Starting phenix.real_space_refine on Wed May 21 17:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vy2_21456/05_2025/6vy2_21456.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vy2_21456/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vy2_21456/05_2025/6vy2_21456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vy2_21456/05_2025/6vy2_21456.map" model { file = "/net/cci-nas-00/data/ceres_data/6vy2_21456/05_2025/6vy2_21456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vy2_21456/05_2025/6vy2_21456.cif" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.52, per 1000 atoms: 0.58 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: 7.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.80 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: 7.48 Time building geometry restraints manager: 7.89 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: 0.00 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 47.910 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.660 ------------------------------------------------------------------------------- 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 : 18.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP H 100 HIS 0.003 0.001 HIS E 355 PHE 0.011 0.002 PHE E 383 TYR 0.015 0.002 TYR E 217 ARG 0.004 0.001 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.09895 ( 72) link_NAG-ASN : angle 8.45718 ( 216) 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_ALPHA1-3 : bond 0.00783 ( 12) link_ALPHA1-3 : angle 1.98995 ( 36) hydrogen bonds : bond 0.15341 ( 726) hydrogen bonds : angle 7.46453 ( 1977) SS BOND : bond 0.03671 ( 33) SS BOND : angle 3.08246 ( 66) covalent geometry : bond 0.00691 (21831) covalent geometry : angle 1.11211 (29631) *********************** 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 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 : 0.004 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: 0.0023 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 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 : 0.004 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 : 0.449 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: 0.9089 (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: 0.9382 (tp) REVERT: A 259 LEU cc_start: 0.9363 (mt) cc_final: 0.8912 (mt) REVERT: A 285 ILE cc_start: 0.9426 (mt) cc_final: 0.9223 (tp) REVERT: A 368 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8070 (p0) REVERT: A 426 MET cc_start: 0.8774 (mtp) cc_final: 0.8391 (ttm) REVERT: A 434 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8808 (ptp) REVERT: A 453 LEU cc_start: 0.9130 (tp) cc_final: 0.8926 (tp) outliers start: 21 outliers final: 3 residues processed: 79 average time/residue: 0.1590 time to fit residues: 15.6153 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 : 0.450 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 : 0.120 Fit side-chains 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: 0.9388 (m) REVERT: B 581 LEU cc_start: 0.9806 (tp) cc_final: 0.9472 (tp) REVERT: B 584 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8566 (mp0) REVERT: B 587 LEU cc_start: 0.9680 (mm) cc_final: 0.9364 (pp) REVERT: B 639 THR cc_start: 0.8418 (p) cc_final: 0.7711 (p) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.2148 time to fit residues: 10.6813 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 : 0.106 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 : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8903 (mmm) cc_final: 0.8678 (mmm) REVERT: H 51 MET cc_start: 0.9507 (ttp) cc_final: 0.9086 (tmm) REVERT: H 58 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8799 (p) REVERT: H 72 ASP cc_start: 0.9401 (t0) cc_final: 0.8668 (p0) outliers start: 7 outliers final: 1 residues processed: 40 average time/residue: 0.1060 time to fit residues: 4.7357 Evaluate side-chains 19 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.100 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 : 0.085 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: 0.1473 time to fit residues: 4.9244 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 : 0.094 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0038 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 : 0.003 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.0050 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.2675 r_free = 0.2675 target = 0.053981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.048514 restraints weight = 589.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.050070 restraints weight = 397.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.052677 restraints weight = 313.325| |-----------------------------------------------------------------------------| r_work (final): 0.2620 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.039759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.038098 restraints weight = 417.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.038438 restraints weight = 183.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.038696 restraints weight = 123.154| |-----------------------------------------------------------------------------| r_work (final): 0.2390 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.051974 restraints weight = 836.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.052963 restraints weight = 586.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053875 restraints weight = 459.776| |-----------------------------------------------------------------------------| r_work (final): 0.2822 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.035811 restraints weight = 24488.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.037291 restraints weight = 16083.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.038425 restraints weight = 11681.361| |-----------------------------------------------------------------------------| r_work (final): 0.2800 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.043289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.034320 restraints weight = 7870.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.035652 restraints weight = 4653.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.036603 restraints weight = 3220.571| |-----------------------------------------------------------------------------| r_work (final): 0.2719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.032453 restraints weight = 7336.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.033792 restraints weight = 4611.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.034796 restraints weight = 3312.813| |-----------------------------------------------------------------------------| r_work (final): 0.2667 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.029780 restraints weight = 4809.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.031352 restraints weight = 2741.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.032545 restraints weight = 1855.992| |-----------------------------------------------------------------------------| r_work (final): 0.2545 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.050318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.048486 restraints weight = 666.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049295 restraints weight = 215.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049773 restraints weight = 99.437| |-----------------------------------------------------------------------------| r_work (final): 0.2691 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.046938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.040221 restraints weight = 741.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.040606 restraints weight = 588.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.040605 restraints weight = 518.774| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.666 22044 Z= 0.897 Angle : 2.568 56.471 30237 Z= 0.972 Chirality : 0.109 1.553 3837 Planarity : 0.007 0.098 3516 Dihedral : 24.648 162.438 6294 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.09 % Favored : 93.53 % Rotamer: Outliers : 1.27 % Allowed : 4.67 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2412 helix: -1.65 (0.23), residues: 396 sheet: -0.55 (0.19), residues: 654 loop : -1.91 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 571 HIS 0.003 0.001 HIS L 39 PHE 0.047 0.004 PHE M 32 TYR 0.077 0.004 TYR J 100A ARG 0.034 0.001 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.05505 ( 72) link_NAG-ASN : angle 10.78443 ( 216) link_ALPHA1-6 : bond 0.48941 ( 15) link_ALPHA1-6 : angle 22.38690 ( 45) link_BETA1-4 : bond 0.02172 ( 81) link_BETA1-4 : angle 4.36788 ( 243) link_ALPHA1-3 : bond 0.21547 ( 12) link_ALPHA1-3 : angle 8.89299 ( 36) hydrogen bonds : bond 0.07203 ( 726) hydrogen bonds : angle 6.96560 ( 1977) SS BOND : bond 0.06535 ( 33) SS BOND : angle 3.02935 ( 66) covalent geometry : bond 0.01188 (21831) covalent geometry : angle 2.20224 (29631) *********************** 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 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 : 0.003 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: 0.0025 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0054 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 : 0.004 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.429 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: 0.9471 (ppp) cc_final: 0.9220 (ppp) REVERT: A 107 ASP cc_start: 0.9340 (m-30) cc_final: 0.9117 (m-30) REVERT: A 193 LEU cc_start: 0.9724 (tp) cc_final: 0.9375 (tp) REVERT: A 383 PHE cc_start: 0.9791 (m-80) cc_final: 0.9360 (m-80) REVERT: A 421 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8544 (ttmt) REVERT: A 434 MET cc_start: 0.9682 (ttp) cc_final: 0.9411 (ppp) REVERT: A 453 LEU cc_start: 0.9573 (tp) cc_final: 0.9137 (tp) REVERT: A 475 MET cc_start: 0.7875 (tpt) cc_final: 0.7431 (tpp) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 0.1880 time to fit residues: 11.1155 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 : 0.433 Evaluate side-chains 32 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8884 (mtp) cc_final: 0.8328 (mmt) REVERT: B 584 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 639 THR cc_start: 0.8800 (p) cc_final: 0.8388 (p) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1814 time to fit residues: 6.2412 Evaluate side-chains 23 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.116 Evaluate side-chains 30 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 51 MET cc_start: 0.9302 (ttp) cc_final: 0.8587 (tmm) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.0948 time to fit residues: 3.0548 Evaluate side-chains 20 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.112 Evaluate side-chains 21 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1353 time to fit residues: 3.1389 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 : 0.094 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0041 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 : 0.003 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 162 optimal weight: 0.1980 chunk 126 optimal weight: 0.3980 chunk 106 optimal weight: 0.0370 chunk 86 optimal weight: 0.0570 chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 425 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN B 630 GLN 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... 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 = 0.2669 r_free = 0.2669 target = 0.043229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.036950 restraints weight = 589.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.037608 restraints weight = 411.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.037873 restraints weight = 353.988| |-----------------------------------------------------------------------------| r_work (final): 0.2464 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.044423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.040840 restraints weight = 293.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.041529 restraints weight = 170.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.042105 restraints weight = 121.001| |-----------------------------------------------------------------------------| r_work (final): 0.2218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056180 restraints weight = 742.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056810 restraints weight = 446.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057277 restraints weight = 299.318| |-----------------------------------------------------------------------------| r_work (final): 0.2957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.035329 restraints weight = 24774.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.036881 restraints weight = 16022.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.038036 restraints weight = 11576.303| |-----------------------------------------------------------------------------| r_work (final): 0.2797 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.042706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.033908 restraints weight = 8172.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.035157 restraints weight = 4810.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.036082 restraints weight = 3354.990| |-----------------------------------------------------------------------------| r_work (final): 0.2681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.041255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.031728 restraints weight = 6990.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.032967 restraints weight = 4465.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.033931 restraints weight = 3223.828| |-----------------------------------------------------------------------------| r_work (final): 0.2608 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.030755 restraints weight = 5599.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.032321 restraints weight = 3260.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.033259 restraints weight = 2215.062| |-----------------------------------------------------------------------------| r_work (final): 0.2501 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.051648 restraints weight = 766.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.052401 restraints weight = 331.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.053004 restraints weight = 188.572| |-----------------------------------------------------------------------------| r_work (final): 0.2770 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.047505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.040622 restraints weight = 691.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.040909 restraints weight = 563.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.041213 restraints weight = 505.824| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.660 22044 Z= 0.890 Angle : 2.363 49.695 30237 Z= 0.938 Chirality : 0.130 1.955 3837 Planarity : 0.009 0.142 3516 Dihedral : 23.706 164.617 6294 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 30.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 1.13 % Allowed : 4.39 % Favored : 94.48 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2412 helix: -1.81 (0.22), residues: 396 sheet: -0.41 (0.20), residues: 591 loop : -2.00 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.006 TRP I 47 HIS 0.020 0.003 HIS C 105 PHE 0.078 0.004 PHE M 95B TYR 0.056 0.005 TYR H 100G ARG 0.010 0.001 ARG E 393 Details of bonding type rmsd link_NAG-ASN : bond 0.05639 ( 72) link_NAG-ASN : angle 10.99900 ( 216) link_ALPHA1-6 : bond 0.46009 ( 15) link_ALPHA1-6 : angle 21.36258 ( 45) link_BETA1-4 : bond 0.02061 ( 81) link_BETA1-4 : angle 3.51890 ( 243) link_ALPHA1-3 : bond 0.23771 ( 12) link_ALPHA1-3 : angle 11.78287 ( 36) hydrogen bonds : bond 0.06966 ( 726) hydrogen bonds : angle 7.06981 ( 1977) SS BOND : bond 0.06570 ( 33) SS BOND : angle 2.87961 ( 66) covalent geometry : bond 0.01280 (21831) covalent geometry : angle 1.95769 (29631) *********************** 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 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 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: 0.0023 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 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 : 0.004 Evaluate side-chains 45 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8891 (tp30) REVERT: A 95 MET cc_start: 0.9479 (ppp) cc_final: 0.9197 (ppp) REVERT: A 193 LEU cc_start: 0.9524 (tp) cc_final: 0.9279 (tp) REVERT: A 383 PHE cc_start: 0.9780 (m-80) cc_final: 0.9341 (m-80) REVERT: A 434 MET cc_start: 0.9617 (ttp) cc_final: 0.9397 (ppp) REVERT: A 453 LEU cc_start: 0.9540 (tp) cc_final: 0.9198 (tp) REVERT: A 475 MET cc_start: 0.7899 (tpt) cc_final: 0.7327 (tpt) outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.1511 time to fit residues: 8.6087 Evaluate side-chains 33 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.433 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 : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9860 (m) cc_final: 0.9583 (p) REVERT: B 584 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8601 (mt-10) REVERT: B 639 THR cc_start: 0.8743 (p) cc_final: 0.8284 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1623 time to fit residues: 5.2926 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 : 0.114 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 : 0.111 Fit side-chains REVERT: I 34 MET cc_start: 0.9155 (mmp) cc_final: 0.8954 (mmm) REVERT: I 37 LEU cc_start: 0.8749 (mp) cc_final: 0.8350 (tp) REVERT: I 51 MET cc_start: 0.9550 (ttp) cc_final: 0.9007 (tmm) REVERT: I 72 ASP cc_start: 0.9196 (t70) cc_final: 0.8627 (p0) REVERT: I 100 ASP cc_start: 0.9415 (t0) cc_final: 0.9181 (m-30) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.1159 time to fit residues: 3.5210 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 : 0.111 Evaluate side-chains 19 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.095 Fit side-chains REVERT: N 48 MET cc_start: 0.6983 (tpt) cc_final: 0.6228 (tpp) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1192 time to fit residues: 2.5460 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 : 0.096 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0038 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 : 0.003 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0035 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 0.5980 chunk 225 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 132 optimal weight: 0.0170 chunk 165 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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** ** A 374 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... 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 73 ASN 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: 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 = 0.2669 r_free = 0.2669 target = 0.043229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.037049 restraints weight = 550.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.037659 restraints weight = 401.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.037906 restraints weight = 351.396| |-----------------------------------------------------------------------------| r_work (final): 0.2466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.044423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2223 r_free = 0.2223 target = 0.040806 restraints weight = 291.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.041735 restraints weight = 172.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.042298 restraints weight = 106.668| |-----------------------------------------------------------------------------| r_work (final): 0.2222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056183 restraints weight = 742.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056804 restraints weight = 446.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057284 restraints weight = 298.860| |-----------------------------------------------------------------------------| r_work (final): 0.2957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.047893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035185 restraints weight = 26151.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.036671 restraints weight = 16936.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037801 restraints weight = 12339.562| |-----------------------------------------------------------------------------| r_work (final): 0.2768 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.036572 restraints weight = 9509.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.037818 restraints weight = 5667.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.038698 restraints weight = 3910.559| |-----------------------------------------------------------------------------| r_work (final): 0.2693 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.043178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.033640 restraints weight = 7214.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.034910 restraints weight = 4516.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.035861 restraints weight = 3246.955| |-----------------------------------------------------------------------------| r_work (final): 0.2677 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.038312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.029412 restraints weight = 5737.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.030808 restraints weight = 3564.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.031872 restraints weight = 2539.268| |-----------------------------------------------------------------------------| r_work (final): 0.2489 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.051892 restraints weight = 635.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.052567 restraints weight = 279.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053104 restraints weight = 167.613| |-----------------------------------------------------------------------------| r_work (final): 0.2772 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.047505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.040690 restraints weight = 746.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.040950 restraints weight = 560.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.041234 restraints weight = 501.170| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 1.853 22044 Z= 1.994 Angle : 2.592 53.831 30237 Z= 1.056 Chirality : 0.166 3.974 3837 Planarity : 0.009 0.142 3516 Dihedral : 23.706 164.617 6294 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 45.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2412 helix: -1.81 (0.22), residues: 396 sheet: -0.41 (0.20), residues: 591 loop : -2.00 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.006 TRP H 47 HIS 0.020 0.003 HIS C 105 PHE 0.078 0.004 PHE L 95B TYR 0.056 0.005 TYR H 100G ARG 0.010 0.001 ARG C 393 Details of bonding type rmsd link_NAG-ASN : bond 0.22187 ( 72) link_NAG-ASN : angle 12.26323 ( 216) link_ALPHA1-6 : bond 0.46009 ( 15) link_ALPHA1-6 : angle 21.36258 ( 45) link_BETA1-4 : bond 0.02061 ( 81) link_BETA1-4 : angle 3.51887 ( 243) link_ALPHA1-3 : bond 0.23771 ( 12) link_ALPHA1-3 : angle 11.78286 ( 36) hydrogen bonds : bond 0.06966 ( 726) hydrogen bonds : angle 7.06981 ( 1977) SS BOND : bond 0.86695 ( 33) SS BOND : angle 20.75172 ( 66) covalent geometry : bond 0.01288 (21831) covalent geometry : angle 1.95851 (29631) *********************** 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 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 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: 0.0022 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 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 : 0.004 Evaluate side-chains 36 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8584 (tp30) REVERT: A 95 MET cc_start: 0.9501 (ppp) cc_final: 0.9217 (ppp) REVERT: A 193 LEU cc_start: 0.9446 (tp) cc_final: 0.9228 (tp) REVERT: A 383 PHE cc_start: 0.9784 (m-80) cc_final: 0.9345 (m-80) REVERT: A 453 LEU cc_start: 0.9532 (tp) cc_final: 0.9170 (tp) REVERT: A 475 MET cc_start: 0.7902 (tpt) cc_final: 0.7318 (tpt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1401 time to fit residues: 6.7286 Evaluate side-chains 32 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.385 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 : 0.102 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: 0.9545 (p) REVERT: B 581 LEU cc_start: 0.9831 (mt) cc_final: 0.9612 (mt) REVERT: B 584 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8601 (mt-10) REVERT: B 639 THR cc_start: 0.8745 (p) cc_final: 0.8234 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1630 time to fit residues: 4.9637 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 : 0.117 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 : 0.104 Fit side-chains REVERT: I 34 MET cc_start: 0.9183 (mmp) cc_final: 0.8980 (mmm) REVERT: I 37 LEU cc_start: 0.8444 (mp) cc_final: 0.8098 (mp) REVERT: I 51 MET cc_start: 0.9567 (ttp) cc_final: 0.9022 (tmm) REVERT: I 72 ASP cc_start: 0.9223 (t70) cc_final: 0.8656 (p0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0680 time to fit residues: 1.8241 Evaluate side-chains 16 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.100 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.086 Fit side-chains REVERT: N 48 MET cc_start: 0.7064 (tpt) cc_final: 0.6355 (tpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0614 time to fit residues: 1.1894 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 : 0.105 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0043 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 : 0.003 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: 0.0032 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** A 374 HIS ** 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 73 ASN 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: 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 = 0.2669 r_free = 0.2669 target = 0.043229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.037082 restraints weight = 538.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.037676 restraints weight = 397.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.037901 restraints weight = 349.259| |-----------------------------------------------------------------------------| r_work (final): 0.2466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.044423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2224 r_free = 0.2224 target = 0.040879 restraints weight = 276.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.041723 restraints weight = 166.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2229 r_free = 0.2229 target = 0.042305 restraints weight = 107.481| |-----------------------------------------------------------------------------| r_work (final): 0.2222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056193 restraints weight = 744.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056809 restraints weight = 445.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057281 restraints weight = 298.639| |-----------------------------------------------------------------------------| r_work (final): 0.2957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.047907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035277 restraints weight = 26204.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036742 restraints weight = 17215.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.037870 restraints weight = 12571.240| |-----------------------------------------------------------------------------| r_work (final): 0.2771 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.036612 restraints weight = 9353.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037841 restraints weight = 5602.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.038714 restraints weight = 3879.514| |-----------------------------------------------------------------------------| r_work (final): 0.2693 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034614 restraints weight = 7439.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.035854 restraints weight = 4538.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036821 restraints weight = 3270.999| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.038251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.029164 restraints weight = 5739.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.030488 restraints weight = 3651.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.031536 restraints weight = 2648.104| |-----------------------------------------------------------------------------| r_work (final): 0.2460 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.051727 restraints weight = 706.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052443 restraints weight = 313.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.053026 restraints weight = 183.513| |-----------------------------------------------------------------------------| r_work (final): 0.2770 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.047505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040975 restraints weight = 621.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.041159 restraints weight = 511.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.041159 restraints weight = 479.404| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.040 1.853 22044 Z= 1.994 Angle : 2.592 53.831 30237 Z= 1.056 Chirality : 0.166 3.974 3837 Planarity : 0.009 0.142 3516 Dihedral : 23.706 164.617 6294 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 48.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2412 helix: -1.81 (0.22), residues: 396 sheet: -0.41 (0.20), residues: 591 loop : -2.00 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.006 TRP H 47 HIS 0.020 0.003 HIS A 105 PHE 0.078 0.004 PHE L 95B TYR 0.056 0.005 TYR J 100G ARG 0.010 0.001 ARG C 393 Details of bonding type rmsd link_NAG-ASN : bond 0.22187 ( 72) link_NAG-ASN : angle 12.26323 ( 216) link_ALPHA1-6 : bond 0.46009 ( 15) link_ALPHA1-6 : angle 21.36258 ( 45) link_BETA1-4 : bond 0.02061 ( 81) link_BETA1-4 : angle 3.51887 ( 243) link_ALPHA1-3 : bond 0.23771 ( 12) link_ALPHA1-3 : angle 11.78286 ( 36) hydrogen bonds : bond 0.06966 ( 726) hydrogen bonds : angle 7.06981 ( 1977) SS BOND : bond 0.86695 ( 33) SS BOND : angle 20.75172 ( 66) covalent geometry : bond 0.01288 (21831) covalent geometry : angle 1.95851 (29631) *********************** 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 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 : 0.003 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: 0.0025 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 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 : 0.004 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 : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8585 (tp30) REVERT: A 95 MET cc_start: 0.9480 (ppp) cc_final: 0.9176 (ppp) REVERT: A 193 LEU cc_start: 0.9453 (tp) cc_final: 0.9232 (tp) REVERT: A 383 PHE cc_start: 0.9784 (m-80) cc_final: 0.9344 (m-80) REVERT: A 453 LEU cc_start: 0.9521 (tp) cc_final: 0.9157 (tp) REVERT: A 475 MET cc_start: 0.7872 (tpt) cc_final: 0.7299 (tpt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1331 time to fit residues: 6.3949 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 : 0.467 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 : 0.123 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: 0.9544 (p) REVERT: B 581 LEU cc_start: 0.9831 (mt) cc_final: 0.9612 (mt) REVERT: B 584 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8602 (mt-10) REVERT: B 639 THR cc_start: 0.8744 (p) cc_final: 0.8232 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1744 time to fit residues: 5.3012 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 : 0.118 Evaluate side-chains 21 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.118 Fit side-chains REVERT: I 37 LEU cc_start: 0.8425 (mp) cc_final: 0.8083 (mp) REVERT: I 51 MET cc_start: 0.9564 (ttp) cc_final: 0.9018 (tmm) REVERT: I 72 ASP cc_start: 0.9213 (t70) cc_final: 0.8644 (p0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0790 time to fit residues: 2.0747 Evaluate side-chains 16 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.117 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.100 Fit side-chains REVERT: N 48 MET cc_start: 0.7128 (tpt) cc_final: 0.6416 (tpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0657 time to fit residues: 1.1755 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 : 0.085 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0041 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 : 0.003 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: 0.0030 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 : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0040 chunk 134 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 0.0970 chunk 203 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 48 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 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 630 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 73 ASN 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: 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 = 0.2710 r_free = 0.2710 target = 0.044036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 16)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.036567 restraints weight = 577.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.037423 restraints weight = 415.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.037723 restraints weight = 358.571| |-----------------------------------------------------------------------------| r_work (final): 0.2477 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.046039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.043095 restraints weight = 220.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.043745 restraints weight = 143.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.044216 restraints weight = 101.398| |-----------------------------------------------------------------------------| r_work (final): 0.2285 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.059102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056025 restraints weight = 763.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056680 restraints weight = 479.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057131 restraints weight = 324.134| |-----------------------------------------------------------------------------| r_work (final): 0.2956 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.035244 restraints weight = 25001.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036726 restraints weight = 16358.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.037886 restraints weight = 11898.034| |-----------------------------------------------------------------------------| r_work (final): 0.2777 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.042442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.034154 restraints weight = 8311.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.035437 restraints weight = 4796.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.036388 restraints weight = 3289.069| |-----------------------------------------------------------------------------| r_work (final): 0.2687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.043436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.034289 restraints weight = 7044.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.035543 restraints weight = 4463.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036447 restraints weight = 3216.700| |-----------------------------------------------------------------------------| r_work (final): 0.2673 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.038157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.028759 restraints weight = 5603.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.030266 restraints weight = 3424.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.031432 restraints weight = 2423.943| |-----------------------------------------------------------------------------| r_work (final): 0.2474 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.053401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.052191 restraints weight = 747.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.052793 restraints weight = 221.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053059 restraints weight = 89.207| |-----------------------------------------------------------------------------| r_work (final): 0.2719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.047248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.040518 restraints weight = 755.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.041004 restraints weight = 561.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.041261 restraints weight = 488.390| |-----------------------------------------------------------------------------| r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.642 22044 Z= 0.900 Angle : 2.456 48.593 30237 Z= 0.989 Chirality : 0.144 2.513 3837 Planarity : 0.010 0.160 3516 Dihedral : 23.563 166.415 6294 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.15), residues: 2412 helix: -1.91 (0.21), residues: 396 sheet: -0.45 (0.19), residues: 627 loop : -2.10 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP C 96 HIS 0.020 0.004 HIS E 105 PHE 0.053 0.004 PHE N 95B TYR 0.106 0.007 TYR M 30 ARG 0.030 0.002 ARG I 30 Details of bonding type rmsd link_NAG-ASN : bond 0.05717 ( 72) link_NAG-ASN : angle 12.84302 ( 216) link_ALPHA1-6 : bond 0.45227 ( 15) link_ALPHA1-6 : angle 21.19239 ( 45) link_BETA1-4 : bond 0.01783 ( 81) link_BETA1-4 : angle 3.57350 ( 243) link_ALPHA1-3 : bond 0.24019 ( 12) link_ALPHA1-3 : angle 11.61179 ( 36) hydrogen bonds : bond 0.06854 ( 726) hydrogen bonds : angle 7.05007 ( 1977) SS BOND : bond 0.06663 ( 33) SS BOND : angle 6.27220 ( 66) covalent geometry : bond 0.01366 (21831) covalent geometry : angle 1.97806 (29631) *********************** 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 : 0.002 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 : 0.002 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: 0.0021 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 : 0.002 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 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 : 0.004 Evaluate side-chains 40 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9512 (ppp) cc_final: 0.9182 (ppp) REVERT: A 193 LEU cc_start: 0.9498 (tp) cc_final: 0.9231 (tp) REVERT: A 383 PHE cc_start: 0.9780 (m-80) cc_final: 0.9341 (m-80) REVERT: A 453 LEU cc_start: 0.9544 (tp) cc_final: 0.9184 (tp) REVERT: A 475 MET cc_start: 0.7835 (tpt) cc_final: 0.7232 (tpt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1485 time to fit residues: 7.7283 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 : 0.420 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 : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9858 (m) cc_final: 0.9518 (p) REVERT: B 581 LEU cc_start: 0.9811 (mt) cc_final: 0.9526 (mm) REVERT: B 584 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8492 (mt-10) REVERT: B 639 THR cc_start: 0.8777 (p) cc_final: 0.8335 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1744 time to fit residues: 5.6582 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 : 0.118 Evaluate side-chains 21 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.100 Fit side-chains REVERT: I 34 MET cc_start: 0.9221 (mmp) cc_final: 0.8983 (mmm) REVERT: I 37 LEU cc_start: 0.8815 (mp) cc_final: 0.8017 (tt) REVERT: I 51 MET cc_start: 0.9579 (ttp) cc_final: 0.9010 (tmm) REVERT: I 82 MET cc_start: 0.9322 (pmm) cc_final: 0.9116 (pmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0689 time to fit residues: 1.7774 Evaluate side-chains 16 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.099 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.093 Fit side-chains REVERT: N 48 MET cc_start: 0.7116 (tpt) cc_final: 0.6830 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0616 time to fit residues: 1.1798 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 : 0.097 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0037 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 : 0.003 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 0.0770 chunk 137 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.0370 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- 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 374 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... Flipped N/Q/H residues before XYZ refinement: ** I 73 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: 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 = 0.2677 r_free = 0.2677 target = 0.045923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.040548 restraints weight = 516.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.041977 restraints weight = 403.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.042724 restraints weight = 285.168| |-----------------------------------------------------------------------------| r_work (final): 0.2591 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.046039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.043174 restraints weight = 208.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.043812 restraints weight = 138.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.044200 restraints weight = 98.320| |-----------------------------------------------------------------------------| r_work (final): 0.2284 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.059102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.055951 restraints weight = 804.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.056642 restraints weight = 497.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057113 restraints weight = 333.424| |-----------------------------------------------------------------------------| r_work (final): 0.2956 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.035261 restraints weight = 24482.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.036746 restraints weight = 15891.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.038008 restraints weight = 11555.177| |-----------------------------------------------------------------------------| r_work (final): 0.2784 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.035503 restraints weight = 8217.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.036770 restraints weight = 4773.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.037735 restraints weight = 3277.422| |-----------------------------------------------------------------------------| r_work (final): 0.2677 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.042544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.033311 restraints weight = 7172.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.034587 restraints weight = 4490.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035506 restraints weight = 3225.826| |-----------------------------------------------------------------------------| r_work (final): 0.2682 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.039322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.029791 restraints weight = 5734.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.031274 restraints weight = 3307.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.032377 restraints weight = 2275.024| |-----------------------------------------------------------------------------| r_work (final): 0.2515 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.053401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.052245 restraints weight = 681.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.052814 restraints weight = 208.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.053048 restraints weight = 85.636| |-----------------------------------------------------------------------------| r_work (final): 0.2719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.047248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.040593 restraints weight = 699.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040924 restraints weight = 548.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041415 restraints weight = 483.982| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 1.131 22044 Z= 1.228 Angle : 2.584 56.903 30237 Z= 1.049 Chirality : 0.144 2.513 3837 Planarity : 0.010 0.160 3516 Dihedral : 23.562 166.415 6294 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 41.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.15), residues: 2412 helix: -1.91 (0.21), residues: 396 sheet: -0.45 (0.19), residues: 627 loop : -2.10 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP C 96 HIS 0.020 0.004 HIS E 105 PHE 0.053 0.004 PHE M 95B TYR 0.106 0.007 TYR M 30 ARG 0.030 0.002 ARG I 30 Details of bonding type rmsd link_NAG-ASN : bond 0.23775 ( 72) link_NAG-ASN : angle 13.91653 ( 216) link_ALPHA1-6 : bond 0.45226 ( 15) link_ALPHA1-6 : angle 21.19238 ( 45) link_BETA1-4 : bond 0.01782 ( 81) link_BETA1-4 : angle 3.57341 ( 243) link_ALPHA1-3 : bond 0.24019 ( 12) link_ALPHA1-3 : angle 11.61202 ( 36) hydrogen bonds : bond 0.06854 ( 726) hydrogen bonds : angle 7.05007 ( 1977) SS BOND : bond 0.27408 ( 33) SS BOND : angle 15.52047 ( 66) covalent geometry : bond 0.01366 (21831) covalent geometry : angle 1.97805 (29631) *********************** 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 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 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: 0.0024 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0060 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 : 0.004 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 : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9531 (ppp) cc_final: 0.9179 (ppp) REVERT: A 193 LEU cc_start: 0.9485 (tp) cc_final: 0.9247 (tp) REVERT: A 383 PHE cc_start: 0.9806 (m-80) cc_final: 0.9367 (m-80) REVERT: A 453 LEU cc_start: 0.9592 (tp) cc_final: 0.9240 (tp) REVERT: A 475 MET cc_start: 0.7851 (tpt) cc_final: 0.7265 (tpt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1265 time to fit residues: 6.6581 Evaluate side-chains 32 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.478 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 : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9854 (m) cc_final: 0.9496 (p) REVERT: B 581 LEU cc_start: 0.9814 (mt) cc_final: 0.9509 (mm) REVERT: B 584 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 639 THR cc_start: 0.8770 (p) cc_final: 0.8298 (p) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1846 time to fit residues: 5.7833 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 : 0.121 Evaluate side-chains 21 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.117 Fit side-chains REVERT: I 34 MET cc_start: 0.9213 (mmp) cc_final: 0.8979 (mmm) REVERT: I 37 LEU cc_start: 0.8822 (mp) cc_final: 0.8032 (tt) REVERT: I 51 MET cc_start: 0.9582 (ttp) cc_final: 0.9000 (tmm) REVERT: I 82 MET cc_start: 0.9351 (pmm) cc_final: 0.9115 (pmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0728 time to fit residues: 1.9174 Evaluate side-chains 16 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.104 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.094 Fit side-chains REVERT: N 48 MET cc_start: 0.6967 (tpt) cc_final: 0.6686 (tpt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0645 time to fit residues: 1.1423 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 : 0.096 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0041 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 : 0.003 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: 0.0032 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 : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2482 > 50: distance: 0 - 1: 8.381 distance: 1 - 2: 6.718 distance: 1 - 4: 6.010 distance: 2 - 3: 6.832 distance: 2 - 9: 3.847 distance: 4 - 5: 17.854 distance: 5 - 6: 25.930 distance: 6 - 7: 29.810 distance: 7 - 8: 47.408 distance: 9 - 10: 14.058 distance: 10 - 11: 20.610 distance: 10 - 13: 8.137 distance: 11 - 12: 27.388 distance: 11 - 17: 34.225 distance: 12 - 31: 39.232 distance: 13 - 14: 14.693 distance: 14 - 15: 7.129 distance: 14 - 16: 5.912 distance: 17 - 18: 28.441 distance: 18 - 19: 32.363 distance: 18 - 21: 41.895 distance: 19 - 20: 30.010 distance: 19 - 24: 40.564 distance: 20 - 39: 29.702 distance: 21 - 22: 28.901 distance: 21 - 23: 25.143 distance: 24 - 25: 35.045 distance: 24 - 30: 36.593 distance: 25 - 26: 39.401 distance: 25 - 28: 35.028 distance: 26 - 27: 26.380 distance: 26 - 31: 48.525 distance: 28 - 29: 33.635 distance: 29 - 30: 35.740 distance: 31 - 32: 14.943 distance: 32 - 33: 36.824 distance: 32 - 35: 37.502 distance: 33 - 34: 20.488 distance: 33 - 39: 48.605 distance: 35 - 36: 32.096 distance: 36 - 37: 31.529 distance: 36 - 38: 25.648 distance: 39 - 40: 9.644 distance: 40 - 41: 20.743 distance: 40 - 43: 34.200 distance: 41 - 42: 19.847 distance: 41 - 45: 43.421 distance: 43 - 44: 12.878 distance: 45 - 46: 33.469 distance: 46 - 47: 31.964 distance: 46 - 49: 46.482 distance: 47 - 48: 26.936 distance: 47 - 52: 21.791 distance: 49 - 50: 52.132 distance: 49 - 51: 32.893 distance: 52 - 53: 14.742 distance: 53 - 54: 45.283 distance: 53 - 56: 40.028 distance: 54 - 55: 30.742 distance: 54 - 59: 28.911 distance: 56 - 57: 35.726 distance: 56 - 58: 48.496 distance: 59 - 60: 28.535 distance: 60 - 61: 34.796 distance: 60 - 63: 38.436 distance: 61 - 62: 19.580 distance: 61 - 67: 28.191 distance: 63 - 64: 34.319 distance: 64 - 65: 35.238 distance: 64 - 66: 39.317 distance: 67 - 68: 10.357 distance: 68 - 69: 9.190 distance: 68 - 71: 10.167 distance: 69 - 70: 9.801 distance: 71 - 72: 14.906 distance: 72 - 73: 3.136 distance: 72 - 74: 7.729