Starting phenix.real_space_refine on Sun Sep 29 07:26:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_21456.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_21456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_21456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_21456.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vy2_21456/09_2024/6vy2_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 14.28, per 1000 atoms: 0.67 Number of scatterers: 21426 At special positions: 0 Unit cell: (151.96, 148.48, 131.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4542 8.00 N 3456 7.00 C 13296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=1.84 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.12 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM20874 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 4 3 " - " MAN 4 4 " " MAN 4 4 " - " MAN 4 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 4 " " MAN o 4 " - " MAN o 5 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA 4 3 " - " MAN 4 6 " " MAN 4 6 " - " MAN 4 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 6 " - " MAN Y 7 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 6 " " MAN o 6 " - " MAN o 7 " " BMA w 3 " - " MAN w 4 " " MAN w 4 " - " MAN w 5 " " BMA z 3 " - " MAN z 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 276 " " NAG 1 1 " - " ASN E 289 " " NAG 2 1 " - " ASN E 334 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 386 " " NAG 5 1 " - " ASN E 392 " " NAG 6 1 " - " ASN E 448 " " NAG 7 1 " - " ASN E 461 " " NAG A 608 " - " ASN A 156 " " NAG A 611 " - " ASN A 187 " " NAG A 635 " - " ASN A 301 " " NAG A 641 " - " ASN A 358 " " NAG A 652 " - " ASN A 442 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 608 " - " ASN C 156 " " NAG C 611 " - " ASN C 187 " " NAG C 635 " - " ASN C 301 " " NAG C 641 " - " ASN C 358 " " NAG C 652 " - " ASN C 442 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 608 " - " ASN E 156 " " NAG E 611 " - " ASN E 187 " " NAG E 635 " - " ASN E 301 " " NAG E 641 " - " ASN E 358 " " NAG E 652 " - " ASN E 442 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 136 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 230 " " NAG S 1 " - " ASN A 241 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN A 289 " " NAG W 1 " - " ASN A 334 " " NAG X 1 " - " ASN A 339 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 461 " " NAG c 1 " - " ASN C 88 " " NAG d 1 " - " ASN C 130 " " NAG e 1 " - " ASN C 136 " " NAG f 1 " - " ASN C 160 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 230 " " NAG i 1 " - " ASN C 241 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 289 " " NAG m 1 " - " ASN C 334 " " NAG n 1 " - " ASN C 339 " " NAG o 1 " - " ASN C 386 " " NAG p 1 " - " ASN C 392 " " NAG q 1 " - " ASN C 448 " " NAG r 1 " - " ASN C 461 " " NAG s 1 " - " ASN E 88 " " NAG t 1 " - " ASN E 130 " " NAG u 1 " - " ASN E 136 " " NAG v 1 " - " ASN E 160 " " NAG w 1 " - " ASN E 197 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN E 262 " Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 2.3 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 22.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 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: 7.32 Time building geometry restraints manager: 8.31 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: 3.030 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 50.930 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.460 ------------------------------------------------------------------------------- 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 : 0.007 0.088 21831 Z= 0.419 Angle : 1.112 10.094 29631 Z= 0.542 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 *********************** 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 84 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.424 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: 0.1508 time to fit residues: 14.8930 Evaluate side-chains 44 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.404 Evaluate side-chains 49 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.103 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: 0.2019 time to fit residues: 10.0361 Evaluate side-chains 25 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.102 Evaluate side-chains 43 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.113 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: 0.1094 time to fit residues: 4.8568 Evaluate side-chains 19 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.099 Evaluate side-chains 32 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.098 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: 0.1450 time to fit residues: 4.8593 Evaluate side-chains 14 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.091 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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: 0.0034 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.202 21831 Z= 0.740 Angle : 2.202 41.760 29631 Z= 0.868 Chirality : 0.109 1.553 3837 Planarity : 0.007 0.098 3516 Dihedral : 24.648 162.438 6294 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.09 % Favored : 93.53 % Rotamer: Outliers : 1.27 % Allowed : 4.67 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2412 helix: -1.65 (0.23), residues: 396 sheet: -0.55 (0.19), residues: 654 loop : -1.91 (0.14), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 571 HIS 0.003 0.001 HIS L 39 PHE 0.047 0.004 PHE M 32 TYR 0.077 0.004 TYR J 100A ARG 0.034 0.001 ARG A 393 *********************** 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 fitting. 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 fitting. 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0060 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 107 ASP cc_start: 0.9252 (m-30) cc_final: 0.9044 (m-30) REVERT: A 193 LEU cc_start: 0.9648 (tp) cc_final: 0.9415 (tp) REVERT: A 285 ILE cc_start: 0.9419 (mt) cc_final: 0.9211 (tp) REVERT: A 453 LEU cc_start: 0.9201 (tp) cc_final: 0.8803 (tp) REVERT: A 475 MET cc_start: 0.7349 (tpt) cc_final: 0.7009 (tpp) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 0.2565 time to fit residues: 14.9347 Evaluate side-chains 34 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.390 Evaluate side-chains 32 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9022 (mtp) cc_final: 0.8398 (mmt) REVERT: B 584 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8689 (mt-10) REVERT: B 587 LEU cc_start: 0.9777 (mm) cc_final: 0.9553 (pp) REVERT: B 639 THR cc_start: 0.8647 (p) cc_final: 0.7748 (p) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1787 time to fit residues: 6.1492 Evaluate side-chains 23 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.101 Evaluate side-chains 30 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 51 MET cc_start: 0.9049 (ttp) cc_final: 0.8698 (tmm) REVERT: J 69 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8845 (p) REVERT: J 100 LEU cc_start: 0.9236 (pt) cc_final: 0.9005 (pp) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.0920 time to fit residues: 3.0041 Evaluate side-chains 22 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.113 Evaluate side-chains 21 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1272 time to fit residues: 2.9633 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.091 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 0.0970 chunk 235 optimal weight: 0.1980 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 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... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.176 21831 Z= 0.665 Angle : 1.801 46.374 29631 Z= 0.766 Chirality : 0.133 2.060 3837 Planarity : 0.008 0.066 3516 Dihedral : 23.357 168.530 6294 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.84 % Favored : 92.91 % Rotamer: Outliers : 1.13 % Allowed : 4.25 % Favored : 94.62 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 1.03 % 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: -1.68 (0.22), residues: 396 sheet: -0.40 (0.20), residues: 591 loop : -1.94 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP I 47 HIS 0.024 0.003 HIS A 105 PHE 0.040 0.004 PHE L 95B TYR 0.100 0.006 TYR E 61 ARG 0.006 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 45 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9381 (ppp) cc_final: 0.9174 (ppp) REVERT: A 453 LEU cc_start: 0.9212 (tp) cc_final: 0.8903 (tp) REVERT: A 475 MET cc_start: 0.7304 (tpt) cc_final: 0.6789 (tpt) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.1506 time to fit residues: 8.3717 Evaluate side-chains 32 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.446 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9794 (m) cc_final: 0.9473 (p) REVERT: B 581 LEU cc_start: 0.9784 (mt) cc_final: 0.9402 (mm) REVERT: B 584 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 639 THR cc_start: 0.8594 (p) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1819 time to fit residues: 5.8884 Evaluate side-chains 25 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.100 Evaluate side-chains 24 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.9310 (mp) cc_final: 0.9022 (mp) REVERT: J 100 LEU cc_start: 0.9226 (pt) cc_final: 0.8988 (pp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.0875 time to fit residues: 2.4377 Evaluate side-chains 21 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.098 Evaluate side-chains 20 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.084 Fit side-chains REVERT: N 48 MET cc_start: 0.7301 (tpt) cc_final: 0.6273 (tpp) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1218 time to fit residues: 2.7293 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.096 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 215 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 0.0870 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.0170 chunk 62 optimal weight: 0.0050 overall best weight: 0.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.176 21831 Z= 0.674 Angle : 1.802 46.374 29631 Z= 0.767 Chirality : 0.169 4.011 3837 Planarity : 0.008 0.066 3516 Dihedral : 23.357 168.530 6294 Min Nonbonded Distance : 0.963 Molprobity Statistics. All-atom Clashscore : 42.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.84 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 1.03 % 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: -1.68 (0.22), residues: 396 sheet: -0.40 (0.20), residues: 591 loop : -1.94 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP I 47 HIS 0.024 0.003 HIS E 105 PHE 0.040 0.004 PHE L 95B TYR 0.100 0.006 TYR E 61 ARG 0.006 0.001 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 4 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 33 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9221 (tp) cc_final: 0.8920 (tp) REVERT: A 475 MET cc_start: 0.7292 (tpt) cc_final: 0.6789 (tpt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1060 time to fit residues: 5.1677 Evaluate side-chains 31 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.419 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9795 (m) cc_final: 0.9472 (p) REVERT: B 581 LEU cc_start: 0.9785 (mt) cc_final: 0.9402 (mm) REVERT: B 584 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8560 (mt-10) REVERT: B 639 THR cc_start: 0.8542 (p) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1761 time to fit residues: 5.3347 Evaluate side-chains 24 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.100 Evaluate side-chains 23 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.8495 (mp) cc_final: 0.8220 (mp) REVERT: J 100 LEU cc_start: 0.9231 (pt) cc_final: 0.8988 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0987 time to fit residues: 2.6286 Evaluate side-chains 20 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.109 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 Fit side-chains REVERT: N 48 MET cc_start: 0.7345 (tpt) cc_final: 0.6270 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0689 time to fit residues: 1.4533 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.110 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.176 21831 Z= 0.674 Angle : 1.802 46.374 29631 Z= 0.767 Chirality : 0.169 4.007 3837 Planarity : 0.008 0.066 3516 Dihedral : 23.358 168.530 6294 Min Nonbonded Distance : 0.964 Molprobity Statistics. All-atom Clashscore : 44.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.84 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 1.03 % 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: -1.68 (0.22), residues: 396 sheet: -0.40 (0.20), residues: 591 loop : -1.94 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP I 47 HIS 0.024 0.003 HIS C 105 PHE 0.040 0.004 PHE L 95B TYR 0.100 0.006 TYR C 61 ARG 0.006 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 5 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 32 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9219 (tp) cc_final: 0.8920 (tp) REVERT: A 475 MET cc_start: 0.7289 (tpt) cc_final: 0.6790 (tpt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1018 time to fit residues: 4.9010 Evaluate side-chains 30 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.463 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9795 (m) cc_final: 0.9472 (p) REVERT: B 581 LEU cc_start: 0.9785 (mt) cc_final: 0.9402 (mm) REVERT: B 584 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8560 (mt-10) REVERT: B 639 THR cc_start: 0.8542 (p) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1686 time to fit residues: 5.1311 Evaluate side-chains 24 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.103 Evaluate side-chains 23 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.8495 (mp) cc_final: 0.8220 (mp) REVERT: J 100 LEU cc_start: 0.9231 (pt) cc_final: 0.8988 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0911 time to fit residues: 2.4394 Evaluate side-chains 20 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.115 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.101 Fit side-chains REVERT: N 48 MET cc_start: 0.7349 (tpt) cc_final: 0.6274 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0685 time to fit residues: 1.4432 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.107 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0060 chunk 208 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 40.0000 chunk 192 optimal weight: 0.0010 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 0.0770 overall best weight: 0.1774 ------------------------------------------------------------------------------- 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 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 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.155 21831 Z= 0.639 Angle : 1.778 45.798 29631 Z= 0.770 Chirality : 0.138 2.305 3837 Planarity : 0.009 0.103 3516 Dihedral : 23.046 166.846 6294 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.28 % Allowed : 3.12 % Favored : 96.60 % Cbeta Deviations : 0.27 % 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: -2.24 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 396 sheet: -0.32 (0.19), residues: 621 loop : -2.05 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP C 96 HIS 0.025 0.003 HIS C 105 PHE 0.035 0.004 PHE M 95B TYR 0.061 0.005 TYR M 30 ARG 0.011 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 6 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 fitting. 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: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 Evaluate side-chains 36 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9239 (tp) cc_final: 0.8966 (tp) REVERT: A 475 MET cc_start: 0.7210 (tpt) cc_final: 0.6693 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1464 time to fit residues: 7.0315 Evaluate side-chains 31 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.481 Evaluate side-chains 29 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9789 (m) cc_final: 0.9443 (p) REVERT: B 581 LEU cc_start: 0.9781 (mt) cc_final: 0.9427 (mm) REVERT: B 584 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8537 (mt-10) REVERT: B 639 THR cc_start: 0.8526 (p) cc_final: 0.7511 (p) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1881 time to fit residues: 5.8862 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.118 Evaluate side-chains 27 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 MET cc_start: 0.8506 (mmp) cc_final: 0.8256 (mmm) REVERT: J 37 LEU cc_start: 0.9091 (mp) cc_final: 0.8610 (tt) REVERT: J 100 LEU cc_start: 0.9195 (pt) cc_final: 0.8914 (pp) REVERT: J 101 ASP cc_start: 0.6098 (t0) cc_final: 0.5827 (t70) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0952 time to fit residues: 2.8739 Evaluate side-chains 21 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.118 Evaluate side-chains 20 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.100 Fit side-chains REVERT: N 48 MET cc_start: 0.7615 (tpt) cc_final: 0.6568 (tpp) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0974 time to fit residues: 2.2605 Evaluate side-chains 11 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.109 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 132 optimal weight: 0.0870 chunk 169 optimal weight: 0.0670 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 0.0010 chunk 106 optimal weight: 0.6980 overall best weight: 0.0680 ------------------------------------------------------------------------------- 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 404 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.155 21831 Z= 0.639 Angle : 1.777 45.799 29631 Z= 0.770 Chirality : 0.138 2.306 3837 Planarity : 0.009 0.103 3516 Dihedral : 23.046 166.846 6294 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 35.82 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -2.24 (0.15), residues: 2412 helix: -1.69 (0.23), residues: 396 sheet: -0.32 (0.19), residues: 621 loop : -2.05 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP C 96 HIS 0.025 0.003 HIS A 105 PHE 0.035 0.004 PHE M 95B TYR 0.061 0.005 TYR N 30 ARG 0.011 0.001 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 7 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 fitting. 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: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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: 0.0051 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 37 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9403 (ppp) cc_final: 0.9199 (ppp) REVERT: A 98 ASN cc_start: 0.8090 (p0) cc_final: 0.7859 (p0) REVERT: A 453 LEU cc_start: 0.9237 (tp) cc_final: 0.8966 (tp) REVERT: A 475 MET cc_start: 0.7209 (tpt) cc_final: 0.6709 (tpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1421 time to fit residues: 6.9068 Evaluate side-chains 30 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.389 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9788 (m) cc_final: 0.9444 (p) REVERT: B 581 LEU cc_start: 0.9781 (mt) cc_final: 0.9428 (mm) REVERT: B 584 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8539 (mt-10) REVERT: B 639 THR cc_start: 0.8518 (p) cc_final: 0.7490 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1769 time to fit residues: 5.7186 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.117 Evaluate side-chains 23 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.9111 (mp) cc_final: 0.8608 (tt) REVERT: J 100 LEU cc_start: 0.9192 (pt) cc_final: 0.8915 (pp) REVERT: J 101 ASP cc_start: 0.6048 (t0) cc_final: 0.5830 (t70) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0995 time to fit residues: 2.6520 Evaluate side-chains 20 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.098 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.084 Fit side-chains REVERT: N 48 MET cc_start: 0.7593 (tpt) cc_final: 0.6577 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0928 time to fit residues: 1.8315 Evaluate side-chains 11 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.102 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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: 0.0033 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0010 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 0.2980 overall best weight: 1.6708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.422 21831 Z= 0.860 Angle : 1.841 46.047 29631 Z= 0.790 Chirality : 0.143 2.512 3837 Planarity : 0.010 0.100 3516 Dihedral : 23.026 166.681 6294 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.27 % 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: -2.30 (0.15), residues: 2412 helix: -1.78 (0.22), residues: 396 sheet: -0.33 (0.19), residues: 621 loop : -2.08 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP C 96 HIS 0.140 0.010 HIS E 72 PHE 0.039 0.004 PHE L 62 TYR 0.087 0.006 TYR L 30 ARG 0.011 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 8 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 fitting. 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: 0.0033 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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: 0.0047 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 33 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9404 (ppp) cc_final: 0.9200 (ppp) REVERT: A 98 ASN cc_start: 0.8138 (p0) cc_final: 0.7837 (p0) REVERT: A 453 LEU cc_start: 0.9239 (tp) cc_final: 0.8968 (tp) REVERT: A 475 MET cc_start: 0.7242 (tpt) cc_final: 0.6938 (tpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1338 time to fit residues: 5.9711 Evaluate side-chains 26 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.393 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9789 (m) cc_final: 0.9464 (p) REVERT: B 581 LEU cc_start: 0.9783 (mt) cc_final: 0.9420 (mm) REVERT: B 584 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8544 (mt-10) REVERT: B 639 THR cc_start: 0.8522 (p) cc_final: 0.7484 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1748 time to fit residues: 5.6417 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.100 Evaluate side-chains 23 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.9107 (mp) cc_final: 0.8634 (tt) REVERT: J 96 LEU cc_start: 0.8956 (mp) cc_final: 0.8433 (mt) REVERT: J 100 LEU cc_start: 0.9195 (pt) cc_final: 0.8926 (pp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0886 time to fit residues: 2.3726 Evaluate side-chains 19 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.097 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.087 Fit side-chains REVERT: N 48 MET cc_start: 0.7609 (tpt) cc_final: 0.6565 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0910 time to fit residues: 1.8013 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 0.0770 chunk 93 optimal weight: 0.0470 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 0.0270 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.422 21831 Z= 0.860 Angle : 1.841 46.047 29631 Z= 0.790 Chirality : 0.143 2.512 3837 Planarity : 0.010 0.100 3516 Dihedral : 23.026 166.681 6294 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 37.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -2.30 (0.15), residues: 2412 helix: -1.78 (0.22), residues: 396 sheet: -0.33 (0.19), residues: 621 loop : -2.08 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP A 96 HIS 0.140 0.010 HIS C 72 PHE 0.039 0.004 PHE M 62 TYR 0.087 0.006 TYR L 30 ARG 0.011 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. 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: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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 fitting. 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: 0.0051 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 31 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9400 (ppp) cc_final: 0.9199 (ppp) REVERT: A 98 ASN cc_start: 0.8136 (p0) cc_final: 0.7837 (p0) REVERT: A 193 LEU cc_start: 0.9473 (tp) cc_final: 0.9263 (tp) REVERT: A 453 LEU cc_start: 0.9210 (tp) cc_final: 0.8941 (tp) REVERT: A 475 MET cc_start: 0.8038 (tpt) cc_final: 0.6940 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1134 time to fit residues: 5.1872 Evaluate side-chains 27 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.426 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9789 (m) cc_final: 0.9464 (p) REVERT: B 581 LEU cc_start: 0.9783 (mt) cc_final: 0.9420 (mm) REVERT: B 584 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 639 THR cc_start: 0.8521 (p) cc_final: 0.7484 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1822 time to fit residues: 5.8722 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.110 Evaluate side-chains 22 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.9105 (mp) cc_final: 0.8635 (tt) REVERT: J 100 LEU cc_start: 0.9199 (pt) cc_final: 0.8924 (pp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0946 time to fit residues: 2.4200 Evaluate side-chains 19 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.110 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: N 48 MET cc_start: 0.7603 (tpt) cc_final: 0.6567 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0946 time to fit residues: 1.8719 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.101 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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: 0.0033 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0050 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.0770 chunk 158 optimal weight: 0.0040 chunk 239 optimal weight: 0.1980 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.0060 overall best weight: 0.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.422 21831 Z= 0.860 Angle : 1.841 46.047 29631 Z= 0.790 Chirality : 0.143 2.512 3837 Planarity : 0.010 0.100 3516 Dihedral : 23.026 166.681 6294 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 36.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -2.30 (0.15), residues: 2412 helix: -1.78 (0.22), residues: 396 sheet: -0.33 (0.19), residues: 621 loop : -2.08 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP C 96 HIS 0.140 0.010 HIS C 72 PHE 0.039 0.004 PHE L 62 TYR 0.087 0.006 TYR L 30 ARG 0.011 0.001 ARG E 308 ********************** REFINEMENT MACRO_CYCLE 10 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0057 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 31 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9399 (ppp) cc_final: 0.9199 (ppp) REVERT: A 98 ASN cc_start: 0.8135 (p0) cc_final: 0.7837 (p0) REVERT: A 193 LEU cc_start: 0.9474 (tp) cc_final: 0.9266 (tp) REVERT: A 453 LEU cc_start: 0.9210 (tp) cc_final: 0.8941 (tp) REVERT: A 475 MET cc_start: 0.8038 (tpt) cc_final: 0.6940 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1073 time to fit residues: 4.8987 Evaluate side-chains 26 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.427 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9789 (m) cc_final: 0.9464 (p) REVERT: B 581 LEU cc_start: 0.9783 (mt) cc_final: 0.9420 (mm) REVERT: B 584 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 639 THR cc_start: 0.8521 (p) cc_final: 0.7484 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1887 time to fit residues: 6.1134 Evaluate side-chains 28 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.101 Evaluate side-chains 22 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 LEU cc_start: 0.9110 (mp) cc_final: 0.8635 (tt) REVERT: J 100 LEU cc_start: 0.9198 (pt) cc_final: 0.8924 (pp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1003 time to fit residues: 2.5636 Evaluate side-chains 19 residues out of total 101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.111 Evaluate side-chains 17 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: N 48 MET cc_start: 0.7601 (tpt) cc_final: 0.6565 (tpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0981 time to fit residues: 1.9384 Evaluate side-chains 12 residues out of total 90 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.096 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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 fitting. 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 fitting. 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 fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.7980 chunk 202 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2555 r_free = 0.2555 target = 0.038684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036263 restraints weight = 593.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.037262 restraints weight = 233.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.038195 restraints weight = 143.135| |-----------------------------------------------------------------------------| r_work (final): 0.2541 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.045426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.041483 restraints weight = 276.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.042113 restraints weight = 165.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.042660 restraints weight = 116.714| |-----------------------------------------------------------------------------| r_work (final): 0.2228 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052608 restraints weight = 662.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.053551 restraints weight = 466.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.054170 restraints weight = 348.582| |-----------------------------------------------------------------------------| r_work (final): 0.2865 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035095 restraints weight = 26014.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036537 restraints weight = 16815.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.037640 restraints weight = 12179.067| |-----------------------------------------------------------------------------| r_work (final): 0.2768 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041557 restraints weight = 7672.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.043040 restraints weight = 4221.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044114 restraints weight = 2817.781| |-----------------------------------------------------------------------------| r_work (final): 0.3034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.033305 restraints weight = 7509.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.034647 restraints weight = 4796.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.035770 restraints weight = 3468.948| |-----------------------------------------------------------------------------| r_work (final): 0.2685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.030327 restraints weight = 5136.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.031831 restraints weight = 3054.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.032896 restraints weight = 2144.410| |-----------------------------------------------------------------------------| r_work (final): 0.2491 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060968 restraints weight = 969.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061829 restraints weight = 482.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062206 restraints weight = 331.686| |-----------------------------------------------------------------------------| r_work (final): 0.2978 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.040642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.038047 restraints weight = 723.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.038608 restraints weight = 293.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.038880 restraints weight = 190.784| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.422 21831 Z= 0.860 Angle : 1.841 46.047 29631 Z= 0.790 Chirality : 0.143 2.512 3837 Planarity : 0.010 0.100 3516 Dihedral : 23.026 166.681 6294 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 36.64 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -2.30 (0.15), residues: 2412 helix: -1.78 (0.22), residues: 396 sheet: -0.33 (0.19), residues: 621 loop : -2.08 (0.14), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP C 96 HIS 0.140 0.010 HIS C 72 PHE 0.039 0.004 PHE M 62 TYR 0.087 0.006 TYR L 30 ARG 0.011 0.001 ARG A 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.00 seconds wall clock time: 92 minutes 22.70 seconds (5542.70 seconds total)