Starting phenix.real_space_refine on Tue Jul 23 04:06:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/07_2024/8dvd_27735.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.056 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 134 5.16 5 C 12814 2.51 5 N 3101 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 167": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20804 Number of models: 1 Model: "" Number of chains: 83 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1059 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "C" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "G" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "f" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "5" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "CA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "EA" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "FA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "GA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "HA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "IA" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "KA" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "LA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "NA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "OA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "PA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "QA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "RA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.27, per 1000 atoms: 0.54 Number of scatterers: 20804 At special positions: 0 Unit cell: (147.288, 139.707, 162.45, 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 134 16.00 O 4755 8.00 N 3101 7.00 C 12814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149E" - pdb=" SG CYS E 149K" distance=2.02 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 191 " 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=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 149E" - pdb=" SG CYS F 149K" distance=2.03 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.02 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 149E" - pdb=" SG CYS G 149K" distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " 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=2.04 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Y 4 " - " MAN Y 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " " MAN t 4 " - " MAN t 5 " " MAN x 4 " - " MAN x 5 " " MAN z 4 " - " MAN z 5 " " MANEA 4 " - " MANEA 5 " " MANIA 4 " - " MANIA 5 " " MANKA 4 " - " MANKA 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 4 3 " - " MAN 4 4 " " BMA 5 3 " - " MAN 5 4 " " BMA 7 3 " - " MAN 7 4 " " BMA 9 3 " - " MAN 9 4 " " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 6 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " " BMAEA 3 " - " MANEA 4 " " BMAGA 3 " - " MANGA 4 " " BMAIA 3 " - " MANIA 4 " " BMAJA 3 " - " MANJA 4 " " BMAKA 3 " - " MANKA 4 " " MANKA 6 " - " MANKA 7 " " BMALA 3 " - " MANLA 4 " " BMAPA 3 " - " MANPA 4 " " BMAQA 3 " - " MANQA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 4 3 " - " MAN 4 5 " " BMA 9 3 " - " MAN 9 5 " " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 6 " " BMA a 3 " - " MAN a 5 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA e 3 " - " MAN e 6 " " MAN e 6 " - " MAN e 8 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 5 " " BMA s 3 " - " MAN s 5 " " BMA t 3 " - " MAN t 6 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 5 " " BMA x 3 " - " MAN x 6 " " MAN x 6 " - " MAN x 7 " " BMA z 3 " - " MAN z 6 " " BMADA 3 " - " MANDA 5 " " BMAEA 3 " - " MANEA 6 " " BMAFA 3 " - " MANFA 4 " " BMAGA 3 " - " MANGA 5 " " BMAIA 3 " - " MANIA 6 " " MANIA 6 " - " MANIA 7 " " BMAKA 3 " - " MANKA 6 " " MANKA 6 " - " MANKA 8 " " BMALA 3 " - " MANLA 5 " " BMAPA 3 " - " MANPA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGLA 2 " - " BMALA 3 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGPA 2 " - " BMAPA 3 " " NAGQA 1 " - " NAGQA 2 " " NAGQA 2 " - " BMAQA 3 " " NAGRA 1 " - " NAGRA 2 " " NAGRA 2 " - " BMARA 3 " NAG-ASN " NAG 0 1 " - " ASN F 160 " " NAG 1 1 " - " ASN F 173 " " NAG 2 1 " - " ASN F 185B" " NAG 3 1 " - " ASN F 354E" " NAG 4 1 " - " ASN F 280 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 468 " " NAG 7 1 " - " ASN G 97 " " NAG 8 1 " - " ASN G 88 " " NAG 9 1 " - " ASN G 132 " " NAG D 1 " - " ASN A 612 " " NAG E 601 " - " ASN E 464 " " NAG F 602 " - " ASN F 464 " " NAG G 601 " - " ASN G 464 " " NAG I 1 " - " ASN A 625 " " NAG J 1 " - " ASN A 641 " " NAG K 1 " - " ASN B 612 " " NAG M 1 " - " ASN B 625 " " NAG N 1 " - " ASN B 641 " " NAG O 1 " - " ASN C 612 " " NAG P 1 " - " ASN C 625 " " NAG Q 1 " - " ASN C 641 " " NAG R 1 " - " ASN E 97 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN E 132 " " NAG U 1 " - " ASN E 187 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 229 " " NAG X 1 " - " ASN E 446 " " NAG Y 1 " - " ASN E 360 " " NAG Z 1 " - " ASN E 267A" " NAG a 1 " - " ASN E 291 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 149J" " NAG e 1 " - " ASN E 47 " " NAG f 1 " - " ASN E 160 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 185B" " NAG i 1 " - " ASN E 354E" " NAG j 1 " - " ASN E 280 " " NAG k 1 " - " ASN E 468 " " NAG l 1 " - " ASN E 173 " " NAG m 1 " - " ASN F 97 " " NAG n 1 " - " ASN F 88 " " NAG o 1 " - " ASN F 132 " " NAG p 1 " - " ASN F 187 " " NAG q 1 " - " ASN F 197 " " NAG r 1 " - " ASN F 229 " " NAG s 1 " - " ASN F 446 " " NAG t 1 " - " ASN F 360 " " NAG u 1 " - " ASN F 267A" " NAG v 1 " - " ASN F 291 " " NAG w 1 " - " ASN F 149 " " NAG x 1 " - " ASN F 262 " " NAG y 1 " - " ASN F 149J" " NAG z 1 " - " ASN F 47 " " NAGAA 1 " - " ASN G 187 " " NAGBA 1 " - " ASN G 197 " " NAGCA 1 " - " ASN G 229 " " NAGDA 1 " - " ASN G 446 " " NAGEA 1 " - " ASN G 360 " " NAGFA 1 " - " ASN G 267A" " NAGGA 1 " - " ASN G 291 " " NAGHA 1 " - " ASN G 149 " " NAGIA 1 " - " ASN G 262 " " NAGJA 1 " - " ASN G 149J" " NAGKA 1 " - " ASN G 47 " " NAGLA 1 " - " ASN G 160 " " NAGMA 1 " - " ASN G 173 " " NAGNA 1 " - " ASN G 185B" " NAGOA 1 " - " ASN G 354E" " NAGPA 1 " - " ASN G 280 " " NAGQA 1 " - " ASN G 468 " " NAGRA 1 " - " ASN G 301 " Time building additional restraints: 12.92 Conformation dependent library (CDL) restraints added in 3.1 seconds 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 32 sheets defined 25.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.943A pdb=" N PHE A 522 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.751A pdb=" N GLY A 527 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.570A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.569A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 664 removed outlier: 4.561A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.020A pdb=" N THR B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.966A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 597 removed outlier: 3.535A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 589 " --> pdb=" O LYS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 664 removed outlier: 4.493A pdb=" N PHE B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 521 Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.744A pdb=" N THR C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 removed outlier: 3.728A pdb=" N ALA C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 597 Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.510A pdb=" N ARG C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 664 Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 132 through 139 removed outlier: 4.015A pdb=" N ARG E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 149D through 149I removed outlier: 3.613A pdb=" N GLN E 149H" --> pdb=" O SER E 149D" (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 338 through 352 removed outlier: 3.958A pdb=" N GLU E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.638A pdb=" N GLU E 395 " --> pdb=" O LEU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 474 through 477 Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.520A pdb=" N GLU E 482 " --> pdb=" O LEU E 478 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 483 " --> pdb=" O TYR E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 478 through 483' Processing helix chain 'F' and resid 98 through 116 removed outlier: 3.592A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.520A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 139 removed outlier: 3.764A pdb=" N TRP F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 149D through 149I removed outlier: 3.647A pdb=" N GLN F 149H" --> pdb=" O SER F 149D" (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 149I" --> pdb=" O CYS F 149E" (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149D through 149I' Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.880A pdb=" N TYR F 290 " --> pdb=" O ASN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 removed outlier: 3.536A pdb=" N LYS F 343 " --> pdb=" O LYS F 339 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.716A pdb=" N PHE F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 396 removed outlier: 3.556A pdb=" N LEU F 391 " --> pdb=" O MET F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.849A pdb=" N ARG F 480 " --> pdb=" O ALA F 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.616A pdb=" N TRP G 109 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.600A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 139 removed outlier: 3.749A pdb=" N ARG G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 149D through 149I removed outlier: 3.820A pdb=" N GLN G 149H" --> pdb=" O SER G 149D" (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 338 through 352 removed outlier: 3.572A pdb=" N GLU G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 359 removed outlier: 3.687A pdb=" N ILE G 359 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.637A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 395 removed outlier: 3.550A pdb=" N LEU G 391 " --> pdb=" O MET G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 476 No H-bonds generated for 'chain 'G' and resid 474 through 476' Processing helix chain 'G' and resid 477 through 483 removed outlier: 3.620A pdb=" N LEU G 481 " --> pdb=" O GLU G 477 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 483 " --> pdb=" O TYR G 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 477 through 483' Processing helix chain 'H' and resid 26 through 31 removed outlier: 5.834A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 9.532A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 603 through 609 removed outlier: 9.376A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.052A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 74 through 76 Processing sheet with id=AA5, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.696A pdb=" N GLU E 174 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 159 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.548A pdb=" N VAL E 182 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.894A pdb=" N GLN E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.511A pdb=" N THR E 282 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 454 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN E 360 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N MET E 471 " --> pdb=" O ASN E 360 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E 362 " --> pdb=" O MET E 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.717A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 305 through 308 removed outlier: 3.593A pdb=" N SER E 317 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.876A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 132 removed outlier: 3.993A pdb=" N TYR F 192 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 182 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159 removed outlier: 3.557A pdb=" N PHE F 159 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.884A pdb=" N GLN F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 424 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.378A pdb=" N GLY F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN F 360 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET F 471 " --> pdb=" O ASN F 360 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR F 362 " --> pdb=" O MET F 471 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 271 through 273 removed outlier: 5.899A pdb=" N GLY F 441 " --> pdb=" O GLY F 300 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.759A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'G' and resid 155 through 159 removed outlier: 3.658A pdb=" N CYS G 157 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.534A pdb=" N GLN G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 256 through 257 removed outlier: 4.063A pdb=" N TRP G 375 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG G 298 " --> pdb=" O LEU G 443 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLY G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLY G 441 " --> pdb=" O GLY G 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA G 454 " --> pdb=" O THR G 282 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.614A pdb=" N GLY G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN G 360 " --> pdb=" O ILE G 469 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.801A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.767A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.528A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.704A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1374 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: 6.60 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2963 1.31 - 1.44: 6629 1.44 - 1.57: 11427 1.57 - 1.70: 3 1.70 - 1.83: 181 Bond restraints: 21203 Sorted by residual: bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.576 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.599 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C2 MAN c 5 " pdb=" O2 MAN c 5 " ideal model delta sigma weight residual 1.407 1.471 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CZ TYS H 100I" pdb=" OH TYS H 100I" ideal model delta sigma weight residual 1.371 1.433 -0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" CZ TYS H 100F" pdb=" OH TYS H 100F" ideal model delta sigma weight residual 1.371 1.428 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 21198 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.17: 455 106.17 - 113.15: 13594 113.15 - 120.14: 6390 120.14 - 127.13: 8115 127.13 - 134.12: 274 Bond angle restraints: 28828 Sorted by residual: angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" N ASN C 664 " ideal model delta sigma weight residual 117.07 110.48 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" CA CYS G 205 " pdb=" CB CYS G 205 " pdb=" SG CYS G 205 " ideal model delta sigma weight residual 114.40 124.92 -10.52 2.30e+00 1.89e-01 2.09e+01 angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" O LEU C 663 " ideal model delta sigma weight residual 120.82 125.16 -4.34 1.05e+00 9.07e-01 1.71e+01 angle pdb=" CA LEU A 663 " pdb=" C LEU A 663 " pdb=" N ASN A 664 " ideal model delta sigma weight residual 117.07 112.70 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N ASN E 149J" pdb=" CA ASN E 149J" pdb=" CB ASN E 149J" ideal model delta sigma weight residual 112.63 107.46 5.17 1.61e+00 3.86e-01 1.03e+01 ... (remaining 28823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 14883 25.15 - 50.30: 822 50.30 - 75.45: 188 75.45 - 100.60: 357 100.60 - 125.76: 225 Dihedral angle restraints: 16475 sinusoidal: 10260 harmonic: 6215 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -162.71 76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA CYS G 119 " pdb=" C CYS G 119 " pdb=" N VAL G 120 " pdb=" CA VAL G 120 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 16472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 4103 0.286 - 0.572: 9 0.572 - 0.858: 4 0.858 - 1.144: 1 1.144 - 1.429: 1 Chirality restraints: 4118 Sorted by residual: chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.77e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN E 160 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.99e+01 ... (remaining 4115 not shown) Planarity restraints: 3247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 160 " -0.032 2.00e-02 2.50e+03 3.69e-02 1.70e+01 pdb=" CG ASN E 160 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 160 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 160 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 120 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C VAL G 120 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL G 120 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 318 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 319 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.036 5.00e-02 4.00e+02 ... (remaining 3244 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 213 2.53 - 3.12: 17336 3.12 - 3.71: 28722 3.71 - 4.31: 41658 4.31 - 4.90: 65854 Nonbonded interactions: 153783 Sorted by model distance: nonbonded pdb=" O3 NAGKA 1 " pdb=" O5 NAGKA 2 " model vdw 1.932 2.440 nonbonded pdb=" O3 NAGNA 1 " pdb=" O5 NAGNA 2 " model vdw 2.052 2.440 nonbonded pdb=" O3 NAG e 1 " pdb=" O5 NAG e 2 " model vdw 2.059 2.440 nonbonded pdb=" O3 NAG 2 1 " pdb=" O5 NAG 2 2 " model vdw 2.061 2.440 nonbonded pdb=" O3 NAG T 2 " pdb=" O5 BMA T 3 " model vdw 2.099 2.440 ... (remaining 153778 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 '4' selection = chain '9' selection = chain 'DA' selection = chain 'GA' selection = chain 'LA' selection = chain 'M' selection = chain 'P' selection = chain 'PA' selection = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'j' selection = chain 'o' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '6' selection = chain 'HA' selection = chain 'J' selection = chain 'MA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'RA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'k' selection = chain 'l' selection = chain 'w' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '8' selection = chain 'AA' selection = chain 'NA' selection = chain 'OA' selection = chain 'S' selection = chain 'h' selection = chain 'i' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'BA' selection = chain 'CA' selection = chain 'D' selection = chain 'FA' selection = chain 'I' selection = chain 'JA' selection = chain 'K' selection = chain 'O' selection = chain 'QA' selection = chain 'V' selection = chain 'W' selection = chain 'd' selection = chain 'g' selection = chain 'm' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 512 through 557 or resid 572 through 664)) selection = (chain 'C' and (resid 512 through 557 or resid 572 through 664)) } ncs_group { reference = (chain 'E' and resid 33 through 505) selection = (chain 'F' and resid 33 through 505) selection = (chain 'G' and resid 33 through 505) } ncs_group { reference = (chain 'EA' and (resid 1 or resid 4 through 6)) selection = (chain 'IA' and (resid 2 or resid 5 through 7)) selection = (chain 'Y' and (resid 1 or resid 4 through 6)) selection = (chain 't' and (resid 1 or resid 4 through 6)) selection = (chain 'x' and (resid 2 or resid 5 through 7)) selection = (chain 'z' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'KA' selection = chain 'c' selection = chain 'e' selection = chain 'f' } 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: 1.800 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 58.130 Find NCS groups from input model: 4.950 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 21203 Z= 0.372 Angle : 1.071 10.524 28828 Z= 0.416 Chirality : 0.069 1.429 4118 Planarity : 0.003 0.065 3172 Dihedral : 24.441 125.756 12342 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.97 % Favored : 91.94 % Rotamer: Outliers : 0.69 % Allowed : 0.80 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -0.76 (0.19), residues: 2109 helix: 1.71 (0.28), residues: 354 sheet: -0.33 (0.23), residues: 551 loop : -1.31 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.003 0.001 HIS E 411 PHE 0.015 0.001 PHE L 10 TYR 0.010 0.001 TYR H 101 ARG 0.005 0.000 ARG G 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 350 time to evaluate : 2.202 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9198 (t0) cc_final: 0.8975 (t0) REVERT: A 651 ILE cc_start: 0.8629 (mt) cc_final: 0.7661 (mm) REVERT: C 585 LYS cc_start: 0.8618 (tptp) cc_final: 0.8317 (tptp) REVERT: C 624 ASN cc_start: 0.8495 (m-40) cc_final: 0.7993 (t0) REVERT: G 161 MET cc_start: 0.8335 (tmm) cc_final: 0.7947 (tmm) REVERT: G 354 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7564 (p0) REVERT: H 33 ASP cc_start: 0.8662 (m-30) cc_final: 0.8283 (t0) REVERT: H 110 HIS cc_start: 0.6301 (m-70) cc_final: 0.5838 (p-80) REVERT: L 32 TYR cc_start: 0.8358 (m-80) cc_final: 0.8057 (m-80) outliers start: 13 outliers final: 5 residues processed: 363 average time/residue: 0.3531 time to fit residues: 189.3409 Evaluate side-chains 166 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 629 GLN B 629 GLN C 629 GLN E 103 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 328 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21203 Z= 0.272 Angle : 0.885 10.425 28828 Z= 0.402 Chirality : 0.054 0.597 4118 Planarity : 0.005 0.054 3172 Dihedral : 20.420 119.188 8339 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 0.48 % Allowed : 5.33 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.09 (0.18), residues: 2109 helix: 1.14 (0.26), residues: 371 sheet: -0.69 (0.22), residues: 577 loop : -1.37 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 108 HIS 0.004 0.001 HIS H 35 PHE 0.027 0.002 PHE H 29 TYR 0.015 0.002 TYR B 658 ARG 0.012 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 2.114 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 REVERT: A 594 ASN cc_start: 0.9228 (t0) cc_final: 0.8850 (t0) REVERT: C 576 LEU cc_start: 0.8071 (mm) cc_final: 0.7231 (mt) REVERT: C 585 LYS cc_start: 0.9077 (tptp) cc_final: 0.8798 (tptp) REVERT: E 52 LEU cc_start: 0.8621 (mt) cc_final: 0.8419 (mt) REVERT: G 161 MET cc_start: 0.8313 (tmm) cc_final: 0.7983 (tmm) REVERT: H 33 ASP cc_start: 0.8713 (m-30) cc_final: 0.8337 (t0) REVERT: H 48 MET cc_start: 0.6025 (mtp) cc_final: 0.5728 (mtp) REVERT: H 110 HIS cc_start: 0.6206 (m-70) cc_final: 0.5887 (p-80) REVERT: L 32 TYR cc_start: 0.8434 (m-80) cc_final: 0.7903 (m-80) outliers start: 9 outliers final: 2 residues processed: 220 average time/residue: 0.3245 time to fit residues: 109.8443 Evaluate side-chains 145 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 629 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 540 GLN C 551 GLN C 602 GLN C 629 GLN ** E 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 323 ASN F 347 GLN G 254 GLN G 392 ASN L 90 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21203 Z= 0.218 Angle : 0.829 10.848 28828 Z= 0.375 Chirality : 0.051 0.498 4118 Planarity : 0.004 0.052 3172 Dihedral : 16.982 111.968 8339 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 0.27 % Allowed : 4.21 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.17 (0.18), residues: 2109 helix: 1.02 (0.27), residues: 369 sheet: -0.85 (0.22), residues: 559 loop : -1.33 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 176 HIS 0.004 0.001 HIS G 352 PHE 0.039 0.002 PHE H 100D TYR 0.019 0.001 TYR C 586 ARG 0.008 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 2.360 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: A 530 MET cc_start: 0.7011 (mmp) cc_final: 0.6473 (mmt) REVERT: A 594 ASN cc_start: 0.9226 (t0) cc_final: 0.8800 (t0) REVERT: E 52 LEU cc_start: 0.8609 (mt) cc_final: 0.8273 (mt) REVERT: E 377 ASN cc_start: 0.7571 (t0) cc_final: 0.6879 (m-40) REVERT: G 161 MET cc_start: 0.8368 (tmm) cc_final: 0.7932 (tmm) REVERT: H 33 ASP cc_start: 0.8621 (m-30) cc_final: 0.8213 (t0) REVERT: H 45 LEU cc_start: 0.8166 (mt) cc_final: 0.7928 (mt) REVERT: H 48 MET cc_start: 0.6004 (mtp) cc_final: 0.5781 (mtp) REVERT: L 32 TYR cc_start: 0.8308 (m-80) cc_final: 0.7840 (m-80) REVERT: L 89 MET cc_start: 0.8676 (tpt) cc_final: 0.7733 (tpt) outliers start: 5 outliers final: 2 residues processed: 203 average time/residue: 0.3182 time to fit residues: 100.1434 Evaluate side-chains 136 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 203 optimal weight: 0.0470 chunk 100 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN B 653 GLN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS F 202 GLN G 254 GLN L 27 HIS L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21203 Z= 0.305 Angle : 0.863 10.264 28828 Z= 0.390 Chirality : 0.052 0.479 4118 Planarity : 0.005 0.057 3172 Dihedral : 14.702 107.848 8339 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.70 % Rotamer: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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 (0.18), residues: 2109 helix: 0.62 (0.26), residues: 394 sheet: -0.70 (0.22), residues: 557 loop : -1.51 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 176 HIS 0.004 0.001 HIS G 195 PHE 0.050 0.003 PHE H 100D TYR 0.019 0.002 TYR B 658 ARG 0.010 0.001 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.205 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: A 530 MET cc_start: 0.7601 (mmp) cc_final: 0.6995 (mmp) REVERT: A 594 ASN cc_start: 0.9259 (t0) cc_final: 0.8858 (t0) REVERT: B 664 ASN cc_start: 0.5837 (p0) cc_final: 0.5622 (p0) REVERT: E 52 LEU cc_start: 0.8654 (mt) cc_final: 0.8450 (mt) REVERT: E 193 MET cc_start: 0.8141 (mtm) cc_final: 0.7905 (mtp) REVERT: G 471 MET cc_start: 0.8048 (mtm) cc_final: 0.7780 (mtm) REVERT: H 33 ASP cc_start: 0.8660 (m-30) cc_final: 0.8403 (t70) REVERT: H 45 LEU cc_start: 0.8541 (mt) cc_final: 0.8206 (mt) REVERT: H 48 MET cc_start: 0.6471 (mtp) cc_final: 0.6151 (mtp) REVERT: L 32 TYR cc_start: 0.8317 (m-80) cc_final: 0.7899 (m-80) REVERT: L 89 MET cc_start: 0.8776 (tpt) cc_final: 0.8167 (tpt) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.3148 time to fit residues: 88.2389 Evaluate side-chains 123 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21203 Z= 0.216 Angle : 0.798 10.586 28828 Z= 0.357 Chirality : 0.050 0.440 4118 Planarity : 0.004 0.052 3172 Dihedral : 13.504 106.414 8339 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.11 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.18), residues: 2109 helix: 0.70 (0.26), residues: 393 sheet: -0.66 (0.23), residues: 486 loop : -1.45 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 258 HIS 0.004 0.001 HIS G 411 PHE 0.032 0.002 PHE H 100D TYR 0.012 0.001 TYR A 658 ARG 0.008 0.001 ARG E 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.120 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: A 530 MET cc_start: 0.7306 (mmp) cc_final: 0.6312 (mmt) REVERT: A 594 ASN cc_start: 0.9211 (t0) cc_final: 0.8908 (t0) REVERT: A 651 ILE cc_start: 0.8653 (mt) cc_final: 0.8259 (mt) REVERT: E 377 ASN cc_start: 0.7950 (t0) cc_final: 0.7730 (t0) REVERT: H 33 ASP cc_start: 0.8666 (m-30) cc_final: 0.8289 (t0) REVERT: L 32 TYR cc_start: 0.8282 (m-80) cc_final: 0.7845 (m-80) REVERT: L 89 MET cc_start: 0.8895 (tpt) cc_final: 0.8340 (tpt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3204 time to fit residues: 87.7693 Evaluate side-chains 121 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 551 GLN E 202 GLN G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21203 Z= 0.198 Angle : 0.784 11.008 28828 Z= 0.350 Chirality : 0.050 0.444 4118 Planarity : 0.004 0.052 3172 Dihedral : 12.507 104.530 8339 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.11 % Favored : 91.75 % Rotamer: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.18), residues: 2109 helix: 0.73 (0.26), residues: 393 sheet: -0.65 (0.23), residues: 477 loop : -1.46 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 258 HIS 0.002 0.001 HIS F 274 PHE 0.020 0.001 PHE H 29 TYR 0.012 0.001 TYR E 354A ARG 0.008 0.000 ARG H 100A *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.198 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: A 530 MET cc_start: 0.7105 (mmp) cc_final: 0.6584 (mmt) REVERT: A 594 ASN cc_start: 0.9207 (t0) cc_final: 0.8911 (t0) REVERT: B 639 GLU cc_start: 0.8503 (pm20) cc_final: 0.8201 (pm20) REVERT: E 52 LEU cc_start: 0.8585 (mt) cc_final: 0.8322 (mt) REVERT: E 377 ASN cc_start: 0.7918 (t0) cc_final: 0.7445 (m-40) REVERT: H 33 ASP cc_start: 0.8623 (m-30) cc_final: 0.8247 (t70) REVERT: L 32 TYR cc_start: 0.8288 (m-80) cc_final: 0.7859 (m-80) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.3125 time to fit residues: 83.9010 Evaluate side-chains 118 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 chunk 149 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 410 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21203 Z= 0.266 Angle : 0.823 11.276 28828 Z= 0.370 Chirality : 0.050 0.463 4118 Planarity : 0.004 0.076 3172 Dihedral : 11.961 103.639 8339 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.82 % Favored : 91.04 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.27 (0.18), residues: 2109 helix: 0.69 (0.26), residues: 393 sheet: -0.64 (0.23), residues: 481 loop : -1.47 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 596 HIS 0.006 0.001 HIS F 274 PHE 0.018 0.002 PHE C 600 TYR 0.017 0.002 TYR C 586 ARG 0.013 0.001 ARG E 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.7083 (mmp) cc_final: 0.6452 (mmt) REVERT: A 589 ASP cc_start: 0.8549 (p0) cc_final: 0.8297 (p0) REVERT: A 594 ASN cc_start: 0.9255 (t0) cc_final: 0.8936 (t0) REVERT: E 52 LEU cc_start: 0.8621 (mt) cc_final: 0.8345 (mt) REVERT: F 69 TRP cc_start: 0.6451 (p90) cc_final: 0.6205 (p90) REVERT: H 33 ASP cc_start: 0.8512 (m-30) cc_final: 0.8102 (t70) REVERT: L 32 TYR cc_start: 0.8348 (m-80) cc_final: 0.7898 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3047 time to fit residues: 77.0936 Evaluate side-chains 114 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 4.9990 chunk 81 optimal weight: 0.0970 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN C 629 GLN E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21203 Z= 0.236 Angle : 0.810 10.733 28828 Z= 0.365 Chirality : 0.049 0.443 4118 Planarity : 0.005 0.084 3172 Dihedral : 11.400 102.286 8339 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.44 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.38 (0.18), residues: 2109 helix: 0.52 (0.26), residues: 408 sheet: -0.70 (0.24), residues: 453 loop : -1.54 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP B 596 HIS 0.005 0.001 HIS F 274 PHE 0.020 0.001 PHE H 29 TYR 0.017 0.001 TYR B 658 ARG 0.017 0.001 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.178 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: A 530 MET cc_start: 0.7138 (mmp) cc_final: 0.6449 (mmt) REVERT: A 594 ASN cc_start: 0.9177 (t0) cc_final: 0.8850 (t0) REVERT: B 574 LYS cc_start: 0.5842 (mttt) cc_final: 0.5146 (mttt) REVERT: B 639 GLU cc_start: 0.8511 (pm20) cc_final: 0.8037 (pm20) REVERT: E 52 LEU cc_start: 0.8615 (mt) cc_final: 0.8364 (mt) REVERT: E 125 LEU cc_start: 0.8936 (pp) cc_final: 0.8700 (pp) REVERT: E 377 ASN cc_start: 0.7979 (t0) cc_final: 0.7350 (m-40) REVERT: H 33 ASP cc_start: 0.8448 (m-30) cc_final: 0.8088 (t70) REVERT: L 32 TYR cc_start: 0.8356 (m-80) cc_final: 0.7893 (m-80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2924 time to fit residues: 76.0976 Evaluate side-chains 116 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN E 103 GLN E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21203 Z= 0.238 Angle : 0.806 13.835 28828 Z= 0.363 Chirality : 0.049 0.444 4118 Planarity : 0.004 0.051 3172 Dihedral : 10.956 100.900 8339 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.37 (0.18), residues: 2109 helix: 0.48 (0.26), residues: 406 sheet: -0.69 (0.24), residues: 447 loop : -1.50 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 596 HIS 0.004 0.001 HIS H 98 PHE 0.021 0.002 PHE C 519 TYR 0.013 0.001 TYR B 658 ARG 0.007 0.001 ARG H 100A *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.172 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: A 530 MET cc_start: 0.7168 (mmp) cc_final: 0.6450 (mmt) REVERT: A 589 ASP cc_start: 0.8452 (p0) cc_final: 0.8144 (p0) REVERT: A 594 ASN cc_start: 0.9175 (t0) cc_final: 0.8856 (t0) REVERT: B 574 LYS cc_start: 0.6054 (mttt) cc_final: 0.5644 (mttt) REVERT: B 639 GLU cc_start: 0.8413 (pm20) cc_final: 0.8145 (pm20) REVERT: E 52 LEU cc_start: 0.8365 (mt) cc_final: 0.8056 (mt) REVERT: E 377 ASN cc_start: 0.7993 (t0) cc_final: 0.7383 (m-40) REVERT: F 69 TRP cc_start: 0.6418 (p90) cc_final: 0.6103 (p90) REVERT: H 33 ASP cc_start: 0.8378 (m-30) cc_final: 0.8103 (t70) REVERT: L 32 TYR cc_start: 0.8432 (m-80) cc_final: 0.7984 (m-80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2860 time to fit residues: 74.0761 Evaluate side-chains 114 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 0.0570 chunk 122 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21203 Z= 0.209 Angle : 0.798 17.155 28828 Z= 0.358 Chirality : 0.048 0.444 4118 Planarity : 0.004 0.059 3172 Dihedral : 10.616 99.457 8339 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.30 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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 (0.18), residues: 2109 helix: 0.52 (0.26), residues: 406 sheet: -0.67 (0.24), residues: 448 loop : -1.52 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 596 HIS 0.003 0.001 HIS G 411 PHE 0.020 0.001 PHE C 600 TYR 0.020 0.001 TYR H 100C ARG 0.007 0.000 ARG H 100A ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.333 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: A 530 MET cc_start: 0.7100 (mmp) cc_final: 0.6322 (mmt) REVERT: A 594 ASN cc_start: 0.9167 (t0) cc_final: 0.8852 (t0) REVERT: B 574 LYS cc_start: 0.5743 (mttt) cc_final: 0.5328 (mttt) REVERT: B 639 GLU cc_start: 0.8377 (pm20) cc_final: 0.8098 (pm20) REVERT: B 651 ILE cc_start: 0.8652 (pt) cc_final: 0.8033 (pt) REVERT: E 52 LEU cc_start: 0.8388 (mt) cc_final: 0.8116 (mt) REVERT: E 125 LEU cc_start: 0.8921 (pp) cc_final: 0.8696 (pp) REVERT: E 129 MET cc_start: 0.7681 (mmm) cc_final: 0.7399 (mtp) REVERT: E 377 ASN cc_start: 0.7985 (t0) cc_final: 0.7438 (m-40) REVERT: H 33 ASP cc_start: 0.8323 (m-30) cc_final: 0.7849 (m-30) REVERT: L 32 TYR cc_start: 0.8457 (m-80) cc_final: 0.7998 (m-80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3125 time to fit residues: 81.2146 Evaluate side-chains 117 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 254 GLN G 411 HIS G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.044382 restraints weight = 124517.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045753 restraints weight = 71262.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.046631 restraints weight = 51510.327| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21203 Z= 0.327 Angle : 0.866 16.111 28828 Z= 0.394 Chirality : 0.049 0.465 4118 Planarity : 0.005 0.062 3172 Dihedral : 10.702 101.518 8339 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.77 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % 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: -1.49 (0.18), residues: 2109 helix: 0.37 (0.26), residues: 408 sheet: -0.96 (0.24), residues: 476 loop : -1.50 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 596 HIS 0.006 0.001 HIS G 411 PHE 0.020 0.002 PHE C 600 TYR 0.018 0.002 TYR B 658 ARG 0.009 0.001 ARG E 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.78 seconds wall clock time: 63 minutes 3.70 seconds (3783.70 seconds total)