Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 18:12:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fuu_3308/04_2023/5fuu_3308_neut_updated.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 116 5.16 5 C 12882 2.51 5 N 3274 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20735 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3553 Classifications: {'peptide': 449} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1150 Classifications: {'peptide': 144} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3537 Classifications: {'peptide': 448} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1209 Classifications: {'peptide': 153} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 148} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} 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 chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "S" 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 chiralities: 3 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 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 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 chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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 chiralities: 2 Chain: "Y" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 160 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 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 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 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 chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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 chiralities: 5 Chain: "f" 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 chiralities: 7 Chain: "g" 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 chiralities: 3 Chain: "h" 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 chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" 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 chiralities: 2 Chain: "p" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 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 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 chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 chiralities: 2 Chain: "x" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 7 Chain: "z" 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 chiralities: 2 Chain: "0" 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 chiralities: 2 Chain: "1" 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 chiralities: 2 Chain: "2" 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 chiralities: 3 Chain: "3" 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 chiralities: 2 Chain: "4" 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 chiralities: 2 Chain: "5" 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 chiralities: 2 Chain: "6" 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 chiralities: 4 Chain: "7" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "8" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "9" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 149 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" 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 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 chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.91, per 1000 atoms: 0.53 Number of scatterers: 20735 At special positions: 0 Unit cell: (137.55, 153.27, 140.17, 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 116 16.00 O 4463 8.00 N 3274 7.00 C 12882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 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 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 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 22 " - pdb=" SG CYS M 92 " 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM20028 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18843 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 8 4 " - " MAN 8 5 " " MAN O 4 " - " MAN O 5 " " MAN f 4 " - " MAN f 5 " " MAN p 4 " - " MAN p 5 " " MAN x 4 " - " MAN x 5 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA 8 3 " - " MAN 8 4 " " MAN 8 6 " - " MAN 8 7 " " BMA 9 3 " - " MAN 9 9 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA Y 3 " - " MAN Y 9 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 6 " - " MAN y 7 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 6 3 " - " MAN 6 4 " " BMA 8 3 " - " MAN 8 6 " " MAN 8 6 " - " MAN 8 8 " " BMA 9 3 " - " MAN 9 4 " " BMA O 3 " - " MAN O 6 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 9 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA x 3 " - " MAN x 6 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 9 " BETA1-2 " MAN 9 4 " - " NAG 9 5 " " MAN 9 9 " - " NAG 9 10 " " MAN Y 4 " - " NAG Y 5 " " MAN Y 9 " - " NAG Y 10 " " MAN Z 4 " - " NAG Z 5 " " MAN Z 9 " - " NAG Z 10 " " MANBA 4 " - " NAGBA 5 " " MANBA 9 " - " NAGBA 10 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG 9 5 " - " GAL 9 6 " " NAG 9 7 " - " GAL 9 8 " " NAG G 1 " - " NAG G 2 " " 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 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Y 5 " - " GAL Y 6 " " NAG Y 7 " - " GAL Y 8 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " MAN Z 4 " - " NAG Z 7 " " NAG Z 5 " - " GAL Z 6 " " NAG Z 7 " - " GAL Z 8 " " NAG Z 10 " - " GAL Z 11 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG 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 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " MANBA 4 " - " NAGBA 7 " " NAGBA 5 " - " GALBA 6 " " NAGBA 7 " - " GALBA 8 " BETA1-6 " NAG 9 1 " - " FUC 9 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN 9 4 " - " NAG 9 7 " " NAG Y 1 " - " FUC Y 11 " " MAN Y 4 " - " NAG Y 7 " " NAG Z 1 " - " FUC Z 13 " " MAN Z 9 " - " NAG Z 12 " " NAG q 1 " - " FUC q 3 " " NAGBA 1 " - " FUCBA 12 " " MANBA 9 " - " NAGBA 11 " NAG-ASN " NAG 0 1 " - " ASN E 295 " " NAG 1 1 " - " ASN E 301 " " NAG 2 1 " - " ASN E 332 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 355 " " NAG 5 1 " - " ASN E 362 " " NAG 6 1 " - " ASN E 386 " " NAG 7 1 " - " ASN E 392 " " NAG 8 1 " - " ASN E 448 " " NAG 9 1 " - " ASN F 611 " " NAG A1135 " - " ASN A 135 " " NAG A1355 " - " ASN A 355 " " NAG A1397 " - " ASN A 397 " " NAG B1600 " - " ASN B 616 " " NAG B1625 " - " ASN B 625 " " NAG C1397 " - " ASN C 397 " " NAG D1600 " - " ASN D 616 " " NAG E1187 " - " ASN E 187 " " NAG E1397 " - " ASN E 397 " " NAG F1600 " - " ASN F 616 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 339 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN B 611 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 135 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 241 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 276 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 339 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 362 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 611 " " NAG r 1 " - " ASN D 625 " " NAG s 1 " - " ASN D 637 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 135 " " NAG v 1 " - " ASN E 156 " " NAG w 1 " - " ASN E 160 " " NAG x 1 " - " ASN E 241 " " NAG y 1 " - " ASN E 262 " " NAG z 1 " - " ASN E 276 " " NAGAA 1 " - " ASN F 625 " " NAGBA 1 " - " ASN F 637 " Time building additional restraints: 13.07 Conformation dependent library (CDL) restraints added in 2.9 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 43 sheets defined 21.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.549A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 Processing helix chain 'B' and resid 530 through 540 removed outlier: 6.551A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.110A pdb=" N ALA B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.802A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.581A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 4.402A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 662 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.550A pdb=" N ASP C 107 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 108 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 112 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.689A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'D' and resid 524 through 527 removed outlier: 3.649A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 530 through 533 No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing helix chain 'D' and resid 537 through 543 removed outlier: 4.379A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.511A pdb=" N GLN D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.852A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 656 removed outlier: 5.435A pdb=" N ASN D 637 " --> pdb=" O ARG D 633 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 352 removed outlier: 3.668A pdb=" N VAL E 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 475 through 483 removed outlier: 4.272A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.874A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.719A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 568 removed outlier: 3.843A pdb=" N GLN F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU F 568 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.170A pdb=" N LEU F 592 " --> pdb=" O GLY F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 651 removed outlier: 3.619A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN F 637 " --> pdb=" O ARG F 633 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER F 640 " --> pdb=" O ASP F 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 184 removed outlier: 4.593A pdb=" N SER A 190 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= H, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.048A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 413 through 417 removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 374 through 378 Processing sheet with id= K, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.705A pdb=" N GLU A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.080A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= P, first strand: chain 'C' and resid 155 through 157 Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.741A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.127A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ASN C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 445 through 449 removed outlier: 3.575A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.942A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= W, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.934A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= Y, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= Z, first strand: chain 'E' and resid 154 through 162 Processing sheet with id= AA, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AC, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.615A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 443 through 449 Processing sheet with id= AE, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.409A pdb=" N GLU E 466 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN E 362 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE E 468 " --> pdb=" O ASN E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'E' and resid 374 through 377 Processing sheet with id= AG, first strand: chain 'E' and resid 302 through 308 removed outlier: 3.692A pdb=" N GLU E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AI, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.843A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.631A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.599A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.389A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP L 105 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 4 through 7 Processing sheet with id= AN, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.811A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.701A pdb=" N VAL M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= AQ, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.887A pdb=" N LYS N 103 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1479 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: 6.93 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4977 1.33 - 1.45: 5227 1.45 - 1.57: 10733 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 21101 Sorted by residual: bond pdb=" CA ASN A 229 " pdb=" CB ASN A 229 " ideal model delta sigma weight residual 1.530 1.412 0.117 1.64e-02 3.72e+03 5.11e+01 bond pdb=" N PRO E 118 " pdb=" CD PRO E 118 " ideal model delta sigma weight residual 1.473 1.553 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" N PRO A 118 " pdb=" CD PRO A 118 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.91e+01 bond pdb=" CA SER F 599 " pdb=" C SER F 599 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.28e-02 6.10e+03 2.58e+01 bond pdb=" C ASN E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.11e-02 8.12e+03 2.45e+01 ... (remaining 21096 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.78: 1038 106.78 - 114.32: 12689 114.32 - 121.86: 10639 121.86 - 129.40: 4096 129.40 - 136.95: 168 Bond angle restraints: 28630 Sorted by residual: angle pdb=" C GLY M 100 " pdb=" N PRO M 100A" pdb=" CA PRO M 100A" ideal model delta sigma weight residual 119.66 128.29 -8.63 7.30e-01 1.88e+00 1.40e+02 angle pdb=" C ASN C 80 " pdb=" N PRO C 81 " pdb=" CA PRO C 81 " ideal model delta sigma weight residual 119.99 130.47 -10.48 1.08e+00 8.57e-01 9.42e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 128.86 -9.10 1.00e+00 1.00e+00 8.29e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.32 129.28 -9.96 1.14e+00 7.69e-01 7.64e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.92 -6.26 7.20e-01 1.93e+00 7.57e+01 ... (remaining 28625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 10858 26.70 - 53.39: 176 53.39 - 80.09: 49 80.09 - 106.78: 7 106.78 - 133.48: 1 Dihedral angle restraints: 11091 sinusoidal: 4521 harmonic: 6570 Sorted by residual: dihedral pdb=" CA ASN E 412 " pdb=" C ASN E 412 " pdb=" N THR E 413 " pdb=" CA THR E 413 " ideal model delta harmonic sigma weight residual -180.00 -46.52 -133.48 0 5.00e+00 4.00e-02 7.13e+02 dihedral pdb=" CA VAL C 65 " pdb=" C VAL C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta harmonic sigma weight residual 0.00 -37.56 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" C GLN C 352 " pdb=" N GLN C 352 " pdb=" CA GLN C 352 " pdb=" CB GLN C 352 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 11088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3170 0.158 - 0.317: 638 0.317 - 0.475: 19 0.475 - 0.634: 13 0.634 - 0.792: 10 Chirality restraints: 3850 Sorted by residual: chirality pdb=" C1 MAN f 7 " pdb=" O3 MAN f 6 " pdb=" C2 MAN f 7 " pdb=" O5 MAN f 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN O 7 " pdb=" O3 MAN O 6 " pdb=" C2 MAN O 7 " pdb=" O5 MAN O 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 chirality pdb=" C1 MAN y 7 " pdb=" O3 MAN y 6 " pdb=" C2 MAN y 7 " pdb=" O5 MAN y 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 ... (remaining 3847 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.300 2.00e-02 2.50e+03 3.39e-01 1.44e+03 pdb=" CG ASN C 301 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.446 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 156 " 0.258 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN A 156 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASN A 156 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 156 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.450 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.308 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN C 156 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.474 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.440 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 173 2.47 - 3.08: 15582 3.08 - 3.68: 28470 3.68 - 4.29: 45074 4.29 - 4.90: 70402 Nonbonded interactions: 159701 Sorted by model distance: nonbonded pdb=" NE ARG A 298 " pdb=" CD1 ILE A 443 " model vdw 1.862 3.540 nonbonded pdb=" CA PRO E 183 " pdb=" CD1 TYR E 191 " model vdw 1.869 3.770 nonbonded pdb=" OD1 ASN A 339 " pdb=" N ASP A 340 " model vdw 1.900 2.520 nonbonded pdb=" O ALA E 336 " pdb=" OD1 ASN E 339 " model vdw 1.967 3.040 nonbonded pdb=" OE1 GLU A 87 " pdb=" O7 NAG G 1 " model vdw 1.996 3.040 ... (remaining 159696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AA' selection = chain 'G' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'z' } ncs_group { reference = (chain '2' and resid 1 through 2) selection = (chain '7' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = (chain '8' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 2 or resid 5 through 8)) selection = (chain 'y' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '9' and (resid 1 or resid 10 through 11)) selection = (chain 'BA' and (resid 2 or resid 11 through 12)) selection = (chain 'Y' and (resid 1 or resid 10 through 11)) } ncs_group { reference = (chain 'A' and (resid 31 through 136 or resid 152 through 401 or resid 410 throu \ gh 506 or resid 1397)) selection = (chain 'C' and (resid 31 through 57 or resid 64 through 401 or resid 410 through \ 506 or resid 1397)) selection = (chain 'E' and (resid 31 through 57 or resid 64 through 136 or resid 152 through \ 401 or resid 410 through 506 or resid 1397)) } ncs_group { reference = (chain 'B' and resid 521 through 658) selection = (chain 'D' and resid 521 through 658) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.020 Extract box with map and model: 5.580 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 57.690 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.014 0.117 21101 Z= 0.872 Angle : 1.862 13.033 28630 Z= 1.055 Chirality : 0.120 0.792 3850 Planarity : 0.017 0.137 3338 Dihedral : 11.136 133.475 6749 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 1.69 % Allowed : 6.15 % Favored : 92.15 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.38 (0.15), residues: 2243 helix: -1.70 (0.20), residues: 431 sheet: -1.02 (0.20), residues: 600 loop : -1.82 (0.16), residues: 1212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 562 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 583 average time/residue: 0.3818 time to fit residues: 320.9354 Evaluate side-chains 238 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 2.478 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 0.2055 time to fit residues: 7.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS C 99 ASN C 389 GLN D 624 ASN E 66 HIS E 428 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 624 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 76 ASN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21101 Z= 0.237 Angle : 0.940 11.528 28630 Z= 0.438 Chirality : 0.054 0.779 3850 Planarity : 0.005 0.047 3338 Dihedral : 5.468 58.835 2444 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.59 % Favored : 94.69 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.59 (0.16), residues: 2243 helix: -0.68 (0.23), residues: 433 sheet: -0.63 (0.20), residues: 591 loop : -1.40 (0.16), residues: 1219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 362 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 364 average time/residue: 0.3288 time to fit residues: 184.2866 Evaluate side-chains 221 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 55 optimal weight: 0.0570 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 201 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 overall best weight: 2.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 553 ASN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN M 76 ASN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN N 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 21101 Z= 0.310 Angle : 0.887 29.076 28630 Z= 0.410 Chirality : 0.048 0.375 3850 Planarity : 0.004 0.044 3338 Dihedral : 5.289 38.422 2444 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.97 % Favored : 93.31 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.43 (0.17), residues: 2243 helix: -0.58 (0.24), residues: 431 sheet: -0.55 (0.20), residues: 622 loop : -1.27 (0.17), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 299 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 303 average time/residue: 0.3169 time to fit residues: 149.5218 Evaluate side-chains 211 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 2.344 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1988 time to fit residues: 4.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 0.7980 chunk 152 optimal weight: 0.0040 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 21101 Z= 0.273 Angle : 0.824 26.784 28630 Z= 0.383 Chirality : 0.047 0.360 3850 Planarity : 0.004 0.051 3338 Dihedral : 5.124 39.017 2444 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.69 % Favored : 92.82 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.28 (0.17), residues: 2243 helix: -0.39 (0.24), residues: 430 sheet: -0.35 (0.20), residues: 594 loop : -1.26 (0.18), residues: 1219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 289 average time/residue: 0.3285 time to fit residues: 147.1619 Evaluate side-chains 212 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1866 time to fit residues: 3.7529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 21101 Z= 0.304 Angle : 0.831 25.224 28630 Z= 0.387 Chirality : 0.047 0.365 3850 Planarity : 0.005 0.063 3338 Dihedral : 5.155 37.452 2444 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.60 % Favored : 92.96 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.31 (0.17), residues: 2243 helix: -0.33 (0.25), residues: 427 sheet: -0.41 (0.20), residues: 626 loop : -1.31 (0.18), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.3312 time to fit residues: 141.1791 Evaluate side-chains 193 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN B 577 GLN B 656 ASN E 82 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21101 Z= 0.214 Angle : 0.765 27.268 28630 Z= 0.357 Chirality : 0.045 0.353 3850 Planarity : 0.004 0.051 3338 Dihedral : 4.999 37.415 2444 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.29 % Favored : 93.22 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.23 (0.17), residues: 2243 helix: -0.17 (0.26), residues: 423 sheet: -0.37 (0.20), residues: 621 loop : -1.29 (0.18), residues: 1199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.3221 time to fit residues: 141.2544 Evaluate side-chains 197 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 134 optimal weight: 0.2980 chunk 131 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN E 249 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21101 Z= 0.216 Angle : 0.757 26.682 28630 Z= 0.353 Chirality : 0.045 0.355 3850 Planarity : 0.004 0.050 3338 Dihedral : 4.896 37.039 2444 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.51 % Favored : 92.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.21 (0.17), residues: 2243 helix: -0.05 (0.26), residues: 420 sheet: -0.44 (0.20), residues: 625 loop : -1.25 (0.18), residues: 1198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3217 time to fit residues: 130.8656 Evaluate side-chains 194 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 553 ASN B 590 GLN B 652 GLN B 656 ASN C 461 ASN E 67 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN H 73 ASN M 76 ASN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 21101 Z= 0.339 Angle : 0.836 27.098 28630 Z= 0.391 Chirality : 0.047 0.377 3850 Planarity : 0.005 0.053 3338 Dihedral : 5.148 36.048 2444 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.09 % Favored : 92.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.42 (0.17), residues: 2243 helix: -0.29 (0.25), residues: 426 sheet: -0.53 (0.20), residues: 624 loop : -1.39 (0.17), residues: 1193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3112 time to fit residues: 116.9087 Evaluate side-chains 175 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 200 optimal weight: 0.0470 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21101 Z= 0.210 Angle : 0.776 26.186 28630 Z= 0.362 Chirality : 0.046 0.356 3850 Planarity : 0.004 0.087 3338 Dihedral : 4.993 35.996 2444 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.11 % Favored : 93.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.33 (0.17), residues: 2243 helix: -0.11 (0.25), residues: 426 sheet: -0.42 (0.20), residues: 623 loop : -1.42 (0.17), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3193 time to fit residues: 129.0868 Evaluate side-chains 195 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN H 76 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 21101 Z= 0.287 Angle : 0.816 23.590 28630 Z= 0.382 Chirality : 0.047 0.360 3850 Planarity : 0.004 0.080 3338 Dihedral : 5.108 35.523 2444 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.27 % Favored : 92.15 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.17), residues: 2243 helix: -0.15 (0.26), residues: 416 sheet: -0.47 (0.20), residues: 612 loop : -1.40 (0.17), residues: 1215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.3077 time to fit residues: 116.9564 Evaluate side-chains 182 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN C 229 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.060484 restraints weight = 70667.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062123 restraints weight = 43967.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063248 restraints weight = 32341.505| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 21101 Z= 0.243 Angle : 0.783 21.555 28630 Z= 0.370 Chirality : 0.046 0.348 3850 Planarity : 0.004 0.075 3338 Dihedral : 5.079 36.202 2444 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.82 % Favored : 92.60 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.30 (0.17), residues: 2243 helix: -0.04 (0.26), residues: 417 sheet: -0.40 (0.20), residues: 621 loop : -1.41 (0.17), residues: 1205 =============================================================================== Job complete usr+sys time: 3701.45 seconds wall clock time: 69 minutes 29.54 seconds (4169.54 seconds total)