Starting phenix.real_space_refine on Wed Jun 18 22:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vy2_21456/06_2025/6vy2_21456.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vy2_21456/06_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_21456/06_2025/6vy2_21456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vy2_21456/06_2025/6vy2_21456.map" model { file = "/net/cci-nas-00/data/ceres_data/6vy2_21456/06_2025/6vy2_21456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vy2_21456/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.16, per 1000 atoms: 0.66 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: 8.16 Conformation dependent library (CDL) restraints added in 2.9 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: 3.31 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: 7.79 Time building geometry restraints manager: 9.14 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: 2.970 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.230 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.180 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.840 ------------------------------------------------------------------------------- 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: 0.0029 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: 0.0038 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 : 0.002 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: 0.0053 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 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 : 0.435 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: 0.1612 time to fit residues: 15.8889 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 : 0.417 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 : 0.109 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: 0.2165 time to fit residues: 10.7408 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 : 0.110 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 : 0.109 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: 0.1153 time to fit residues: 5.1384 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 : 0.128 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 : 0.109 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: 0.1562 time to fit residues: 5.2338 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 : 0.092 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: 0.0040 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=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 = 0.2674 r_free = 0.2674 target = 0.053891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.048520 restraints weight = 590.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.050059 restraints weight = 398.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.052527 restraints weight = 314.242| |-----------------------------------------------------------------------------| r_work (final): 0.2613 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.039350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.037710 restraints weight = 424.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.038034 restraints weight = 186.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.038256 restraints weight = 124.970| |-----------------------------------------------------------------------------| r_work (final): 0.2366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.052257 restraints weight = 850.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053152 restraints weight = 608.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.053980 restraints weight = 488.451| |-----------------------------------------------------------------------------| r_work (final): 0.2839 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035679 restraints weight = 23921.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.037192 restraints weight = 15516.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.038325 restraints weight = 11229.388| |-----------------------------------------------------------------------------| r_work (final): 0.2797 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.043297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.034332 restraints weight = 7872.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.035658 restraints weight = 4653.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.036597 restraints weight = 3240.968| |-----------------------------------------------------------------------------| r_work (final): 0.2719 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.032368 restraints weight = 7336.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.033737 restraints weight = 4586.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.034747 restraints weight = 3278.226| |-----------------------------------------------------------------------------| r_work (final): 0.2648 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.029666 restraints weight = 4747.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.031222 restraints weight = 2706.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.032296 restraints weight = 1845.843| |-----------------------------------------------------------------------------| r_work (final): 0.2513 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.051452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.047423 restraints weight = 594.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.048183 restraints weight = 238.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.048624 restraints weight = 147.577| |-----------------------------------------------------------------------------| r_work (final): 0.2623 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.046962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.040441 restraints weight = 741.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.040642 restraints weight = 558.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.040654 restraints weight = 507.189| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.651 22044 Z= 0.879 Angle : 2.530 56.491 30237 Z= 0.958 Chirality : 0.116 1.568 3837 Planarity : 0.007 0.100 3516 Dihedral : 24.518 161.419 6294 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.34 % Favored : 93.41 % 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: -1.64 (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 0.040 0.003 TRP F 571 HIS 0.002 0.001 HIS C 249 PHE 0.042 0.004 PHE N 32 TYR 0.076 0.004 TYR H 100G ARG 0.031 0.001 ARG E 393 Details of bonding type rmsd link_NAG-ASN : bond 0.05605 ( 72) link_NAG-ASN : angle 10.73172 ( 216) link_ALPHA1-6 : bond 0.47899 ( 15) link_ALPHA1-6 : angle 22.39960 ( 45) link_BETA1-4 : bond 0.02722 ( 81) link_BETA1-4 : angle 4.31340 ( 243) link_ALPHA1-3 : bond 0.22240 ( 12) link_ALPHA1-3 : angle 8.78623 ( 36) hydrogen bonds : bond 0.07156 ( 726) hydrogen bonds : angle 6.95946 ( 1977) SS BOND : bond 0.06538 ( 33) SS BOND : angle 2.94713 ( 66) covalent geometry : bond 0.01140 (21831) covalent geometry : angle 2.15991 (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 : 0.002 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 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: 0.0055 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 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.421 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: 0.9481 (ppp) cc_final: 0.9222 (ppp) REVERT: A 107 ASP cc_start: 0.9337 (m-30) cc_final: 0.9115 (m-30) REVERT: A 193 LEU cc_start: 0.9725 (tp) cc_final: 0.9375 (tp) REVERT: A 383 PHE cc_start: 0.9794 (m-80) cc_final: 0.9364 (m-80) REVERT: A 421 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8528 (ttmt) REVERT: A 434 MET cc_start: 0.9686 (ttp) cc_final: 0.9412 (ppp) REVERT: A 453 LEU cc_start: 0.9592 (tp) cc_final: 0.9162 (tp) REVERT: A 475 MET cc_start: 0.8023 (tpt) cc_final: 0.7555 (tpp) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 0.1912 time to fit residues: 11.2928 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 : 0.483 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 : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8927 (mtp) cc_final: 0.8296 (mmt) REVERT: B 584 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 639 THR cc_start: 0.8800 (p) cc_final: 0.8389 (p) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1918 time to fit residues: 6.6053 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 : 0.128 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 : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 51 MET cc_start: 0.9300 (ttp) cc_final: 0.8594 (tmm) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.0995 time to fit residues: 3.2238 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 : 0.130 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 : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1277 time to fit residues: 2.9714 Evaluate side-chains 13 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.104 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 : 0.003 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 92 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 106 optimal weight: 0.0000 chunk 86 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.2684 r_free = 0.2684 target = 0.043419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.037308 restraints weight = 593.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.037924 restraints weight = 422.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.038184 restraints weight = 365.561| |-----------------------------------------------------------------------------| r_work (final): 0.2480 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.044199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.040625 restraints weight = 295.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.041557 restraints weight = 171.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.042103 restraints weight = 105.681| |-----------------------------------------------------------------------------| r_work (final): 0.2220 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055845 restraints weight = 767.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056499 restraints weight = 496.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056961 restraints weight = 337.479| |-----------------------------------------------------------------------------| r_work (final): 0.2943 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.035777 restraints weight = 24864.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.037255 restraints weight = 16245.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.038392 restraints weight = 11773.602| |-----------------------------------------------------------------------------| r_work (final): 0.2799 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.042713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.034392 restraints weight = 8433.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.035627 restraints weight = 5006.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.036536 restraints weight = 3488.504| |-----------------------------------------------------------------------------| r_work (final): 0.2681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.031568 restraints weight = 7280.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.032822 restraints weight = 4538.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.033788 restraints weight = 3250.843| |-----------------------------------------------------------------------------| r_work (final): 0.2590 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.039339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.030239 restraints weight = 5634.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.031791 restraints weight = 3196.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.032896 restraints weight = 2152.102| |-----------------------------------------------------------------------------| r_work (final): 0.2490 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067739 restraints weight = 658.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.068782 restraints weight = 323.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.069489 restraints weight = 199.802| |-----------------------------------------------------------------------------| r_work (final): 0.2865 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.040509 restraints weight = 700.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.040908 restraints weight = 559.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.040956 restraints weight = 495.062| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4050 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= 0.901 Angle : 2.376 50.058 30237 Z= 0.944 Chirality : 0.129 1.915 3837 Planarity : 0.010 0.150 3516 Dihedral : 23.704 163.940 6294 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % Rotamer: Outliers : 1.27 % Allowed : 4.11 % Favored : 94.62 % Cbeta Deviations : 0.40 % 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: -2.34 (0.15), residues: 2412 helix: -1.82 (0.21), residues: 396 sheet: -0.48 (0.19), residues: 618 loop : -2.04 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.006 TRP I 47 HIS 0.019 0.003 HIS C 105 PHE 0.095 0.005 PHE L 95B TYR 0.055 0.005 TYR H 100G ARG 0.011 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.05598 ( 72) link_NAG-ASN : angle 11.16114 ( 216) link_ALPHA1-6 : bond 0.45998 ( 15) link_ALPHA1-6 : angle 21.41121 ( 45) link_BETA1-4 : bond 0.02140 ( 81) link_BETA1-4 : angle 3.65526 ( 243) link_ALPHA1-3 : bond 0.23807 ( 12) link_ALPHA1-3 : angle 11.57240 ( 36) hydrogen bonds : bond 0.06939 ( 726) hydrogen bonds : angle 7.07915 ( 1977) SS BOND : bond 0.06602 ( 33) SS BOND : angle 2.78172 ( 66) covalent geometry : bond 0.01319 (21831) covalent geometry : angle 1.96682 (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: 0.0033 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: 0.0026 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 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 42 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9489 (ppp) cc_final: 0.9207 (ppp) REVERT: A 193 LEU cc_start: 0.9503 (tp) cc_final: 0.9084 (tp) REVERT: A 383 PHE cc_start: 0.9785 (m-80) cc_final: 0.9352 (m-80) REVERT: A 434 MET cc_start: 0.9614 (ttp) cc_final: 0.9397 (ppp) REVERT: A 453 LEU cc_start: 0.9545 (tp) cc_final: 0.9206 (tp) REVERT: A 475 MET cc_start: 0.7926 (tpt) cc_final: 0.7380 (tpp) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1342 time to fit residues: 7.3283 Evaluate side-chains 32 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.477 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 : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9881 (m) cc_final: 0.9570 (p) REVERT: B 584 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8550 (mt-10) REVERT: B 639 THR cc_start: 0.8769 (p) cc_final: 0.8270 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1696 time to fit residues: 5.1420 Evaluate side-chains 26 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.119 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 : 0.106 Fit side-chains revert: symmetry clash REVERT: I 37 LEU cc_start: 0.8748 (mp) cc_final: 0.8357 (tp) REVERT: I 51 MET cc_start: 0.9552 (ttp) cc_final: 0.9014 (tmm) REVERT: I 72 ASP cc_start: 0.9206 (t70) cc_final: 0.8636 (p0) REVERT: I 100 ASP cc_start: 0.9423 (t0) cc_final: 0.9179 (m-30) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.1144 time to fit residues: 3.4749 Evaluate side-chains 19 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.107 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 : 0.090 Fit side-chains REVERT: N 48 MET cc_start: 0.6749 (tpt) cc_final: 0.6537 (tpt) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1215 time to fit residues: 2.5986 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 : 0.094 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: 0.0035 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 : 0.002 ------------------------------------------------------------------------------- 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: 0.6980 chunk 225 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 171 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 221 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.2678 r_free = 0.2678 target = 0.043432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.037343 restraints weight = 555.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.037881 restraints weight = 417.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.038152 restraints weight = 368.622| |-----------------------------------------------------------------------------| r_work (final): 0.2477 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.044196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2220 r_free = 0.2220 target = 0.040627 restraints weight = 293.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.041349 restraints weight = 171.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2231 r_free = 0.2231 target = 0.041944 restraints weight = 118.572| |-----------------------------------------------------------------------------| r_work (final): 0.2216 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055972 restraints weight = 768.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056550 restraints weight = 469.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056983 restraints weight = 324.850| |-----------------------------------------------------------------------------| r_work (final): 0.2944 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.035418 restraints weight = 25770.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.036886 restraints weight = 16614.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.038038 restraints weight = 12068.581| |-----------------------------------------------------------------------------| r_work (final): 0.2787 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.036139 restraints weight = 9552.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.037381 restraints weight = 5611.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.038259 restraints weight = 3860.959| |-----------------------------------------------------------------------------| r_work (final): 0.2674 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.042414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.033585 restraints weight = 7225.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.034834 restraints weight = 4400.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.035821 restraints weight = 3095.303| |-----------------------------------------------------------------------------| r_work (final): 0.2642 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.038485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.029250 restraints weight = 5981.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.030579 restraints weight = 3832.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.031552 restraints weight = 2788.445| |-----------------------------------------------------------------------------| r_work (final): 0.2477 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.056471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.053537 restraints weight = 634.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.054339 restraints weight = 310.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.054928 restraints weight = 189.191| |-----------------------------------------------------------------------------| r_work (final): 0.2798 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.047277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.040520 restraints weight = 756.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040813 restraints weight = 560.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.041099 restraints weight = 500.945| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.039 1.726 22044 Z= 1.924 Angle : 2.592 51.214 30237 Z= 1.054 Chirality : 0.164 3.900 3837 Planarity : 0.010 0.150 3516 Dihedral : 23.713 163.947 6294 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 46.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.40 % 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: -2.34 (0.15), residues: 2412 helix: -1.82 (0.21), residues: 396 sheet: -0.48 (0.19), residues: 618 loop : -2.05 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.006 TRP I 47 HIS 0.019 0.002 HIS C 105 PHE 0.095 0.005 PHE L 95B TYR 0.055 0.005 TYR I 100G ARG 0.011 0.001 ARG M 54 Details of bonding type rmsd link_NAG-ASN : bond 0.21097 ( 72) link_NAG-ASN : angle 12.36878 ( 216) link_ALPHA1-6 : bond 0.46018 ( 15) link_ALPHA1-6 : angle 21.40401 ( 45) link_BETA1-4 : bond 0.02181 ( 81) link_BETA1-4 : angle 3.66228 ( 243) link_ALPHA1-3 : bond 0.23759 ( 12) link_ALPHA1-3 : angle 11.59146 ( 36) hydrogen bonds : bond 0.06939 ( 726) hydrogen bonds : angle 7.07869 ( 1977) SS BOND : bond 0.82747 ( 33) SS BOND : angle 20.14534 ( 66) covalent geometry : bond 0.01327 (21831) covalent geometry : angle 1.96616 (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: 0.0033 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: 0.0049 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 : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9517 (ppp) cc_final: 0.9240 (ppp) REVERT: A 193 LEU cc_start: 0.9429 (tp) cc_final: 0.9211 (tp) REVERT: A 383 PHE cc_start: 0.9788 (m-80) cc_final: 0.9354 (m-80) REVERT: A 453 LEU cc_start: 0.9530 (tp) cc_final: 0.9184 (tp) REVERT: A 475 MET cc_start: 0.7925 (tpt) cc_final: 0.7372 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1518 time to fit residues: 7.2330 Evaluate side-chains 31 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.428 Evaluate side-chains 27 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9877 (m) cc_final: 0.9541 (p) REVERT: B 581 LEU cc_start: 0.9834 (mt) cc_final: 0.9613 (mt) REVERT: B 584 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 639 THR cc_start: 0.8771 (p) cc_final: 0.8289 (p) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1757 time to fit residues: 5.1618 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 : 0.110 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 : 0.106 Fit side-chains revert: symmetry clash REVERT: I 34 MET cc_start: 0.9211 (mmp) cc_final: 0.8994 (mmm) REVERT: I 37 LEU cc_start: 0.8505 (mp) cc_final: 0.8159 (mp) REVERT: I 51 MET cc_start: 0.9565 (ttp) cc_final: 0.9028 (tmm) REVERT: I 72 ASP cc_start: 0.9209 (t70) cc_final: 0.8630 (p0) REVERT: I 100 ASP cc_start: 0.9402 (t0) cc_final: 0.9173 (m-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0758 time to fit residues: 2.0357 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 : 0.109 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 : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0669 time to fit residues: 1.2647 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 : 0.091 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: 0.0041 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 ------------------------------------------------------------------------------- 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: 0.0060 chunk 170 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 166 optimal weight: 0.0050 chunk 63 optimal weight: 0.0370 chunk 219 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 158 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 overall best weight: 0.1826 ------------------------------------------------------------------------------- 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 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 = 0.2764 r_free = 0.2764 target = 0.045149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.035927 restraints weight = 557.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.036755 restraints weight = 428.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.037008 restraints weight = 376.835| |-----------------------------------------------------------------------------| r_work (final): 0.2475 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.045584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.041959 restraints weight = 253.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.042551 restraints weight = 141.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.043057 restraints weight = 105.942| |-----------------------------------------------------------------------------| r_work (final): 0.2232 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056555 restraints weight = 746.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057300 restraints weight = 421.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057789 restraints weight = 291.722| |-----------------------------------------------------------------------------| r_work (final): 0.2980 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.035506 restraints weight = 24123.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.037113 restraints weight = 15645.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.038314 restraints weight = 11296.472| |-----------------------------------------------------------------------------| r_work (final): 0.2805 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.037083 restraints weight = 9172.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038374 restraints weight = 5384.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.039327 restraints weight = 3701.718| |-----------------------------------------------------------------------------| r_work (final): 0.2699 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.041654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.032035 restraints weight = 7147.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.033295 restraints weight = 4517.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.034267 restraints weight = 3233.260| |-----------------------------------------------------------------------------| r_work (final): 0.2641 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.038537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.028520 restraints weight = 5515.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.029981 restraints weight = 3390.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.031091 restraints weight = 2421.797| |-----------------------------------------------------------------------------| r_work (final): 0.2464 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.048083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.047007 restraints weight = 667.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.047515 restraints weight = 204.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.047716 restraints weight = 87.050| |-----------------------------------------------------------------------------| r_work (final): 0.2529 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.047217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040782 restraints weight = 621.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.041032 restraints weight = 473.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.041326 restraints weight = 436.758| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.595 22044 Z= 0.749 Angle : 2.123 46.626 30237 Z= 0.838 Chirality : 0.141 2.869 3837 Planarity : 0.007 0.085 3516 Dihedral : 22.982 167.276 6294 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.34 % Favored : 92.41 % Rotamer: Outliers : 0.42 % Allowed : 3.40 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -2.35 (0.15), residues: 2412 helix: -1.94 (0.22), residues: 396 sheet: -0.31 (0.19), residues: 621 loop : -2.11 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP C 96 HIS 0.027 0.003 HIS E 105 PHE 0.066 0.004 PHE L 95B TYR 0.050 0.004 TYR N 30 ARG 0.008 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.05623 ( 72) link_NAG-ASN : angle 10.99516 ( 216) link_ALPHA1-6 : bond 0.42851 ( 15) link_ALPHA1-6 : angle 21.01873 ( 45) link_BETA1-4 : bond 0.01445 ( 81) link_BETA1-4 : angle 3.14027 ( 243) link_ALPHA1-3 : bond 0.24060 ( 12) link_ALPHA1-3 : angle 11.52579 ( 36) hydrogen bonds : bond 0.06315 ( 726) hydrogen bonds : angle 7.00405 ( 1977) SS BOND : bond 0.06538 ( 33) SS BOND : angle 3.29542 ( 66) covalent geometry : bond 0.00777 (21831) covalent geometry : angle 1.66816 (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 : 0.002 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: 0.0055 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 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9327 (mt) cc_final: 0.9050 (mp) REVERT: A 95 MET cc_start: 0.9567 (ppp) cc_final: 0.9342 (ppp) REVERT: A 193 LEU cc_start: 0.9557 (tp) cc_final: 0.9304 (tp) REVERT: A 383 PHE cc_start: 0.9770 (m-80) cc_final: 0.9310 (m-80) REVERT: A 453 LEU cc_start: 0.9554 (tp) cc_final: 0.9251 (tp) REVERT: A 475 MET cc_start: 0.7635 (tpt) cc_final: 0.7227 (tpp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1599 time to fit residues: 9.0818 Evaluate side-chains 27 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.421 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 : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9846 (m) cc_final: 0.9474 (p) REVERT: B 581 LEU cc_start: 0.9808 (mt) cc_final: 0.9511 (mm) REVERT: B 584 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8488 (mt-10) REVERT: B 633 LYS cc_start: 0.9583 (mtmm) cc_final: 0.9365 (mttt) REVERT: B 639 THR cc_start: 0.8693 (p) cc_final: 0.8102 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1907 time to fit residues: 5.7416 Evaluate side-chains 27 residues out of total 105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.110 Evaluate side-chains 25 residues out of total 101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: I 37 LEU cc_start: 0.8792 (mp) cc_final: 0.8139 (tt) REVERT: I 51 MET cc_start: 0.9557 (ttp) cc_final: 0.8980 (tmm) REVERT: I 80 LEU cc_start: 0.9440 (tp) cc_final: 0.9239 (tp) REVERT: I 82 MET cc_start: 0.9390 (pmm) cc_final: 0.8899 (pmm) REVERT: I 100 ASP cc_start: 0.9337 (t0) cc_final: 0.9119 (m-30) outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.0720 time to fit residues: 2.1130 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 : 0.108 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 : 0.092 Fit side-chains REVERT: N 30 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7439 (m-10) REVERT: N 95 PHE cc_start: 0.7878 (t80) cc_final: 0.7633 (p90) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1209 time to fit residues: 2.5820 Evaluate side-chains 13 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.092 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: 0.0039 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 : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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: 54.4352 > 50: distance: 1 - 2: 3.249 distance: 1 - 3: 3.077 distance: 6 - 7: 6.477 distance: 7 - 8: 6.412 distance: 7 - 10: 7.962 distance: 8 - 9: 5.025 distance: 8 - 15: 6.479 distance: 9 - 38: 19.769 distance: 10 - 11: 6.515 distance: 15 - 16: 8.892 distance: 16 - 17: 14.458 distance: 16 - 19: 9.118 distance: 17 - 18: 6.095 distance: 17 - 23: 5.321 distance: 18 - 44: 19.437 distance: 19 - 20: 6.319 distance: 20 - 21: 10.300 distance: 20 - 22: 6.395 distance: 23 - 24: 20.167 distance: 24 - 25: 34.576 distance: 24 - 27: 18.221 distance: 25 - 26: 41.402 distance: 25 - 30: 30.177 distance: 26 - 52: 27.820 distance: 27 - 28: 17.359 distance: 27 - 29: 15.128 distance: 30 - 31: 12.099 distance: 31 - 32: 10.806 distance: 31 - 34: 8.401 distance: 32 - 33: 14.015 distance: 32 - 38: 26.144 distance: 33 - 66: 11.606 distance: 34 - 35: 24.937 distance: 34 - 36: 21.677 distance: 35 - 37: 10.290 distance: 38 - 39: 32.506 distance: 39 - 40: 41.523 distance: 39 - 42: 21.744 distance: 40 - 41: 23.007 distance: 40 - 44: 37.288 distance: 41 - 74: 12.446 distance: 42 - 43: 29.223 distance: 44 - 45: 27.614 distance: 45 - 46: 9.791 distance: 45 - 48: 19.286 distance: 46 - 47: 23.637 distance: 46 - 52: 16.180 distance: 48 - 49: 6.777 distance: 49 - 50: 8.833 distance: 52 - 53: 10.258 distance: 53 - 54: 7.564 distance: 53 - 56: 9.877 distance: 54 - 55: 8.550 distance: 54 - 66: 8.225 distance: 56 - 57: 9.056 distance: 57 - 58: 6.050 distance: 57 - 59: 6.263 distance: 58 - 60: 4.584 distance: 59 - 61: 17.931 distance: 59 - 62: 5.159 distance: 60 - 61: 11.543 distance: 61 - 63: 18.866 distance: 62 - 64: 3.981 distance: 63 - 65: 10.062 distance: 64 - 65: 7.130 distance: 67 - 68: 5.031 distance: 67 - 70: 3.764 distance: 68 - 69: 9.366 distance: 68 - 74: 7.132 distance: 70 - 71: 5.493 distance: 71 - 72: 5.216 distance: 71 - 73: 6.449 distance: 74 - 75: 4.191 distance: 75 - 78: 6.850 distance: 76 - 77: 5.105