Starting phenix.real_space_refine on Fri Jul 26 12:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cde_7459/07_2024/6cde_7459_neut.cif" } resolution = 3.8 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= 0.004 sd= 0.093 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 177 5.16 5 C 20661 2.51 5 N 5319 2.21 5 O 6816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "h TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 108": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "q ARG 61": "NH1" <-> "NH2" Residue "q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32973 Number of models: 1 Model: "" Number of chains: 81 Chain: "h" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "l" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "r" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "c" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "7" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "8" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 813 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "5" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "2" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3556 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "3" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "4" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 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: "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: 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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" 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: "g" 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: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "o" 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: "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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: "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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "EA" 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: "FA" 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: "GA" 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "JA" 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: "KA" 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: "LA" 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: "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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 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: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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 Time building chain proxies: 17.95, per 1000 atoms: 0.54 Number of scatterers: 32973 At special positions: 0 Unit cell: (163.24, 159, 154.76, 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 177 16.00 O 6816 8.00 N 5319 7.00 C 20661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.13 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.09 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.19 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 87 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.34 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.13 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 95 " distance=2.25 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.05 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.16 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 605 " - pdb=" SG CYS c 501 " distance=2.03 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.27 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.02 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.02 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 95 " distance=2.40 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 87 " distance=2.05 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 98 " - pdb=" SG CYS 5 100A" distance=2.17 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 605 " - pdb=" SG CYS 2 501 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.42 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.13 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM31432 O5 NAG j 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32304 O5 NAGDA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30560 O5 NAG K 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31266 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30394 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32138 O5 NAGBA 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN P 5 " - " MAN P 6 " " MAN P 7 " - " MAN P 8 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN g 4 " - " MAN g 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN o 5 " - " MAN o 6 " " MAN o 7 " - " MAN o 8 " " MAN t 5 " - " MAN t 6 " " MAN t 8 " - " MAN t 9 " " MANBA 4 " - " MANBA 5 " " MANCA 4 " - " MANCA 5 " " MANCA 5 " - " MANCA 6 " " MANFA 5 " - " MANFA 6 " " MANFA 7 " - " MANFA 8 " " MANIA 5 " - " MANIA 6 " " MANIA 8 " - " MANIA 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA k 3 " - " MAN k 4 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA t 3 " - " MAN t 8 " " MAN t 4 " - " MAN t 5 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " MANCA 7 " - " MANCA 8 " " BMAEA 3 " - " MANEA 4 " " BMAFA 3 " - " MANFA 7 " " MANFA 4 " - " MANFA 5 " " BMAIA 3 " - " MANIA 8 " " MANIA 4 " - " MANIA 5 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA J 3 " - " MAN J 7 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 7 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 6 " " BMA i 3 " - " MAN i 7 " " BMA k 3 " - " MAN k 5 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " " MAN t 4 " - " MAN t 7 " " BMA v 3 " - " MAN v 4 " " BMABA 3 " - " MANBA 6 " " BMACA 3 " - " MANCA 7 " " BMAEA 3 " - " MANEA 5 " " BMAFA 3 " - " MANFA 4 " " BMAIA 3 " - " MANIA 4 " " MANIA 4 " - " MANIA 7 " " BMAKA 3 " - " MANKA 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 9 1 " - " NAG 9 2 " " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 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 O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 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 e 1 " - " NAG e 2 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG 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 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " 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 " NAG-ASN " NAG 0 1 " - " ASN 2 88 " " NAG 1 701 " - " ASN 1 618 " " NAG 2 653 " - " ASN 2 339 " " NAG 2 654 " - " ASN 2 355 " " NAG 9 1 " - " ASN 2 133 " " NAG A 1 " - " ASN D 637 " " NAG B 1 " - " ASN D 611 " " NAG C 653 " - " ASN C 339 " " NAG C 654 " - " ASN C 355 " " NAG D 701 " - " ASN D 618 " " NAG E 1 " - " ASN C 88 " " NAG F 1 " - " ASN C 133 " " NAG G 1 " - " ASN C 137 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 160 " " NAG K 1 " - " ASN C 197 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN d 637 " " NAG a 1 " - " ASN d 611 " " NAG b 1 " - " ASN c 88 " " NAG c 653 " - " ASN c 339 " " NAG c 654 " - " ASN c 355 " " NAG d 701 " - " ASN d 618 " " NAG e 1 " - " ASN c 133 " " NAG f 1 " - " ASN c 137 " " NAG g 1 " - " ASN c 156 " " NAG i 1 " - " ASN c 160 " " NAG j 1 " - " ASN c 197 " " NAG k 1 " - " ASN c 234 " " NAG o 1 " - " ASN c 262 " " NAG p 1 " - " ASN c 295 " " NAG s 1 " - " ASN c 301 " " NAG t 1 " - " ASN c 332 " " NAG u 1 " - " ASN c 363 " " NAG v 1 " - " ASN c 386 " " NAG w 1 " - " ASN c 392 " " NAG x 1 " - " ASN c 448 " " NAG y 1 " - " ASN 1 637 " " NAG z 1 " - " ASN 1 611 " " NAGAA 1 " - " ASN 2 137 " " NAGBA 1 " - " ASN 2 156 " " NAGCA 1 " - " ASN 2 160 " " NAGDA 1 " - " ASN 2 197 " " NAGEA 1 " - " ASN 2 234 " " NAGFA 1 " - " ASN 2 262 " " NAGGA 1 " - " ASN 2 295 " " NAGHA 1 " - " ASN 2 301 " " NAGIA 1 " - " ASN 2 332 " " NAGJA 1 " - " ASN 2 363 " " NAGKA 1 " - " ASN 2 386 " " NAGLA 1 " - " ASN 2 392 " " NAGMA 1 " - " ASN 2 448 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.11 Conformation dependent library (CDL) restraints added in 6.2 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 84 sheets defined 13.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP M 89 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER M 90 " --> pdb=" O ALA M 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 90' Processing helix chain 'M' and resid 107 through 111 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 633 Processing helix chain 'D' and resid 638 through 663 removed outlier: 4.039A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.438A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'm' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP m 89 " --> pdb=" O THR m 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER m 90 " --> pdb=" O ALA m 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 86 through 90' Processing helix chain 'm' and resid 107 through 111 Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.685A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 527 removed outlier: 4.213A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 4.113A pdb=" N SER d 534 " --> pdb=" O MET d 530 " (cutoff:3.500A) Processing helix chain 'd' and resid 537 through 543 removed outlier: 3.854A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 633 Processing helix chain 'd' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 Processing helix chain 'c' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 179 No H-bonds generated for 'chain 'c' and resid 177 through 179' Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 354 removed outlier: 4.439A pdb=" N LYS c 351 " --> pdb=" O LYS c 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS c 352 " --> pdb=" O GLN c 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE c 353 " --> pdb=" O LEU c 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 476 through 481 Processing helix chain '7' and resid 86 through 90 removed outlier: 3.511A pdb=" N ASP 7 89 " --> pdb=" O THR 7 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER 7 90 " --> pdb=" O ALA 7 87 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 86 through 90' Processing helix chain '7' and resid 107 through 111 Processing helix chain '5' and resid 61 through 64 removed outlier: 3.684A pdb=" N GLN 5 64 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 61 through 64' Processing helix chain '5' and resid 83 through 87 removed outlier: 3.678A pdb=" N THR 5 87 " --> pdb=" O PRO 5 84 " (cutoff:3.500A) Processing helix chain '1' and resid 515 through 520 removed outlier: 3.798A pdb=" N PHE 1 519 " --> pdb=" O ILE 1 515 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 527 removed outlier: 4.214A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 534 removed outlier: 4.112A pdb=" N SER 1 534 " --> pdb=" O MET 1 530 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 543 removed outlier: 3.855A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 Processing helix chain '1' and resid 620 through 625 Processing helix chain '1' and resid 627 through 633 Processing helix chain '1' and resid 638 through 663 removed outlier: 4.038A pdb=" N LEU 1 663 " --> pdb=" O ASP 1 659 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 63 Processing helix chain '2' and resid 99 through 115 removed outlier: 3.693A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 354 removed outlier: 4.437A pdb=" N LYS 2 351 " --> pdb=" O LYS 2 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N HIS 2 352 " --> pdb=" O GLN 2 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE 2 353 " --> pdb=" O LEU 2 349 " (cutoff:3.500A) Processing helix chain '2' and resid 368 through 373 removed outlier: 3.824A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 476 through 481 Processing sheet with id=AA1, first strand: chain 'h' and resid 10 through 11 removed outlier: 6.540A pdb=" N ASP h 10 " --> pdb=" O THR h 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'h' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'h' and resid 44 through 51 removed outlier: 6.581A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER h 93 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG h 94 " --> pdb=" O ASP h 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'l' and resid 5 through 7 removed outlier: 4.152A pdb=" N THR l 5 " --> pdb=" O LYS l 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS l 24 " --> pdb=" O THR l 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'l' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU l 104 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL M 12 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL M 128 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA M 91 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR M 33 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 96 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 13 removed outlier: 5.736A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'N' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP R 69 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU R 11 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.984A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.507A pdb=" N VAL m 12 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL m 128 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA m 91 " --> pdb=" O VAL m 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR m 33 " --> pdb=" O THR m 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA m 96 " --> pdb=" O SER m 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'm' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'n' and resid 11 through 13 removed outlier: 5.743A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'n' and resid 19 through 22 Processing sheet with id=AE3, first strand: chain 'n' and resid 31 through 38 removed outlier: 3.882A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'r' and resid 5 through 7 removed outlier: 3.580A pdb=" N ASP r 69 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU r 11 " --> pdb=" O GLU r 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AE8, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR q 102 " --> pdb=" O ARG q 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 35 through 40 Processing sheet with id=AF2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS c 487 " --> pdb=" O LEU c 226 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE c 53 " --> pdb=" O CYS c 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 84 through 85 removed outlier: 3.514A pdb=" N THR c 244 " --> pdb=" O ILE c 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 130 through 133 Processing sheet with id=AF7, first strand: chain 'c' and resid 181 through 183 Processing sheet with id=AF8, first strand: chain 'c' and resid 202 through 203 removed outlier: 7.198A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR c 450 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL c 292 " --> pdb=" O VAL c 446 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N VAL c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE c 294 " --> pdb=" O ARG c 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 271 through 273 removed outlier: 6.790A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS c 330 " --> pdb=" O THR c 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 304 through 312 removed outlier: 7.068A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP 7 34 " --> pdb=" O TYR 7 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR 7 50 " --> pdb=" O TRP 7 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP 7 36 " --> pdb=" O ILE 7 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '7' and resid 11 through 12 removed outlier: 3.506A pdb=" N VAL 7 12 " --> pdb=" O THR 7 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 7 128 " --> pdb=" O ALA 7 91 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 7 91 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR 7 33 " --> pdb=" O THR 7 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 7 96 " --> pdb=" O SER 7 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '7' and resid 71 through 72 Processing sheet with id=AG6, first strand: chain '8' and resid 11 through 13 removed outlier: 5.730A pdb=" N VAL 8 11 " --> pdb=" O ILE 8 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain '8' and resid 19 through 22 Processing sheet with id=AG8, first strand: chain '8' and resid 31 through 38 removed outlier: 3.881A pdb=" N TYR 8 87 " --> pdb=" O TYR 8 36 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '6' and resid 5 through 7 removed outlier: 3.579A pdb=" N ASP 6 69 " --> pdb=" O SER 6 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP 6 34 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '6' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU 6 11 " --> pdb=" O GLU 6 100 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '5' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain '5' and resid 10 through 11 removed outlier: 3.664A pdb=" N GLY 5 49 " --> pdb=" O TRP 5 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG 5 38 " --> pdb=" O TRP 5 47 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP 5 47 " --> pdb=" O ARG 5 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE 5 40 " --> pdb=" O PHE 5 45 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE 5 45 " --> pdb=" O ILE 5 40 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '5' and resid 10 through 11 removed outlier: 3.983A pdb=" N TYR 5 102 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 35 through 40 Processing sheet with id=AH7, first strand: chain '2' and resid 45 through 47 removed outlier: 3.532A pdb=" N LYS 2 487 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 75 through 76 removed outlier: 3.875A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE 2 53 " --> pdb=" O CYS 2 218 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 84 through 85 removed outlier: 3.513A pdb=" N THR 2 244 " --> pdb=" O ILE 2 84 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '2' and resid 91 through 94 removed outlier: 4.127A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AI3, first strand: chain '2' and resid 181 through 183 Processing sheet with id=AI4, first strand: chain '2' and resid 202 through 203 removed outlier: 7.199A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.385A pdb=" N THR 2 450 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR 2 290 " --> pdb=" O ASN 2 448 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN 2 448 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N VAL 2 292 " --> pdb=" O VAL 2 446 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL 2 446 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ILE 2 294 " --> pdb=" O ARG 2 444 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N ARG 2 444 " --> pdb=" O ILE 2 294 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '2' and resid 271 through 273 removed outlier: 6.791A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS 2 330 " --> pdb=" O THR 2 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '2' and resid 304 through 312 removed outlier: 7.058A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '3' and resid 10 through 11 removed outlier: 6.539A pdb=" N ASP 3 10 " --> pdb=" O THR 3 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain '3' and resid 21 through 23 Processing sheet with id=AJ1, first strand: chain '3' and resid 44 through 51 removed outlier: 6.580A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER 3 93 " --> pdb=" O HIS 3 35 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG 3 94 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '4' and resid 5 through 7 removed outlier: 4.153A pdb=" N THR 4 5 " --> pdb=" O LYS 4 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS 4 24 " --> pdb=" O THR 4 5 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '4' and resid 33 through 38 removed outlier: 4.422A pdb=" N GLY 4 84 " --> pdb=" O LEU 4 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2223 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: 13.59 Time building geometry restraints manager: 17.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9936 1.34 - 1.46: 9053 1.46 - 1.59: 14446 1.59 - 1.71: 0 1.71 - 1.83: 240 Bond restraints: 33675 Sorted by residual: bond pdb=" C1 MAN i 4 " pdb=" O5 MAN i 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 MANCA 4 " pdb=" O5 MANCA 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C5 BMAAA 3 " pdb=" O5 BMAAA 3 " ideal model delta sigma weight residual 1.417 1.493 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 BMA f 3 " pdb=" O5 BMA f 3 " ideal model delta sigma weight residual 1.417 1.493 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 33670 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.46: 363 103.46 - 111.11: 14026 111.11 - 118.77: 13693 118.77 - 126.43: 16996 126.43 - 134.08: 654 Bond angle restraints: 45732 Sorted by residual: angle pdb=" N GLN R 89 " pdb=" CA GLN R 89 " pdb=" C GLN R 89 " ideal model delta sigma weight residual 108.41 98.37 10.04 1.63e+00 3.76e-01 3.80e+01 angle pdb=" C SER 1 615 " pdb=" N ASN 1 616 " pdb=" CA ASN 1 616 " ideal model delta sigma weight residual 122.46 129.36 -6.90 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER D 615 " pdb=" N ASN D 616 " pdb=" CA ASN D 616 " ideal model delta sigma weight residual 122.46 129.35 -6.89 1.41e+00 5.03e-01 2.39e+01 angle pdb=" C SER d 615 " pdb=" N ASN d 616 " pdb=" CA ASN d 616 " ideal model delta sigma weight residual 122.46 129.34 -6.88 1.41e+00 5.03e-01 2.38e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 120.28 -10.47 2.21e+00 2.05e-01 2.24e+01 ... (remaining 45727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 21475 23.24 - 46.48: 759 46.48 - 69.71: 186 69.71 - 92.95: 230 92.95 - 116.19: 132 Dihedral angle restraints: 22782 sinusoidal: 11763 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS 2 54 " pdb=" SG CYS 2 54 " pdb=" SG CYS 2 74 " pdb=" CB CYS 2 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.53 85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS c 54 " pdb=" SG CYS c 54 " pdb=" SG CYS c 74 " pdb=" CB CYS c 74 " ideal model delta sinusoidal sigma weight residual -86.00 -169.43 83.43 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 22779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 5688 0.327 - 0.653: 18 0.653 - 0.980: 9 0.980 - 1.307: 9 1.307 - 1.633: 6 Chirality restraints: 5730 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 332 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.67e+01 chirality pdb=" C1 NAG t 1 " pdb=" ND2 ASN c 332 " pdb=" C2 NAG t 1 " pdb=" O5 NAG t 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" C1 NAGIA 1 " pdb=" ND2 ASN 2 332 " pdb=" C2 NAGIA 1 " pdb=" O5 NAGIA 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.65e+01 ... (remaining 5727 not shown) Planarity restraints: 5529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN c 392 " -0.073 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" CG ASN c 392 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN c 392 " -0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN c 392 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG w 1 " -0.344 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.519 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 392 " 0.073 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" CG ASN 2 392 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 392 " 0.193 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 392 " -0.518 2.00e-02 2.50e+03 pdb=" C1 NAGLA 1 " 0.343 2.00e-02 2.50e+03 ... (remaining 5526 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 47 2.30 - 2.95: 15387 2.95 - 3.60: 42730 3.60 - 4.25: 71011 4.25 - 4.90: 116013 Nonbonded interactions: 245188 Sorted by model distance: nonbonded pdb=" O GLY 2 263 " pdb=" CG2 THR 2 450 " model vdw 1.655 3.460 nonbonded pdb=" O GLY C 263 " pdb=" CG2 THR C 450 " model vdw 1.664 3.460 nonbonded pdb=" O GLY c 263 " pdb=" CG2 THR c 450 " model vdw 1.664 3.460 nonbonded pdb=" O LYS c 502 " pdb=" CD2 LEU 1 661 " model vdw 1.865 3.460 nonbonded pdb=" CD2 LEU D 661 " pdb=" O LYS 2 502 " model vdw 1.918 3.460 ... (remaining 245183 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 '9' selection = chain 'DA' selection = chain 'E' selection = chain 'F' selection = chain 'GA' selection = chain 'K' selection = chain 'S' selection = chain 'b' selection = chain 'e' selection = chain 'j' selection = chain 'p' } ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '6' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '7' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '8' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'HA' selection = chain 'JA' selection = chain 'LA' selection = chain 'MA' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'AA' selection = chain 'G' selection = chain 'KA' selection = chain 'W' selection = chain 'f' selection = chain 'v' } ncs_group { reference = chain 'BA' selection = chain 'I' selection = chain 'g' } ncs_group { reference = (chain 'CA' and (resid 1 or resid 4 through 8)) selection = (chain 'FA' and (resid 1 or resid 4 through 8)) selection = (chain 'IA' and (resid 2 or resid 5 through 9)) selection = (chain 'J' and (resid 1 or resid 4 through 8)) selection = (chain 'P' and (resid 1 or resid 4 through 8)) selection = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'i' and (resid 1 or resid 4 through 8)) selection = (chain 'o' and (resid 1 or resid 4 through 8)) selection = (chain 't' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'EA' selection = chain 'O' selection = chain 'k' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 91.120 Find NCS groups from input model: 5.840 Set up NCS constraints: 0.660 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: 0.020 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.008 0.081 33675 Z= 0.524 Angle : 1.113 11.145 45732 Z= 0.537 Chirality : 0.101 1.633 5730 Planarity : 0.006 0.067 5469 Dihedral : 17.575 116.188 15561 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.29 (0.12), residues: 3774 helix: -2.28 (0.20), residues: 405 sheet: -1.48 (0.14), residues: 1221 loop : -2.67 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP c 479 HIS 0.010 0.002 HIS H 35 PHE 0.044 0.004 PHE 2 288 TYR 0.025 0.003 TYR L 49 ARG 0.010 0.001 ARG 4 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 709 time to evaluate : 3.408 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: h 96 LYS cc_start: 0.8219 (mttt) cc_final: 0.7769 (tptt) REVERT: l 4 MET cc_start: 0.7185 (mtt) cc_final: 0.6447 (mmm) REVERT: l 24 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7895 (mttt) REVERT: l 27 GLN cc_start: 0.8328 (mt0) cc_final: 0.7849 (mt0) REVERT: l 30 ASN cc_start: 0.8361 (m110) cc_final: 0.8024 (m-40) REVERT: l 70 ASP cc_start: 0.6993 (p0) cc_final: 0.6787 (p0) REVERT: N 17 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7776 (mt0) REVERT: N 87 TYR cc_start: 0.8464 (m-80) cc_final: 0.8144 (m-10) REVERT: N 104 LEU cc_start: 0.8452 (tp) cc_final: 0.7840 (tp) REVERT: R 33 THR cc_start: 0.9351 (m) cc_final: 0.9084 (p) REVERT: Q 39 LEU cc_start: 0.9054 (tp) cc_final: 0.8742 (tt) REVERT: D 542 ARG cc_start: 0.8844 (ttm110) cc_final: 0.8497 (ttp-170) REVERT: D 571 TRP cc_start: 0.8222 (m100) cc_final: 0.7964 (m100) REVERT: D 657 GLU cc_start: 0.8837 (tp30) cc_final: 0.8613 (tp30) REVERT: C 475 MET cc_start: 0.8753 (tpt) cc_final: 0.8343 (tpp) REVERT: L 27 GLN cc_start: 0.8227 (mt0) cc_final: 0.7927 (mt0) REVERT: n 17 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7676 (mt0) REVERT: n 53 ASP cc_start: 0.7771 (m-30) cc_final: 0.7561 (m-30) REVERT: n 87 TYR cc_start: 0.8466 (m-80) cc_final: 0.8213 (m-80) REVERT: q 39 LEU cc_start: 0.9161 (tp) cc_final: 0.8918 (tt) REVERT: q 76 ASP cc_start: 0.8095 (p0) cc_final: 0.7777 (p0) REVERT: d 571 TRP cc_start: 0.8035 (m100) cc_final: 0.7652 (m100) REVERT: d 574 LYS cc_start: 0.8814 (mttp) cc_final: 0.8546 (mtpt) REVERT: d 647 GLU cc_start: 0.8456 (tt0) cc_final: 0.8202 (tt0) REVERT: d 657 GLU cc_start: 0.8937 (tp30) cc_final: 0.8569 (tp30) REVERT: d 659 ASP cc_start: 0.8647 (m-30) cc_final: 0.8400 (t0) REVERT: c 475 MET cc_start: 0.8729 (tpt) cc_final: 0.8400 (tpp) REVERT: 8 17 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7807 (mt0) REVERT: 8 49 TYR cc_start: 0.8410 (p90) cc_final: 0.8184 (p90) REVERT: 8 87 TYR cc_start: 0.8402 (m-80) cc_final: 0.8047 (m-80) REVERT: 6 33 THR cc_start: 0.9488 (m) cc_final: 0.9067 (p) REVERT: 5 39 LEU cc_start: 0.9231 (tp) cc_final: 0.8888 (tt) REVERT: 1 571 TRP cc_start: 0.8100 (m100) cc_final: 0.7848 (m100) REVERT: 1 574 LYS cc_start: 0.8737 (mttp) cc_final: 0.8492 (mtpt) REVERT: 1 657 GLU cc_start: 0.8956 (tp30) cc_final: 0.8700 (tp30) REVERT: 2 180 ASP cc_start: 0.8851 (m-30) cc_final: 0.8637 (m-30) REVERT: 2 475 MET cc_start: 0.8689 (tpt) cc_final: 0.8229 (tpp) REVERT: 3 96 LYS cc_start: 0.8231 (mttt) cc_final: 0.7863 (tptt) REVERT: 4 24 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7657 (mtpt) REVERT: 4 27 GLN cc_start: 0.8382 (mt0) cc_final: 0.7923 (mt0) outliers start: 7 outliers final: 4 residues processed: 716 average time/residue: 0.5019 time to fit residues: 549.2203 Evaluate side-chains 353 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 349 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain r residue 88 GLN Chi-restraints excluded: chain 7 residue 95 CYS Chi-restraints excluded: chain 6 residue 88 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 0.0980 chunk 293 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 340 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN N 50 ASN R 36 GLN D 543 ASN D 625 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 293 GLN L 38 GLN n 50 ASN d 543 ASN d 625 ASN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 ASN c 103 GLN c 293 GLN 8 50 ASN ** 6 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 543 ASN 1 625 ASN 2 293 GLN 3 61 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33675 Z= 0.191 Angle : 0.731 9.823 45732 Z= 0.344 Chirality : 0.048 0.284 5730 Planarity : 0.005 0.044 5469 Dihedral : 15.244 87.334 8607 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.80 % Allowed : 9.31 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.13), residues: 3774 helix: -0.61 (0.24), residues: 426 sheet: -1.21 (0.14), residues: 1320 loop : -2.26 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 112 HIS 0.006 0.001 HIS M 52 PHE 0.034 0.002 PHE 2 53 TYR 0.026 0.002 TYR H 32 ARG 0.007 0.001 ARG 6 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 453 time to evaluate : 3.563 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: h 96 LYS cc_start: 0.7858 (mttt) cc_final: 0.7650 (tptt) REVERT: l 24 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7963 (mttt) REVERT: l 30 ASN cc_start: 0.8244 (m110) cc_final: 0.7996 (m-40) REVERT: M 64 LYS cc_start: 0.8623 (tptt) cc_final: 0.8310 (ttmm) REVERT: N 17 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8118 (mt0) REVERT: N 20 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7760 (mmm-85) REVERT: D 542 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8431 (ttp-170) REVERT: D 633 LYS cc_start: 0.9304 (ptmt) cc_final: 0.8905 (mttp) REVERT: D 657 GLU cc_start: 0.8863 (tp30) cc_final: 0.8529 (tp30) REVERT: C 180 ASP cc_start: 0.8846 (m-30) cc_final: 0.8640 (m-30) REVERT: C 264 SER cc_start: 0.9046 (t) cc_final: 0.8490 (p) REVERT: H 96 LYS cc_start: 0.7826 (mttt) cc_final: 0.7467 (tptt) REVERT: L 4 MET cc_start: 0.6684 (mtt) cc_final: 0.6244 (mmp) REVERT: n 17 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8019 (mt0) REVERT: n 53 ASP cc_start: 0.7736 (m-30) cc_final: 0.7463 (m-30) REVERT: n 87 TYR cc_start: 0.8503 (m-80) cc_final: 0.8228 (m-10) REVERT: q 39 LEU cc_start: 0.8980 (tp) cc_final: 0.8774 (tt) REVERT: d 574 LYS cc_start: 0.8905 (mttp) cc_final: 0.8572 (mtmt) REVERT: d 633 LYS cc_start: 0.9316 (ptpt) cc_final: 0.8619 (mtmm) REVERT: d 657 GLU cc_start: 0.8880 (tp30) cc_final: 0.8498 (tp30) REVERT: d 659 ASP cc_start: 0.8670 (m-30) cc_final: 0.8444 (t0) REVERT: c 264 SER cc_start: 0.9033 (t) cc_final: 0.8570 (p) REVERT: c 416 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8969 (pp) REVERT: 7 3 HIS cc_start: 0.8314 (t-90) cc_final: 0.8058 (t-90) REVERT: 7 31 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8740 (t0) REVERT: 8 17 GLN cc_start: 0.8254 (mm-40) cc_final: 0.8007 (mt0) REVERT: 8 87 TYR cc_start: 0.8422 (m-80) cc_final: 0.8195 (m-10) REVERT: 8 100 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7901 (mm-30) REVERT: 5 39 LEU cc_start: 0.9127 (tp) cc_final: 0.8812 (tt) REVERT: 1 574 LYS cc_start: 0.8894 (mttp) cc_final: 0.8536 (mtpt) REVERT: 1 657 GLU cc_start: 0.8911 (tp30) cc_final: 0.8609 (tp30) REVERT: 1 659 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8581 (t0) REVERT: 2 82 GLN cc_start: 0.7303 (pp30) cc_final: 0.6987 (pp30) REVERT: 2 180 ASP cc_start: 0.8841 (m-30) cc_final: 0.8599 (m-30) REVERT: 2 416 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8952 (pp) REVERT: 3 96 LYS cc_start: 0.7819 (mttt) cc_final: 0.7559 (tptt) REVERT: 4 4 MET cc_start: 0.6672 (mtt) cc_final: 0.6403 (mmp) REVERT: 4 27 GLN cc_start: 0.8386 (mt0) cc_final: 0.8023 (mt0) REVERT: 4 27 ILE cc_start: 0.7650 (mt) cc_final: 0.7370 (mm) outliers start: 60 outliers final: 29 residues processed: 498 average time/residue: 0.4618 time to fit residues: 369.8731 Evaluate side-chains 383 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 350 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 87 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain R residue 51 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 61 GLN Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 87 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 273 optimal weight: 0.0010 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 93 HIS 8 50 ASN 6 36 GLN 2 478 ASN 3 61 GLN 4 90 GLN 4 93 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33675 Z= 0.328 Angle : 0.737 17.463 45732 Z= 0.347 Chirality : 0.050 0.662 5730 Planarity : 0.004 0.036 5469 Dihedral : 12.919 80.586 8598 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.43 % Allowed : 11.59 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3774 helix: 0.17 (0.25), residues: 426 sheet: -0.96 (0.14), residues: 1290 loop : -2.04 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 571 HIS 0.006 0.001 HIS m 52 PHE 0.031 0.002 PHE 2 53 TYR 0.018 0.002 TYR 3 100 ARG 0.008 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 372 time to evaluate : 3.869 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: h 45 LEU cc_start: 0.6284 (tp) cc_final: 0.5959 (tp) REVERT: h 96 LYS cc_start: 0.7722 (mttt) cc_final: 0.7416 (tptt) REVERT: l 27 GLN cc_start: 0.8278 (mt0) cc_final: 0.7890 (mt0) REVERT: l 30 ASN cc_start: 0.8251 (m110) cc_final: 0.7964 (m-40) REVERT: l 37 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8382 (tp) REVERT: l 86 TYR cc_start: 0.6146 (m-80) cc_final: 0.5855 (m-80) REVERT: M 64 LYS cc_start: 0.8725 (tptt) cc_final: 0.8496 (ttmm) REVERT: N 20 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7908 (mmm-85) REVERT: N 104 LEU cc_start: 0.8443 (tp) cc_final: 0.7348 (tp) REVERT: D 633 LYS cc_start: 0.9355 (ptmt) cc_final: 0.8794 (mttp) REVERT: D 657 GLU cc_start: 0.8925 (tp30) cc_final: 0.8637 (tp30) REVERT: C 125 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9339 (tt) REVERT: C 396 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (mm) REVERT: H 39 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7536 (tm-30) REVERT: H 97 LEU cc_start: 0.8587 (mt) cc_final: 0.8232 (tt) REVERT: L 4 MET cc_start: 0.6693 (mtt) cc_final: 0.6153 (mmp) REVERT: m 46 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7863 (tm-30) REVERT: n 17 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8097 (mt0) REVERT: n 26 GLU cc_start: 0.8589 (tt0) cc_final: 0.8189 (mm-30) REVERT: n 53 ASP cc_start: 0.7810 (m-30) cc_final: 0.7592 (m-30) REVERT: n 87 TYR cc_start: 0.8560 (m-80) cc_final: 0.8314 (m-10) REVERT: d 633 LYS cc_start: 0.9370 (ptpt) cc_final: 0.8720 (mtmm) REVERT: d 657 GLU cc_start: 0.8906 (tp30) cc_final: 0.8500 (tp30) REVERT: d 659 ASP cc_start: 0.8774 (m-30) cc_final: 0.8540 (t0) REVERT: c 82 GLN cc_start: 0.8183 (pm20) cc_final: 0.7820 (pm20) REVERT: c 161 MET cc_start: 0.8381 (tpp) cc_final: 0.8113 (tpp) REVERT: c 416 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9246 (pt) REVERT: 7 3 HIS cc_start: 0.8329 (t-90) cc_final: 0.8037 (t-90) REVERT: 7 31 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8835 (t0) REVERT: 8 87 TYR cc_start: 0.8475 (m-80) cc_final: 0.8273 (m-10) REVERT: 8 100 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8045 (mm-30) REVERT: 1 574 LYS cc_start: 0.9011 (mttp) cc_final: 0.8566 (mtpt) REVERT: 1 657 GLU cc_start: 0.8956 (tp30) cc_final: 0.8618 (tp30) REVERT: 1 659 ASP cc_start: 0.9293 (OUTLIER) cc_final: 0.8694 (t0) REVERT: 2 416 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9000 (pp) REVERT: 3 98 LEU cc_start: 0.8281 (tt) cc_final: 0.7950 (mp) REVERT: 4 4 MET cc_start: 0.6621 (mtt) cc_final: 0.6317 (mmp) REVERT: 4 27 GLN cc_start: 0.8445 (mt0) cc_final: 0.8114 (mt0) REVERT: 4 27 ILE cc_start: 0.7698 (mt) cc_final: 0.7301 (mm) REVERT: 4 90 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5828 (tm-30) outliers start: 81 outliers final: 50 residues processed: 441 average time/residue: 0.4403 time to fit residues: 313.1759 Evaluate side-chains 391 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 87 SER Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain r residue 36 GLN Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 620 SER Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 87 SER Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 324 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN l 93 HIS ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN N 50 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN 6 30 ASN 2 249 HIS ** 4 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33675 Z= 0.298 Angle : 0.705 17.734 45732 Z= 0.329 Chirality : 0.049 0.691 5730 Planarity : 0.004 0.035 5469 Dihedral : 11.455 77.793 8598 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.58 % Allowed : 13.54 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.13), residues: 3774 helix: 0.60 (0.26), residues: 426 sheet: -0.85 (0.14), residues: 1281 loop : -1.97 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 571 HIS 0.004 0.001 HIS M 52 PHE 0.026 0.002 PHE 2 53 TYR 0.021 0.002 TYR 7 33 ARG 0.004 0.001 ARG 4 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 352 time to evaluate : 3.701 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: h 37 MET cc_start: 0.8375 (mmm) cc_final: 0.8124 (mmm) REVERT: h 39 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7394 (tm-30) REVERT: h 96 LYS cc_start: 0.7803 (mttt) cc_final: 0.7539 (tptt) REVERT: l 27 GLN cc_start: 0.8321 (mt0) cc_final: 0.8003 (mt0) REVERT: l 30 ASN cc_start: 0.8243 (m110) cc_final: 0.8039 (m-40) REVERT: M 64 LYS cc_start: 0.8727 (tptt) cc_final: 0.8426 (ttmm) REVERT: D 612 SER cc_start: 0.9150 (t) cc_final: 0.8764 (t) REVERT: D 633 LYS cc_start: 0.9349 (ptmt) cc_final: 0.8791 (mttp) REVERT: D 657 GLU cc_start: 0.8928 (tp30) cc_final: 0.8652 (tp30) REVERT: C 161 MET cc_start: 0.8741 (tpp) cc_final: 0.8271 (tpp) REVERT: H 39 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7404 (tm-30) REVERT: H 98 LEU cc_start: 0.8476 (tt) cc_final: 0.8091 (mp) REVERT: L 4 MET cc_start: 0.6630 (mtt) cc_final: 0.6062 (mmp) REVERT: m 46 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7772 (tm-30) REVERT: n 50 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7929 (t0) REVERT: n 53 ASP cc_start: 0.7806 (m-30) cc_final: 0.7594 (m-30) REVERT: d 633 LYS cc_start: 0.9375 (ptpt) cc_final: 0.8708 (mtmm) REVERT: d 657 GLU cc_start: 0.8897 (tp30) cc_final: 0.8479 (tp30) REVERT: d 659 ASP cc_start: 0.8811 (m-30) cc_final: 0.8557 (t0) REVERT: c 161 MET cc_start: 0.8520 (tpp) cc_final: 0.8157 (tpp) REVERT: c 416 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9215 (pt) REVERT: 7 3 HIS cc_start: 0.8225 (t-90) cc_final: 0.7987 (t-90) REVERT: 8 26 GLU cc_start: 0.8557 (tt0) cc_final: 0.8340 (mm-30) REVERT: 8 100 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8065 (mm-30) REVERT: 1 574 LYS cc_start: 0.9046 (mttp) cc_final: 0.8717 (mtpt) REVERT: 1 657 GLU cc_start: 0.8961 (tp30) cc_final: 0.8623 (tp30) REVERT: 1 659 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.8713 (t0) REVERT: 2 416 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8924 (pp) REVERT: 3 39 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7277 (pp30) REVERT: 3 96 LYS cc_start: 0.7871 (mttt) cc_final: 0.7636 (tptt) REVERT: 3 98 LEU cc_start: 0.8393 (tt) cc_final: 0.8036 (mp) REVERT: 4 4 MET cc_start: 0.6603 (mtt) cc_final: 0.6209 (mmp) REVERT: 4 27 GLN cc_start: 0.8485 (mt0) cc_final: 0.8020 (mt0) REVERT: 4 27 ILE cc_start: 0.7657 (mt) cc_final: 0.7411 (mm) REVERT: 4 48 ILE cc_start: 0.7142 (pt) cc_final: 0.6930 (pt) outliers start: 86 outliers final: 54 residues processed: 419 average time/residue: 0.4433 time to fit residues: 302.9867 Evaluate side-chains 383 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 325 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain n residue 50 ASN Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 309 optimal weight: 4.9990 chunk 250 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 0.4980 chunk 325 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN l 38 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 ASN L 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN 2 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33675 Z= 0.253 Angle : 0.675 16.513 45732 Z= 0.314 Chirality : 0.048 0.614 5730 Planarity : 0.003 0.062 5469 Dihedral : 10.763 76.101 8598 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.61 % Allowed : 13.45 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.74 (0.14), residues: 3774 helix: 0.82 (0.26), residues: 426 sheet: -0.79 (0.14), residues: 1299 loop : -1.86 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 571 HIS 0.005 0.001 HIS m 52 PHE 0.022 0.002 PHE 2 53 TYR 0.020 0.002 TYR M 33 ARG 0.010 0.000 ARG c 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 334 time to evaluate : 3.463 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: h 37 MET cc_start: 0.8356 (mmm) cc_final: 0.7982 (mmm) REVERT: M 64 LYS cc_start: 0.8714 (tptt) cc_final: 0.8400 (ttmm) REVERT: D 612 SER cc_start: 0.9144 (t) cc_final: 0.8767 (t) REVERT: D 633 LYS cc_start: 0.9337 (ptmt) cc_final: 0.8780 (mttp) REVERT: D 657 GLU cc_start: 0.8945 (tp30) cc_final: 0.8538 (tp30) REVERT: H 98 LEU cc_start: 0.8580 (tt) cc_final: 0.8250 (mp) REVERT: m 46 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7281 (tm-30) REVERT: n 26 GLU cc_start: 0.8577 (tt0) cc_final: 0.8286 (mm-30) REVERT: n 50 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8325 (t0) REVERT: q 81 GLU cc_start: 0.8530 (tp30) cc_final: 0.8121 (mm-30) REVERT: d 633 LYS cc_start: 0.9379 (ptpt) cc_final: 0.8643 (mtmm) REVERT: d 657 GLU cc_start: 0.8901 (tp30) cc_final: 0.8479 (tp30) REVERT: d 659 ASP cc_start: 0.8786 (m-30) cc_final: 0.8551 (t0) REVERT: c 161 MET cc_start: 0.8590 (tpp) cc_final: 0.8208 (tpp) REVERT: c 416 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9155 (pt) REVERT: 8 26 GLU cc_start: 0.8563 (tt0) cc_final: 0.8330 (mm-30) REVERT: 8 100 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8040 (mm-30) REVERT: 1 574 LYS cc_start: 0.9055 (mttp) cc_final: 0.8730 (mtpt) REVERT: 1 595 ILE cc_start: 0.9335 (pt) cc_final: 0.9006 (mt) REVERT: 1 657 GLU cc_start: 0.8880 (tp30) cc_final: 0.8517 (tp30) REVERT: 1 659 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8707 (t0) REVERT: 2 150 MET cc_start: 0.7140 (mpp) cc_final: 0.6850 (pmm) REVERT: 2 416 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8894 (pp) REVERT: 3 39 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7347 (pp30) REVERT: 3 96 LYS cc_start: 0.7770 (mttt) cc_final: 0.7496 (mmtt) REVERT: 3 98 LEU cc_start: 0.8368 (tt) cc_final: 0.8028 (mp) REVERT: 4 4 MET cc_start: 0.6548 (mtt) cc_final: 0.6202 (mmp) REVERT: 4 27 ILE cc_start: 0.7747 (mt) cc_final: 0.7407 (mm) outliers start: 87 outliers final: 55 residues processed: 404 average time/residue: 0.4258 time to fit residues: 281.1946 Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 312 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 50 ASN Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 50 ASN Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 6 residue 22 PHE Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.9990 chunk 326 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS L 27 GLN m 76 ASN n 50 ASN d 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33675 Z= 0.299 Angle : 0.687 18.248 45732 Z= 0.321 Chirality : 0.048 0.599 5730 Planarity : 0.004 0.063 5469 Dihedral : 10.282 75.672 8598 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.15 % Allowed : 13.24 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.62 (0.14), residues: 3774 helix: 0.90 (0.26), residues: 426 sheet: -0.66 (0.14), residues: 1293 loop : -1.82 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 571 HIS 0.006 0.001 HIS M 52 PHE 0.021 0.002 PHE C 53 TYR 0.025 0.002 TYR M 33 ARG 0.005 0.000 ARG 4 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 333 time to evaluate : 3.864 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: h 37 MET cc_start: 0.8347 (mmm) cc_final: 0.7993 (mmm) REVERT: l 27 GLN cc_start: 0.8344 (mt0) cc_final: 0.7994 (mt0) REVERT: M 64 LYS cc_start: 0.8731 (tptt) cc_final: 0.8446 (ttmm) REVERT: N 20 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: N 26 GLU cc_start: 0.8617 (tt0) cc_final: 0.8335 (mm-30) REVERT: D 612 SER cc_start: 0.9200 (t) cc_final: 0.8834 (t) REVERT: D 633 LYS cc_start: 0.9323 (ptmt) cc_final: 0.8738 (mttp) REVERT: D 657 GLU cc_start: 0.8961 (tp30) cc_final: 0.8535 (tp30) REVERT: H 98 LEU cc_start: 0.8632 (tt) cc_final: 0.8331 (mp) REVERT: m 46 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7311 (tm-30) REVERT: n 26 GLU cc_start: 0.8642 (tt0) cc_final: 0.8319 (mm-30) REVERT: q 81 GLU cc_start: 0.8520 (tp30) cc_final: 0.8195 (mm-30) REVERT: d 633 LYS cc_start: 0.9392 (ptpt) cc_final: 0.8659 (mtmm) REVERT: d 657 GLU cc_start: 0.8942 (tp30) cc_final: 0.8491 (tp30) REVERT: d 659 ASP cc_start: 0.8819 (m-30) cc_final: 0.8555 (t0) REVERT: c 161 MET cc_start: 0.8682 (tpp) cc_final: 0.8280 (tpp) REVERT: c 416 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9197 (pt) REVERT: 8 100 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8121 (mm-30) REVERT: 1 574 LYS cc_start: 0.9081 (mttp) cc_final: 0.8751 (mtpt) REVERT: 1 595 ILE cc_start: 0.9348 (pt) cc_final: 0.9017 (mt) REVERT: 1 657 GLU cc_start: 0.8894 (tp30) cc_final: 0.8535 (tp30) REVERT: 1 659 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8692 (t0) REVERT: 2 150 MET cc_start: 0.7080 (mpp) cc_final: 0.6835 (pmm) REVERT: 2 271 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: 2 416 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8941 (pp) REVERT: 3 39 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7344 (pp30) REVERT: 3 96 LYS cc_start: 0.7791 (mttt) cc_final: 0.7587 (mmtt) REVERT: 3 97 LEU cc_start: 0.8366 (mt) cc_final: 0.8108 (tt) REVERT: 4 27 ILE cc_start: 0.7726 (mt) cc_final: 0.7474 (mm) outliers start: 105 outliers final: 82 residues processed: 415 average time/residue: 0.4293 time to fit residues: 290.0752 Evaluate side-chains 400 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 314 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 31 ASP Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 47 ILE Chi-restraints excluded: chain r residue 99 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 576 LEU Chi-restraints excluded: chain d residue 620 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 396 ILE Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 8 residue 25 GLU Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 6 residue 22 PHE Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 76 ASP Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 271 MET Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 93 SER Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 361 optimal weight: 10.0000 chunk 226 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 61 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN n 50 ASN 7 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33675 Z= 0.161 Angle : 0.647 17.541 45732 Z= 0.296 Chirality : 0.047 0.563 5730 Planarity : 0.003 0.077 5469 Dihedral : 9.405 71.334 8598 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.31 % Allowed : 14.56 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3774 helix: 1.19 (0.27), residues: 426 sheet: -0.52 (0.14), residues: 1278 loop : -1.72 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 47 HIS 0.005 0.001 HIS m 52 PHE 0.020 0.001 PHE 2 53 TYR 0.022 0.001 TYR 3 100 ARG 0.008 0.000 ARG 4 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 354 time to evaluate : 3.598 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: h 37 MET cc_start: 0.8178 (mmm) cc_final: 0.7838 (mmm) REVERT: l 4 MET cc_start: 0.5788 (mmp) cc_final: 0.5263 (mmt) REVERT: l 27 GLN cc_start: 0.8356 (mt0) cc_final: 0.7997 (mt0) REVERT: M 64 LYS cc_start: 0.8729 (tptt) cc_final: 0.8468 (ttmm) REVERT: N 26 GLU cc_start: 0.8578 (tt0) cc_final: 0.8283 (mm-30) REVERT: Q 81 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: D 633 LYS cc_start: 0.9278 (ptmt) cc_final: 0.8821 (mtmm) REVERT: D 657 GLU cc_start: 0.8943 (tp30) cc_final: 0.8568 (tp30) REVERT: C 161 MET cc_start: 0.8764 (tpp) cc_final: 0.8338 (tpp) REVERT: H 10 ASP cc_start: 0.5346 (m-30) cc_final: 0.4935 (t0) REVERT: m 46 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7349 (tm-30) REVERT: n 26 GLU cc_start: 0.8550 (tt0) cc_final: 0.8238 (mm-30) REVERT: q 81 GLU cc_start: 0.8449 (tp30) cc_final: 0.8148 (mm-30) REVERT: d 633 LYS cc_start: 0.9347 (ptpt) cc_final: 0.8886 (mtmm) REVERT: d 657 GLU cc_start: 0.8890 (tp30) cc_final: 0.8475 (tp30) REVERT: d 659 ASP cc_start: 0.8746 (m-30) cc_final: 0.8487 (t0) REVERT: c 161 MET cc_start: 0.8697 (tpp) cc_final: 0.8300 (tpp) REVERT: c 416 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9119 (pt) REVERT: 8 100 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8065 (mm-30) REVERT: 5 39 LEU cc_start: 0.9091 (tp) cc_final: 0.8736 (tt) REVERT: 1 574 LYS cc_start: 0.9068 (mttp) cc_final: 0.8737 (mtpt) REVERT: 1 657 GLU cc_start: 0.8903 (tp30) cc_final: 0.8589 (tp30) REVERT: 1 659 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8663 (t0) REVERT: 2 150 MET cc_start: 0.7028 (mpp) cc_final: 0.6809 (pmm) REVERT: 2 416 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8826 (pp) REVERT: 3 39 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7449 (pp30) REVERT: 3 97 LEU cc_start: 0.8275 (mt) cc_final: 0.8036 (tt) REVERT: 3 98 LEU cc_start: 0.8364 (tt) cc_final: 0.7766 (mp) REVERT: 4 27 GLN cc_start: 0.8405 (mt0) cc_final: 0.8023 (mt0) REVERT: 4 27 ILE cc_start: 0.7598 (mt) cc_final: 0.7387 (mm) outliers start: 77 outliers final: 50 residues processed: 415 average time/residue: 0.4456 time to fit residues: 298.6947 Evaluate side-chains 373 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 319 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain c residue 434 MET Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 546 SER Chi-restraints excluded: chain 1 residue 576 LEU Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 280 ASN Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.4980 chunk 144 optimal weight: 0.0980 chunk 215 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 284 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33675 Z= 0.159 Angle : 0.645 17.560 45732 Z= 0.295 Chirality : 0.046 0.539 5730 Planarity : 0.004 0.093 5469 Dihedral : 8.942 69.853 8598 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.19 % Allowed : 14.92 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.29 (0.14), residues: 3774 helix: 1.36 (0.27), residues: 426 sheet: -0.51 (0.14), residues: 1317 loop : -1.62 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 47 HIS 0.006 0.001 HIS M 52 PHE 0.018 0.001 PHE 2 53 TYR 0.026 0.001 TYR 3 32 ARG 0.011 0.000 ARG 4 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 334 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 37 MET cc_start: 0.8157 (mmm) cc_final: 0.7883 (mmm) REVERT: l 4 MET cc_start: 0.5624 (mmp) cc_final: 0.5099 (mmt) REVERT: l 27 GLN cc_start: 0.8349 (mt0) cc_final: 0.8002 (mt0) REVERT: M 31 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8975 (t0) REVERT: M 64 LYS cc_start: 0.8767 (tptt) cc_final: 0.8485 (ttmm) REVERT: M 77 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5906 (tp) REVERT: N 26 GLU cc_start: 0.8564 (tt0) cc_final: 0.8272 (mm-30) REVERT: Q 81 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: D 633 LYS cc_start: 0.9265 (ptmt) cc_final: 0.8828 (mtmm) REVERT: D 657 GLU cc_start: 0.8964 (tp30) cc_final: 0.8669 (tp30) REVERT: C 161 MET cc_start: 0.8787 (tpp) cc_final: 0.8372 (tpp) REVERT: H 10 ASP cc_start: 0.5333 (m-30) cc_final: 0.4953 (t0) REVERT: L 4 MET cc_start: 0.6380 (mtt) cc_final: 0.5804 (mmp) REVERT: m 46 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7344 (tm-30) REVERT: n 26 GLU cc_start: 0.8569 (tt0) cc_final: 0.8223 (mm-30) REVERT: q 81 GLU cc_start: 0.8449 (tp30) cc_final: 0.8169 (mm-30) REVERT: d 633 LYS cc_start: 0.9379 (ptpt) cc_final: 0.8704 (mtmm) REVERT: d 657 GLU cc_start: 0.8917 (tp30) cc_final: 0.8501 (tp30) REVERT: d 659 ASP cc_start: 0.8728 (m-30) cc_final: 0.8504 (t0) REVERT: c 161 MET cc_start: 0.8693 (tpp) cc_final: 0.8281 (tpp) REVERT: c 416 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9098 (pt) REVERT: 8 95 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8338 (mmt90) REVERT: 5 39 LEU cc_start: 0.9059 (tp) cc_final: 0.8690 (tt) REVERT: 1 574 LYS cc_start: 0.9048 (mttp) cc_final: 0.8731 (mtpt) REVERT: 1 657 GLU cc_start: 0.8907 (tp30) cc_final: 0.8588 (tp30) REVERT: 1 659 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8673 (t0) REVERT: 2 320 THR cc_start: 0.9535 (m) cc_final: 0.9172 (p) REVERT: 2 416 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8851 (pp) REVERT: 3 39 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7453 (pp30) REVERT: 3 97 LEU cc_start: 0.8362 (mt) cc_final: 0.8123 (tt) REVERT: 4 27 GLN cc_start: 0.8505 (mt0) cc_final: 0.8083 (mt0) outliers start: 73 outliers final: 54 residues processed: 392 average time/residue: 0.4561 time to fit residues: 292.4489 Evaluate side-chains 369 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 309 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 595 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 280 ASN Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 318 optimal weight: 6.9990 chunk 335 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 6 GLN 4 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33675 Z= 0.256 Angle : 0.670 15.843 45732 Z= 0.312 Chirality : 0.047 0.540 5730 Planarity : 0.004 0.082 5469 Dihedral : 8.850 71.969 8598 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.49 % Allowed : 14.68 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3774 helix: 1.56 (0.27), residues: 408 sheet: -0.44 (0.14), residues: 1287 loop : -1.59 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 113 HIS 0.004 0.001 HIS 2 374 PHE 0.019 0.002 PHE R 22 TYR 0.024 0.001 TYR h 32 ARG 0.011 0.000 ARG 4 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 310 time to evaluate : 3.503 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: h 37 MET cc_start: 0.8207 (mmm) cc_final: 0.7884 (mmm) REVERT: l 4 MET cc_start: 0.5718 (mmp) cc_final: 0.5224 (mmt) REVERT: l 27 GLN cc_start: 0.8407 (mt0) cc_final: 0.8051 (mt0) REVERT: l 47 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6507 (tt) REVERT: M 64 LYS cc_start: 0.8757 (tptt) cc_final: 0.8407 (ttmm) REVERT: M 77 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5706 (tp) REVERT: N 26 GLU cc_start: 0.8599 (tt0) cc_final: 0.8283 (mm-30) REVERT: D 633 LYS cc_start: 0.9288 (ptmt) cc_final: 0.8688 (mtmm) REVERT: D 657 GLU cc_start: 0.8980 (tp30) cc_final: 0.8661 (tp30) REVERT: C 161 MET cc_start: 0.8784 (tpp) cc_final: 0.8342 (tpp) REVERT: H 10 ASP cc_start: 0.5385 (m-30) cc_final: 0.4969 (t0) REVERT: m 46 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7377 (tm-30) REVERT: n 26 GLU cc_start: 0.8604 (tt0) cc_final: 0.8278 (mm-30) REVERT: q 81 GLU cc_start: 0.8472 (tp30) cc_final: 0.8178 (mm-30) REVERT: d 633 LYS cc_start: 0.9399 (ptpt) cc_final: 0.8748 (mtmm) REVERT: d 657 GLU cc_start: 0.8934 (tp30) cc_final: 0.8485 (tp30) REVERT: d 659 ASP cc_start: 0.8771 (m-30) cc_final: 0.8501 (t0) REVERT: c 161 MET cc_start: 0.8732 (tpp) cc_final: 0.8239 (tpp) REVERT: c 416 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9183 (pt) REVERT: 1 574 LYS cc_start: 0.9070 (mttp) cc_final: 0.8748 (mtpt) REVERT: 1 657 GLU cc_start: 0.8919 (tp30) cc_final: 0.8577 (tp30) REVERT: 1 659 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8673 (t0) REVERT: 2 320 THR cc_start: 0.9568 (m) cc_final: 0.9251 (p) REVERT: 2 416 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8860 (pp) REVERT: 3 34 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6827 (tpt) REVERT: 3 39 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7289 (pp30) outliers start: 83 outliers final: 66 residues processed: 371 average time/residue: 0.4167 time to fit residues: 256.9500 Evaluate side-chains 371 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 299 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 31 ASP Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain n residue 107 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 595 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 47 ILE Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 76 ASP Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 595 ILE Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 280 ASN Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 3.9990 chunk 356 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33675 Z= 0.339 Angle : 0.710 14.791 45732 Z= 0.332 Chirality : 0.048 0.558 5730 Planarity : 0.004 0.085 5469 Dihedral : 8.943 73.762 8598 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.40 % Allowed : 14.92 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.14), residues: 3774 helix: 1.47 (0.27), residues: 408 sheet: -0.44 (0.14), residues: 1293 loop : -1.60 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 113 HIS 0.004 0.001 HIS 2 374 PHE 0.020 0.002 PHE q 100D TYR 0.027 0.002 TYR h 32 ARG 0.010 0.001 ARG l 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 301 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 34 MET cc_start: 0.7469 (tpp) cc_final: 0.7242 (tpt) REVERT: h 37 MET cc_start: 0.8309 (mmm) cc_final: 0.7945 (mmm) REVERT: l 27 GLN cc_start: 0.8402 (mt0) cc_final: 0.8037 (mt0) REVERT: l 45 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7405 (mmmt) REVERT: l 47 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6548 (tt) REVERT: M 77 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5900 (tp) REVERT: N 26 GLU cc_start: 0.8608 (tt0) cc_final: 0.8311 (mm-30) REVERT: D 612 SER cc_start: 0.9077 (t) cc_final: 0.8748 (t) REVERT: D 633 LYS cc_start: 0.9340 (ptmt) cc_final: 0.8745 (mtmm) REVERT: D 657 GLU cc_start: 0.8978 (tp30) cc_final: 0.8638 (tp30) REVERT: C 161 MET cc_start: 0.8851 (tpp) cc_final: 0.8422 (tpp) REVERT: H 33 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7127 (pt0) REVERT: L 45 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7327 (mmmt) REVERT: m 46 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7375 (tm-30) REVERT: m 73 LYS cc_start: 0.8203 (tttt) cc_final: 0.7425 (tttt) REVERT: n 26 GLU cc_start: 0.8665 (tt0) cc_final: 0.8349 (mm-30) REVERT: q 81 GLU cc_start: 0.8465 (tp30) cc_final: 0.8165 (mm-30) REVERT: d 633 LYS cc_start: 0.9413 (ptpt) cc_final: 0.8646 (mtmm) REVERT: d 657 GLU cc_start: 0.8968 (tp30) cc_final: 0.8505 (tp30) REVERT: d 659 ASP cc_start: 0.8842 (m-30) cc_final: 0.8503 (t0) REVERT: c 161 MET cc_start: 0.8726 (tpp) cc_final: 0.8238 (tpp) REVERT: c 416 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9224 (pt) REVERT: 7 73 LYS cc_start: 0.8238 (tttt) cc_final: 0.7221 (tptt) REVERT: 1 574 LYS cc_start: 0.9091 (mttp) cc_final: 0.8765 (mtpt) REVERT: 1 657 GLU cc_start: 0.8932 (tp30) cc_final: 0.8582 (tp30) REVERT: 1 659 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.8669 (t0) REVERT: 2 416 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9050 (pp) REVERT: 3 39 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7206 (pp30) REVERT: 4 27 GLN cc_start: 0.8586 (mt0) cc_final: 0.8214 (mt0) REVERT: 4 45 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7391 (mmmt) outliers start: 80 outliers final: 72 residues processed: 361 average time/residue: 0.4470 time to fit residues: 266.7973 Evaluate side-chains 363 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 286 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 93 SER Chi-restraints excluded: chain h residue 102 VAL Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain n residue 107 LEU Chi-restraints excluded: chain r residue 101 VAL Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 87 THR Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain d residue 546 SER Chi-restraints excluded: chain d residue 595 ILE Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 260 LEU Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 357 THR Chi-restraints excluded: chain c residue 371 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 423 ILE Chi-restraints excluded: chain 7 residue 16 GLU Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 47 ILE Chi-restraints excluded: chain 8 residue 107 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 76 ASP Chi-restraints excluded: chain 5 residue 98 CYS Chi-restraints excluded: chain 1 residue 595 ILE Chi-restraints excluded: chain 1 residue 659 ASP Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 261 LEU Chi-restraints excluded: chain 2 residue 280 ASN Chi-restraints excluded: chain 2 residue 357 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 68 ILE Chi-restraints excluded: chain 3 residue 102 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 305 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 51 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.065411 restraints weight = 86064.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.065407 restraints weight = 60099.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065823 restraints weight = 50147.888| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33675 Z= 0.295 Angle : 0.693 14.196 45732 Z= 0.323 Chirality : 0.047 0.557 5730 Planarity : 0.004 0.072 5469 Dihedral : 8.865 73.627 8598 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.49 % Allowed : 15.05 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3774 helix: 1.54 (0.27), residues: 408 sheet: -0.48 (0.14), residues: 1305 loop : -1.57 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 113 HIS 0.004 0.001 HIS 2 374 PHE 0.019 0.002 PHE q 100D TYR 0.031 0.002 TYR m 33 ARG 0.009 0.001 ARG l 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.77 seconds wall clock time: 118 minutes 59.57 seconds (7139.57 seconds total)