80) cc_final: 0.9345 (m-80) REVERT: A 425 ASN cc_start: 0.5210 (OUTLIER) cc_final: 0.3906 (t0) REVERT: A 453 LEU cc_start: 0.9609 (tp) cc_final: 0.9282 (tp) REVERT: A 475 MET cc_start: 0.7690 (tpt) cc_final: 0.7121 (tpt) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0359 time to fit residues: 1.9489 Evaluate side-chains 32 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.101 Evaluate side-chains 30 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8254 (mtt) cc_final: 0.7997 (mmm) REVERT: B 580 VAL cc_start: 0.9850 (m) cc_final: 0.9567 (p) REVERT: B 584 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8694 (mt-10) REVERT: B 639 THR cc_start: 0.8695 (p) cc_final: 0.8194 (p) REVERT: B 648 GLU cc_start: 0.9030 (pm20) cc_final: 0.8607 (pm20) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0772 time to fit residues: 2.4698 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.030 Evaluate side-chains 23 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.023 Fit side-chains revert: symmetry clash REVERT: I 37 LEU cc_start: 0.8727 (mp) cc_final: 0.8105 (tt) REVERT: I 51 MET cc_start: 0.9551 (ttp) cc_final: 0.8980 (tmm) REVERT: I 80 LEU cc_start: 0.9433 (tp) cc_final: 0.8945 (tp) REVERT: I 82 MET cc_start: 0.9269 (mpp) cc_final: 0.8751 (mpp) REVERT: I 100 ASP cc_start: 0.9390 (t0) cc_final: 0.9147 (m-30) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.0208 time to fit residues: 0.6043 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.034 Evaluate side-chains 19 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.022 Fit side-chains REVERT: N 48 MET cc_start: 0.7591 (tpt) cc_final: 0.6472 (tpp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0390 time to fit residues: 0.8517 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 40 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.039013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.036650 restraints weight = 595.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.037710 restraints weight = 234.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.038769 restraints weight = 144.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.038934 restraints weight = 47.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.038981 restraints weight = 10.486| |-----------------------------------------------------------------------------| r_work (final): 0.2565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.044593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.041621 restraints weight = 291.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.042246 restraints weight = 176.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.042806 restraints weight = 122.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.043289 restraints weight = 88.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.043594 restraints weight = 57.266| |-----------------------------------------------------------------------------| r_work (final): 0.2236 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053838 restraints weight = 722.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054835 restraints weight = 456.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055570 restraints weight = 311.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.056058 restraints weight = 224.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056326 restraints weight = 171.768| |-----------------------------------------------------------------------------| r_work (final): 0.2942 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.047683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.034992 restraints weight = 25121.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.036504 restraints weight = 16196.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.037680 restraints weight = 11688.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038565 restraints weight = 9018.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.039259 restraints weight = 7344.125| |-----------------------------------------------------------------------------| r_work (final): 0.2829 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.036869 restraints weight = 9373.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.038066 restraints weight = 5559.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038886 restraints weight = 3881.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.039522 restraints weight = 3003.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.039951 restraints weight = 2461.849| |-----------------------------------------------------------------------------| r_work (final): 0.2738 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.032467 restraints weight = 7279.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.033726 restraints weight = 4573.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.034616 restraints weight = 3317.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.035345 restraints weight = 2603.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.035847 restraints weight = 2153.532| |-----------------------------------------------------------------------------| r_work (final): 0.2661 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.039044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.029893 restraints weight = 5403.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.031457 restraints weight = 3219.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.032602 restraints weight = 2199.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.033526 restraints weight = 1622.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.034182 restraints weight = 1266.803| |-----------------------------------------------------------------------------| r_work (final): 0.2586 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.052112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051023 restraints weight = 669.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.051570 restraints weight = 215.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.051814 restraints weight = 89.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.051962 restraints weight = 39.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.052037 restraints weight = 18.080| |-----------------------------------------------------------------------------| r_work (final): 0.2672 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040606 restraints weight = 688.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.040980 restraints weight = 515.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.041367 restraints weight = 458.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.041500 restraints weight = 409.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041605 restraints weight = 388.950| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.619 22044 Z= 0.927 Angle : 2.336 46.468 30237 Z= 0.936 Chirality : 0.149 2.710 3837 Planarity : 0.010 0.134 3516 Dihedral : 23.075 167.461 6294 Min Nonbonded Distance : 0.345 Molprobity Statistics. All-atom Clashscore : 36.97 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.21 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 3.12 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.15), residues: 2412 helix: -1.88 (0.22), residues: 393 sheet: -0.23 (0.19), residues: 615 loop : -2.19 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 308 TYR 0.060 0.005 TYR H 100A PHE 0.036 0.004 PHE L 32 TRP 0.055 0.005 TRP E 96 HIS 0.021 0.003 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.01202 (21831) covalent geometry : angle 1.82464 (29631) SS BOND : bond 0.12827 ( 33) SS BOND : angle 7.37039 ( 66) hydrogen bonds : bond 0.06452 ( 726) hydrogen bonds : angle 7.05119 ( 1977) link_ALPHA1-3 : bond 0.23984 ( 12) link_ALPHA1-3 : angle 11.58406 ( 36) link_ALPHA1-6 : bond 0.44010 ( 15) link_ALPHA1-6 : angle 21.06204 ( 45) link_BETA1-4 : bond 0.01591 ( 81) link_BETA1-4 : angle 3.26517 ( 243) link_NAG-ASN : bond 0.11901 ( 72) link_NAG-ASN : angle 12.80493 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 34 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9564 (ppp) cc_final: 0.9289 (ppp) REVERT: A 98 ASN cc_start: 0.8224 (p0) cc_final: 0.7896 (p0) REVERT: A 193 LEU cc_start: 0.9443 (tp) cc_final: 0.9202 (tp) REVERT: A 383 PHE cc_start: 0.9785 (m-80) cc_final: 0.9348 (m-80) REVERT: A 453 LEU cc_start: 0.9615 (tp) cc_final: 0.9286 (tp) REVERT: A 475 MET cc_start: 0.7705 (tpt) cc_final: 0.7133 (tpt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0272 time to fit residues: 1.3741 Evaluate side-chains 30 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.086 Evaluate side-chains 28 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8276 (mtt) cc_final: 0.8066 (mmm) REVERT: B 580 VAL cc_start: 0.9846 (m) cc_final: 0.9557 (p) REVERT: B 584 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8693 (mt-10) REVERT: B 639 THR cc_start: 0.8680 (p) cc_final: 0.8198 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0775 time to fit residues: 2.3415 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.039 Evaluate side-chains 22 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.039 Fit side-chains REVERT: I 37 LEU cc_start: 0.8738 (mp) cc_final: 0.8094 (tt) REVERT: I 51 MET cc_start: 0.9557 (ttp) cc_final: 0.8984 (tmm) REVERT: I 80 LEU cc_start: 0.9422 (tp) cc_final: 0.8914 (tp) REVERT: I 82 MET cc_start: 0.9284 (mpp) cc_final: 0.8744 (mpp) REVERT: I 100 ASP cc_start: 0.9375 (t0) cc_final: 0.9151 (m-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0210 time to fit residues: 0.5645 Evaluate side-chains 17 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.027 Evaluate side-chains 18 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.026 Fit side-chains REVERT: N 48 MET cc_start: 0.7413 (tpt) cc_final: 0.6322 (tpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0289 time to fit residues: 0.6130 Evaluate side-chains 11 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 152 optimal weight: 0.1980 chunk 123 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 0.0270 chunk 215 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.040589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.037248 restraints weight = 505.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.038607 restraints weight = 262.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.039456 restraints weight = 152.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.039967 restraints weight = 86.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.040195 restraints weight = 47.149| |-----------------------------------------------------------------------------| r_work (final): 0.2656 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.045439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.042015 restraints weight = 245.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.042665 restraints weight = 134.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.043291 restraints weight = 95.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.043620 restraints weight = 62.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.043936 restraints weight = 49.145| |-----------------------------------------------------------------------------| r_work (final): 0.2244 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057899 restraints weight = 710.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058591 restraints weight = 487.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059025 restraints weight = 376.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059408 restraints weight = 282.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.059730 restraints weight = 227.751| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.035206 restraints weight = 24774.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036679 restraints weight = 16252.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037831 restraints weight = 11863.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038704 restraints weight = 9217.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039307 restraints weight = 7554.271| |-----------------------------------------------------------------------------| r_work (final): 0.2834 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036630 restraints weight = 9167.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.037792 restraints weight = 5321.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038686 restraints weight = 3751.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.039287 restraints weight = 2870.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.039734 restraints weight = 2361.290| |-----------------------------------------------------------------------------| r_work (final): 0.2721 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.032560 restraints weight = 7341.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.033859 restraints weight = 4493.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.034675 restraints weight = 3190.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.035483 restraints weight = 2508.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.035996 restraints weight = 2025.985| |-----------------------------------------------------------------------------| r_work (final): 0.2650 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.029731 restraints weight = 4878.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.031323 restraints weight = 2869.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.032467 restraints weight = 1938.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.033357 restraints weight = 1418.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033996 restraints weight = 1094.723| |-----------------------------------------------------------------------------| r_work (final): 0.2591 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.053081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.051548 restraints weight = 700.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.052063 restraints weight = 274.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.052389 restraints weight = 146.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.052517 restraints weight = 89.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.052625 restraints weight = 66.252| |-----------------------------------------------------------------------------| r_work (final): 0.2643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.047188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040533 restraints weight = 780.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040843 restraints weight = 512.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.041067 restraints weight = 454.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.041429 restraints weight = 423.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.041477 restraints weight = 389.867| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.606 22044 Z= 0.751 Angle : 2.116 46.119 30237 Z= 0.850 Chirality : 0.140 2.658 3837 Planarity : 0.008 0.097 3516 Dihedral : 22.151 166.326 6294 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.96 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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 aren not related in a simple way. whole: -2.42 (0.15), residues: 2412 helix: -1.80 (0.23), residues: 393 sheet: -0.47 (0.19), residues: 630 loop : -2.17 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 327 TYR 0.053 0.004 TYR I 100A PHE 0.108 0.006 PHE L 95B TRP 0.056 0.004 TRP A 96 HIS 0.023 0.003 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00836 (21831) covalent geometry : angle 1.67141 (29631) SS BOND : bond 0.06579 ( 33) SS BOND : angle 3.46187 ( 66) hydrogen bonds : bond 0.05917 ( 726) hydrogen bonds : angle 6.90686 ( 1977) link_ALPHA1-3 : bond 0.23790 ( 12) link_ALPHA1-3 : angle 11.64016 ( 36) link_ALPHA1-6 : bond 0.42507 ( 15) link_ALPHA1-6 : angle 20.89831 ( 45) link_BETA1-4 : bond 0.01150 ( 81) link_BETA1-4 : angle 3.07071 ( 243) link_NAG-ASN : bond 0.05576 ( 72) link_NAG-ASN : angle 10.74531 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 38 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9323 (mt) cc_final: 0.9081 (mp) REVERT: A 95 MET cc_start: 0.9530 (ppp) cc_final: 0.9193 (ppp) REVERT: A 98 ASN cc_start: 0.8253 (p0) cc_final: 0.7974 (p0) REVERT: A 193 LEU cc_start: 0.9501 (tp) cc_final: 0.9235 (tp) REVERT: A 383 PHE cc_start: 0.9736 (m-80) cc_final: 0.9272 (m-80) REVERT: A 453 LEU cc_start: 0.9590 (tp) cc_final: 0.9300 (tp) REVERT: A 475 MET cc_start: 0.7666 (tpt) cc_final: 0.7238 (tpt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0397 time to fit residues: 2.1957 Evaluate side-chains 30 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.193 Evaluate side-chains 31 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8535 (mtt) cc_final: 0.8109 (mmm) REVERT: B 580 VAL cc_start: 0.9842 (m) cc_final: 0.9555 (p) REVERT: B 581 LEU cc_start: 0.9869 (mt) cc_final: 0.9574 (mm) REVERT: B 584 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 587 LEU cc_start: 0.9880 (mm) cc_final: 0.9656 (pp) REVERT: B 639 THR cc_start: 0.8701 (p) cc_final: 0.8185 (p) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0662 time to fit residues: 2.2009 Evaluate side-chains 27 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.038 Evaluate side-chains 24 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.039 Fit side-chains REVERT: I 37 LEU cc_start: 0.8757 (mp) cc_final: 0.8082 (tt) REVERT: I 51 MET cc_start: 0.9557 (ttp) cc_final: 0.8964 (tmm) REVERT: I 80 LEU cc_start: 0.9458 (tp) cc_final: 0.9005 (tp) REVERT: I 82 MET cc_start: 0.9330 (mpp) cc_final: 0.8796 (mpp) REVERT: I 100 ASP cc_start: 0.9326 (t0) cc_final: 0.9117 (m-30) REVERT: I 101 ASP cc_start: 0.6628 (p0) cc_final: 0.6421 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0204 time to fit residues: 0.6222 Evaluate side-chains 18 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.039 Evaluate side-chains 20 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.032 Fit side-chains REVERT: N 48 MET cc_start: 0.7746 (tpt) cc_final: 0.6439 (tpp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0380 time to fit residues: 0.8776 Evaluate side-chains 13 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0827 > 50: distance: 1 - 2: 13.353 distance: 2 - 3: 10.850 distance: 2 - 5: 10.417 distance: 3 - 4: 18.375 distance: 3 - 7: 6.164 distance: 5 - 6: 7.831 distance: 7 - 8: 7.201 distance: 8 - 9: 7.483 distance: 8 - 11: 6.485 distance: 9 - 10: 9.376 distance: 9 - 14: 17.902 distance: 11 - 12: 7.463 distance: 11 - 13: 20.592 distance: 15 - 16: 10.913 distance: 15 - 18: 12.900 distance: 16 - 17: 13.951 distance: 16 - 21: 14.175 distance: 18 - 19: 19.571 distance: 18 - 20: 19.282 distance: 21 - 22: 16.332 distance: 22 - 23: 12.288 distance: 22 - 25: 27.607 distance: 23 - 24: 6.190 distance: 23 - 29: 8.458 distance: 25 - 26: 50.083 distance: 26 - 27: 11.348 distance: 26 - 28: 24.078 distance: 29 - 30: 5.179 distance: 30 - 31: 8.319 distance: 30 - 33: 6.435 distance: 31 - 32: 12.871 distance: 31 - 37: 3.859 distance: 33 - 34: 4.874 distance: 34 - 35: 4.368 distance: 34 - 36: 4.814 distance: 37 - 38: 4.018 distance: 38 - 39: 7.519 distance: 38 - 41: 3.160 distance: 39 - 40: 19.586 distance: 41 - 42: 20.083 distance: 43 - 44: 10.541 distance: 44 - 45: 4.970 distance: 44 - 47: 17.324 distance: 45 - 46: 4.439 distance: 45 - 50: 7.008 distance: 47 - 48: 9.356 distance: 47 - 49: 17.313 distance: 51 - 52: 5.185 distance: 52 - 53: 5.725 distance: 52 - 58: 16.721 distance: 54 - 55: 3.730 distance: 55 - 56: 5.738 distance: 55 - 57: 4.748 distance: 58 - 59: 13.988 distance: 59 - 62: 12.496 distance: 60 - 61: 6.830 distance: 60 - 63: 22.027 distance: 63 - 64: 12.178 distance: 64 - 65: 13.223 distance: 64 - 67: 8.430 distance: 65 - 66: 14.138 distance: 65 - 70: 5.975 distance: 67 - 68: 12.806 distance: 67 - 69: 12.731 distance: 70 - 71: 14.642 distance: 71 - 72: 8.509 distance: 71 - 74: 4.890 distance: 72 - 73: 4.010 distance: 72 - 75: 8.752 distance: 75 - 76: 4.246 distance: 76 - 79: 8.537 distance: 77 - 78: 15.420 distance: 77 - 81: 4.060 distance: 79 - 80: 7.203 distance: 82 - 83: 5.286 distance: 82 - 85: 3.039 distance: 83 - 89: 3.968 distance: 85 - 86: 3.150 distance: 89 - 90: 7.029