Starting phenix.real_space_refine on Sun Feb 18 02:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u59_20642/02_2024/6u59_20642.pdb" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.096 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 126 5.16 5 C 12780 2.51 5 N 3342 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20439 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "I" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "K" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: 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: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 11.12, per 1000 atoms: 0.54 Number of scatterers: 20439 At special positions: 0 Unit cell: (152.95, 165.6, 124.2, 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 126 16.00 O 4191 8.00 N 3342 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.13 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.13 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.13 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.05 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA W 3 " - " MAN W 4 " " BMA j 3 " - " MAN j 4 " " BMA w 3 " - " MAN w 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 606 " - " ASN A 197 " " NAG A 613 " - " ASN A 301 " " NAG A 614 " - " ASN A 339 " " NAG A 618 " - " ASN A 355 " " NAG A 635 " - " ASN A 396 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG B 704 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 606 " - " ASN C 197 " " NAG C 613 " - " ASN C 301 " " NAG C 614 " - " ASN C 339 " " NAG C 618 " - " ASN C 355 " " NAG C 635 " - " ASN C 396 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 611 " " NAG G 601 " - " ASN G 88 " " NAG G 606 " - " ASN G 197 " " NAG G 613 " - " ASN G 301 " " NAG G 614 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 635 " - " ASN G 396 " " NAG I 701 " - " ASN I 616 " " NAG I 702 " - " ASN I 625 " " NAG I 703 " - " ASN I 637 " " NAG I 704 " - " ASN I 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 362 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 241 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 362 " " NAG g 1 " - " ASN C 386 " " NAG h 1 " - " ASN C 392 " " NAG i 1 " - " ASN C 448 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 241 " " NAG l 1 " - " ASN C 413 " " NAG m 1 " - " ASN G 156 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 332 " " NAG s 1 " - " ASN G 362 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 262 " " NAG x 1 " - " ASN G 241 " " NAG y 1 " - " ASN G 413 " Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 3.5 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 530' Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.791A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 530' Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 662 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 116 removed outlier: 3.586A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 526 through 530' Processing helix chain 'I' and resid 538 through 543 Processing helix chain 'I' and resid 569 through 597 removed outlier: 4.036A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 648 Processing helix chain 'I' and resid 651 through 662 Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.430A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.841A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.111A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 removed outlier: 6.773A pdb=" N THR H 76 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'G' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE G 215 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY G 250 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR G 217 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 176 Processing sheet with id=AD9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR G 357 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE G 468 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE G 359 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE G 323 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 321 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 1980 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: 8.27 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4960 1.32 - 1.46: 6549 1.46 - 1.59: 9164 1.59 - 1.73: 24 1.73 - 1.86: 156 Bond restraints: 20853 Sorted by residual: bond pdb=" CE1 HIS C 374 " pdb=" NE2 HIS C 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.84e+01 bond pdb=" CE1 HIS G 374 " pdb=" NE2 HIS G 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" CE1 HIS A 374 " pdb=" NE2 HIS A 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" CB HIS G 105 " pdb=" CG HIS G 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" CB HIS C 105 " pdb=" CG HIS C 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.37: 818 106.37 - 113.52: 11576 113.52 - 120.68: 8995 120.68 - 127.84: 6759 127.84 - 134.99: 205 Bond angle restraints: 28353 Sorted by residual: angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 114.62 102.65 11.97 1.14e+00 7.69e-01 1.10e+02 angle pdb=" N GLU G 370 " pdb=" CA GLU G 370 " pdb=" C GLU G 370 " ideal model delta sigma weight residual 114.62 102.69 11.93 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N GLU C 370 " pdb=" CA GLU C 370 " pdb=" C GLU C 370 " ideal model delta sigma weight residual 114.62 102.70 11.92 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N ILE I 602 " pdb=" CA ILE I 602 " pdb=" C ILE I 602 " ideal model delta sigma weight residual 111.67 103.88 7.79 9.50e-01 1.11e+00 6.72e+01 angle pdb=" N ILE B 602 " pdb=" CA ILE B 602 " pdb=" C ILE B 602 " ideal model delta sigma weight residual 111.67 103.89 7.78 9.50e-01 1.11e+00 6.70e+01 ... (remaining 28348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 13283 21.95 - 43.90: 454 43.90 - 65.85: 99 65.85 - 87.80: 42 87.80 - 109.75: 30 Dihedral angle restraints: 13908 sinusoidal: 6972 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.59 32.59 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.58 32.58 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.56 32.56 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1736 0.065 - 0.130: 1062 0.130 - 0.195: 496 0.195 - 0.259: 181 0.259 - 0.324: 41 Chirality restraints: 3516 Sorted by residual: chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG y 2 " pdb=" O4 NAG y 1 " pdb=" C2 NAG y 2 " pdb=" O5 NAG y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 3513 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 107 " 0.040 2.00e-02 2.50e+03 8.11e-02 6.58e+01 pdb=" C LYS J 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS J 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS J 107 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 107 " -0.040 2.00e-02 2.50e+03 8.10e-02 6.57e+01 pdb=" C LYS E 107 " 0.140 2.00e-02 2.50e+03 pdb=" O LYS E 107 " -0.051 2.00e-02 2.50e+03 pdb=" OXT LYS E 107 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " 0.040 2.00e-02 2.50e+03 8.09e-02 6.55e+01 pdb=" C LYS L 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS L 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS L 107 " 0.049 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4375 2.77 - 3.30: 18449 3.30 - 3.83: 34553 3.83 - 4.37: 40023 4.37 - 4.90: 65587 Nonbonded interactions: 162987 Sorted by model distance: nonbonded pdb=" O4 NAG k 2 " pdb=" O6 NAG k 2 " model vdw 2.234 2.440 nonbonded pdb=" O4 NAG X 2 " pdb=" O6 NAG X 2 " model vdw 2.234 2.440 nonbonded pdb=" O4 NAG x 2 " pdb=" O6 NAG x 2 " model vdw 2.234 2.440 nonbonded pdb=" O4 NAG f 2 " pdb=" O6 NAG f 2 " model vdw 2.249 2.440 nonbonded pdb=" O4 NAG S 2 " pdb=" O6 NAG S 2 " model vdw 2.249 2.440 ... (remaining 162982 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 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'R' selection = chain 'e' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'j' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.690 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 57.220 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.019 0.116 20853 Z= 1.236 Angle : 1.805 11.971 28353 Z= 1.160 Chirality : 0.102 0.324 3516 Planarity : 0.009 0.081 3465 Dihedral : 12.879 109.747 9357 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.34 % Rotamer: Outliers : 0.72 % Allowed : 0.58 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.59 (0.17), residues: 2364 helix: -0.50 (0.25), residues: 381 sheet: 1.10 (0.19), residues: 675 loop : 0.42 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.011 TRP I 610 HIS 0.019 0.003 HIS H 33 PHE 0.038 0.007 PHE A 383 TYR 0.078 0.008 TYR L 36 ARG 0.007 0.001 ARG L 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 680 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8197 (t0) cc_final: 0.7745 (t0) REVERT: A 256 SER cc_start: 0.8648 (p) cc_final: 0.8380 (p) REVERT: A 279 ASP cc_start: 0.8479 (t0) cc_final: 0.8218 (t0) REVERT: A 317 PHE cc_start: 0.8782 (t80) cc_final: 0.8523 (t80) REVERT: A 439 ILE cc_start: 0.8866 (pt) cc_final: 0.8553 (mm) REVERT: B 542 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5943 (mmt180) REVERT: B 639 THR cc_start: 0.9018 (m) cc_final: 0.8708 (p) REVERT: L 77 ASP cc_start: 0.8015 (t0) cc_final: 0.7252 (t0) REVERT: H 59 TYR cc_start: 0.7810 (m-80) cc_final: 0.7585 (m-80) REVERT: H 79 LEU cc_start: 0.8005 (tp) cc_final: 0.7204 (tp) REVERT: H 82 LEU cc_start: 0.9304 (mt) cc_final: 0.8803 (mt) REVERT: C 78 ASP cc_start: 0.8173 (t0) cc_final: 0.7776 (t0) REVERT: C 107 ASP cc_start: 0.8628 (m-30) cc_final: 0.8186 (m-30) REVERT: C 279 ASP cc_start: 0.8656 (t0) cc_final: 0.8245 (t0) REVERT: C 439 ILE cc_start: 0.9031 (pt) cc_final: 0.8738 (mm) REVERT: D 542 ARG cc_start: 0.6625 (mtp180) cc_final: 0.6072 (mmt180) REVERT: D 639 THR cc_start: 0.9000 (m) cc_final: 0.8653 (p) REVERT: E 77 ASP cc_start: 0.7885 (t0) cc_final: 0.7595 (t0) REVERT: E 95 ASP cc_start: 0.7415 (m-30) cc_final: 0.7170 (m-30) REVERT: F 39 GLN cc_start: 0.8104 (tt0) cc_final: 0.7446 (tm-30) REVERT: F 82 LEU cc_start: 0.9260 (mt) cc_final: 0.8608 (mt) REVERT: G 439 ILE cc_start: 0.8801 (pt) cc_final: 0.8504 (mm) REVERT: I 542 ARG cc_start: 0.6202 (mtp180) cc_final: 0.5839 (mmt180) REVERT: I 627 THR cc_start: 0.8920 (m) cc_final: 0.7957 (p) REVERT: I 639 THR cc_start: 0.9011 (m) cc_final: 0.8436 (p) REVERT: J 77 ASP cc_start: 0.7917 (t0) cc_final: 0.7617 (t0) REVERT: K 39 GLN cc_start: 0.8331 (tt0) cc_final: 0.7739 (tm-30) REVERT: K 82 LEU cc_start: 0.9231 (mt) cc_final: 0.8673 (mt) outliers start: 15 outliers final: 6 residues processed: 692 average time/residue: 0.3321 time to fit residues: 347.6366 Evaluate side-chains 365 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 359 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain I residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 607 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20853 Z= 0.249 Angle : 0.780 9.518 28353 Z= 0.406 Chirality : 0.047 0.267 3516 Planarity : 0.004 0.041 3465 Dihedral : 9.290 66.477 5031 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.29 % Rotamer: Outliers : 3.03 % Allowed : 12.09 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.18 (0.17), residues: 2364 helix: 0.48 (0.26), residues: 381 sheet: 0.50 (0.18), residues: 675 loop : -0.11 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 479 HIS 0.004 0.001 HIS C 374 PHE 0.020 0.003 PHE A 391 TYR 0.019 0.002 TYR K 100C ARG 0.009 0.001 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 476 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7780 (ptm) cc_final: 0.7509 (ptp) REVERT: A 116 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8519 (mt) REVERT: B 566 LEU cc_start: 0.8190 (tt) cc_final: 0.7893 (tt) REVERT: B 595 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9343 (tp) REVERT: B 621 GLU cc_start: 0.7644 (tt0) cc_final: 0.7426 (tt0) REVERT: B 639 THR cc_start: 0.8845 (m) cc_final: 0.8566 (p) REVERT: L 42 GLN cc_start: 0.7872 (mp10) cc_final: 0.7380 (mp10) REVERT: L 75 ILE cc_start: 0.8871 (mp) cc_final: 0.8654 (tp) REVERT: L 77 ASP cc_start: 0.7833 (t0) cc_final: 0.7203 (t0) REVERT: L 95 ASP cc_start: 0.7303 (m-30) cc_final: 0.6972 (m-30) REVERT: H 7 SER cc_start: 0.8265 (p) cc_final: 0.8054 (p) REVERT: C 107 ASP cc_start: 0.8596 (m-30) cc_final: 0.8219 (m-30) REVERT: D 566 LEU cc_start: 0.8648 (tp) cc_final: 0.8158 (tt) REVERT: D 603 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8857 (pt) REVERT: D 627 THR cc_start: 0.8945 (p) cc_final: 0.8581 (t) REVERT: D 630 GLN cc_start: 0.8304 (mt0) cc_final: 0.8090 (mt0) REVERT: E 42 GLN cc_start: 0.8122 (mp10) cc_final: 0.7683 (mp-120) REVERT: E 75 ILE cc_start: 0.8877 (mp) cc_final: 0.8597 (tp) REVERT: E 77 ASP cc_start: 0.8030 (t0) cc_final: 0.7446 (t0) REVERT: E 95 ASP cc_start: 0.7583 (m-30) cc_final: 0.7341 (m-30) REVERT: F 30 SER cc_start: 0.8918 (m) cc_final: 0.8618 (m) REVERT: G 74 CYS cc_start: 0.8010 (m) cc_final: 0.7623 (m) REVERT: G 195 ASN cc_start: 0.7860 (m-40) cc_final: 0.7495 (m-40) REVERT: I 566 LEU cc_start: 0.8490 (tp) cc_final: 0.8010 (tt) REVERT: I 627 THR cc_start: 0.9047 (m) cc_final: 0.8712 (p) REVERT: J 42 GLN cc_start: 0.7891 (mp10) cc_final: 0.7490 (mp10) REVERT: J 75 ILE cc_start: 0.8978 (mp) cc_final: 0.8744 (tp) REVERT: J 77 ASP cc_start: 0.7624 (t0) cc_final: 0.7302 (t0) outliers start: 63 outliers final: 34 residues processed: 512 average time/residue: 0.3012 time to fit residues: 241.7451 Evaluate side-chains 386 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 349 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 658 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN I 658 GLN J 6 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20853 Z= 0.374 Angle : 0.779 16.338 28353 Z= 0.391 Chirality : 0.048 0.245 3516 Planarity : 0.004 0.050 3465 Dihedral : 7.438 42.828 5025 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.95 % Allowed : 14.88 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.14 (0.17), residues: 2364 helix: 0.60 (0.27), residues: 363 sheet: 0.59 (0.19), residues: 651 loop : -0.61 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 479 HIS 0.007 0.001 HIS F 33 PHE 0.030 0.003 PHE J 96 TYR 0.020 0.002 TYR E 49 ARG 0.006 0.001 ARG J 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 372 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7759 (ptm) cc_final: 0.7509 (ptp) REVERT: A 180 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 468 PHE cc_start: 0.8179 (m-80) cc_final: 0.7669 (m-80) REVERT: B 530 MET cc_start: 0.7207 (mmm) cc_final: 0.6645 (mmm) REVERT: B 595 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9375 (tp) REVERT: B 621 GLU cc_start: 0.8074 (tt0) cc_final: 0.7873 (tt0) REVERT: B 629 MET cc_start: 0.8233 (mmt) cc_final: 0.7990 (tpp) REVERT: L 4 MET cc_start: 0.7057 (mmm) cc_final: 0.6633 (tpp) REVERT: L 42 GLN cc_start: 0.7704 (mp10) cc_final: 0.7290 (mp10) REVERT: L 77 ASP cc_start: 0.7606 (t0) cc_final: 0.7277 (t0) REVERT: L 95 ASP cc_start: 0.7468 (m-30) cc_final: 0.7119 (m-30) REVERT: H 13 GLN cc_start: 0.8172 (pp30) cc_final: 0.7959 (pp30) REVERT: C 420 ILE cc_start: 0.9074 (mp) cc_final: 0.8732 (mt) REVERT: D 566 LEU cc_start: 0.8913 (tp) cc_final: 0.8518 (tt) REVERT: D 603 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8910 (pt) REVERT: D 653 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: E 42 GLN cc_start: 0.8028 (mp10) cc_final: 0.7611 (mp10) REVERT: E 77 ASP cc_start: 0.7737 (t0) cc_final: 0.7468 (t0) REVERT: F 6 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.5377 (mt-10) REVERT: F 31 ASP cc_start: 0.8431 (p0) cc_final: 0.8230 (p0) REVERT: G 74 CYS cc_start: 0.8071 (m) cc_final: 0.7562 (m) REVERT: G 95 MET cc_start: 0.7434 (ptp) cc_final: 0.7178 (ptp) REVERT: G 479 TRP cc_start: 0.8581 (m-10) cc_final: 0.8331 (m-90) REVERT: I 530 MET cc_start: 0.7116 (mmm) cc_final: 0.5975 (mmm) REVERT: I 595 ILE cc_start: 0.9621 (tp) cc_final: 0.9125 (tt) REVERT: J 42 GLN cc_start: 0.7803 (mp10) cc_final: 0.7396 (mp10) REVERT: J 82 ASP cc_start: 0.6790 (p0) cc_final: 0.6531 (p0) outliers start: 82 outliers final: 44 residues processed: 425 average time/residue: 0.2917 time to fit residues: 196.4991 Evaluate side-chains 379 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 330 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 564 HIS Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 229 optimal weight: 0.4980 chunk 113 optimal weight: 0.1980 chunk 205 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN J 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20853 Z= 0.258 Angle : 0.700 15.312 28353 Z= 0.348 Chirality : 0.046 0.206 3516 Planarity : 0.004 0.043 3465 Dihedral : 6.413 43.914 5025 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.81 % Allowed : 14.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.27 (0.17), residues: 2364 helix: 0.59 (0.27), residues: 366 sheet: 0.49 (0.19), residues: 684 loop : -0.75 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 36 HIS 0.006 0.001 HIS K 33 PHE 0.021 0.002 PHE H 47 TYR 0.016 0.002 TYR J 49 ARG 0.007 0.000 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 360 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7833 (ptm) cc_final: 0.7617 (ptp) REVERT: A 468 PHE cc_start: 0.8043 (m-80) cc_final: 0.7519 (m-80) REVERT: B 530 MET cc_start: 0.7239 (mmm) cc_final: 0.6261 (mmm) REVERT: B 621 GLU cc_start: 0.8008 (tt0) cc_final: 0.7758 (tt0) REVERT: L 42 GLN cc_start: 0.7671 (mp10) cc_final: 0.7239 (mp10) REVERT: L 77 ASP cc_start: 0.7629 (t0) cc_final: 0.7338 (t0) REVERT: C 420 ILE cc_start: 0.9062 (mp) cc_final: 0.8768 (mt) REVERT: D 566 LEU cc_start: 0.8925 (tp) cc_final: 0.8566 (tt) REVERT: E 42 GLN cc_start: 0.7978 (mp10) cc_final: 0.7658 (mp10) REVERT: E 77 ASP cc_start: 0.7691 (t0) cc_final: 0.7486 (t0) REVERT: E 82 ASP cc_start: 0.6479 (p0) cc_final: 0.6272 (p0) REVERT: F 6 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.5795 (mt-10) REVERT: F 31 ASP cc_start: 0.8487 (p0) cc_final: 0.8266 (p0) REVERT: G 74 CYS cc_start: 0.7942 (m) cc_final: 0.7438 (m) REVERT: G 95 MET cc_start: 0.7354 (ptp) cc_final: 0.7095 (ptp) REVERT: G 104 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8221 (ttm) REVERT: G 479 TRP cc_start: 0.8408 (m-10) cc_final: 0.8203 (m-90) REVERT: I 530 MET cc_start: 0.7273 (mmm) cc_final: 0.6320 (mmm) REVERT: J 42 GLN cc_start: 0.7730 (mp10) cc_final: 0.7373 (mp10) REVERT: J 82 ASP cc_start: 0.6283 (p0) cc_final: 0.5919 (p0) REVERT: K 58 TYR cc_start: 0.7812 (p90) cc_final: 0.7422 (p90) outliers start: 79 outliers final: 58 residues processed: 401 average time/residue: 0.2968 time to fit residues: 188.0434 Evaluate side-chains 376 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 316 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 564 HIS Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 20853 Z= 0.439 Angle : 0.785 15.463 28353 Z= 0.390 Chirality : 0.048 0.219 3516 Planarity : 0.004 0.044 3465 Dihedral : 6.586 45.920 5019 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.38 % Allowed : 15.27 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.45 (0.17), residues: 2364 helix: 0.77 (0.28), residues: 354 sheet: 0.39 (0.19), residues: 693 loop : -0.99 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 479 HIS 0.006 0.001 HIS G 374 PHE 0.021 0.003 PHE H 47 TYR 0.022 0.002 TYR E 49 ARG 0.006 0.001 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 324 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 PHE cc_start: 0.8276 (m-80) cc_final: 0.7809 (m-80) REVERT: B 530 MET cc_start: 0.7531 (mmm) cc_final: 0.6680 (mmm) REVERT: L 42 GLN cc_start: 0.7668 (mp10) cc_final: 0.7265 (mp10) REVERT: L 77 ASP cc_start: 0.7849 (t0) cc_final: 0.7603 (t0) REVERT: C 420 ILE cc_start: 0.9104 (mp) cc_final: 0.8820 (mt) REVERT: D 530 MET cc_start: 0.7387 (mmm) cc_final: 0.6512 (mmm) REVERT: D 595 ILE cc_start: 0.9597 (tp) cc_final: 0.9312 (tp) REVERT: D 647 GLU cc_start: 0.8195 (tp30) cc_final: 0.7942 (tp30) REVERT: E 4 MET cc_start: 0.7382 (mmm) cc_final: 0.6716 (tpp) REVERT: E 42 GLN cc_start: 0.7877 (mp10) cc_final: 0.7596 (mp10) REVERT: E 82 ASP cc_start: 0.6598 (p0) cc_final: 0.6379 (p0) REVERT: F 6 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.5817 (mt-10) REVERT: F 31 ASP cc_start: 0.8588 (p0) cc_final: 0.8277 (p0) REVERT: F 81 MET cc_start: 0.7862 (ttm) cc_final: 0.7577 (mtm) REVERT: G 74 CYS cc_start: 0.7951 (m) cc_final: 0.7449 (m) REVERT: G 104 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8015 (ttm) REVERT: G 479 TRP cc_start: 0.8539 (m-10) cc_final: 0.8125 (m-90) REVERT: I 530 MET cc_start: 0.7303 (mmm) cc_final: 0.6458 (mmm) REVERT: I 629 MET cc_start: 0.8415 (mmm) cc_final: 0.7804 (mmm) REVERT: J 42 GLN cc_start: 0.7626 (mp10) cc_final: 0.7217 (mp10) REVERT: J 82 ASP cc_start: 0.6310 (p0) cc_final: 0.5854 (p0) outliers start: 91 outliers final: 62 residues processed: 375 average time/residue: 0.2994 time to fit residues: 176.5828 Evaluate side-chains 366 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 302 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 564 HIS Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20853 Z= 0.324 Angle : 0.724 17.022 28353 Z= 0.358 Chirality : 0.046 0.285 3516 Planarity : 0.004 0.046 3465 Dihedral : 6.451 51.406 5019 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.81 % Allowed : 16.18 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.54 (0.17), residues: 2364 helix: 0.85 (0.28), residues: 351 sheet: 0.26 (0.19), residues: 711 loop : -1.07 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 36 HIS 0.004 0.001 HIS G 374 PHE 0.024 0.002 PHE H 47 TYR 0.019 0.002 TYR H 59 ARG 0.004 0.001 ARG I 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 317 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 468 PHE cc_start: 0.8251 (m-80) cc_final: 0.7800 (m-80) REVERT: B 530 MET cc_start: 0.7439 (mmm) cc_final: 0.6710 (mmm) REVERT: L 4 MET cc_start: 0.7487 (mmm) cc_final: 0.7158 (tpp) REVERT: L 42 GLN cc_start: 0.7662 (mp10) cc_final: 0.7284 (mp-120) REVERT: L 77 ASP cc_start: 0.7798 (t0) cc_final: 0.7547 (t0) REVERT: C 420 ILE cc_start: 0.9091 (mp) cc_final: 0.8805 (mt) REVERT: D 595 ILE cc_start: 0.9558 (tp) cc_final: 0.9234 (tp) REVERT: D 602 ILE cc_start: 0.9628 (tp) cc_final: 0.9313 (tp) REVERT: E 4 MET cc_start: 0.7360 (mmm) cc_final: 0.6746 (tpp) REVERT: E 42 GLN cc_start: 0.7751 (mp10) cc_final: 0.7510 (mp10) REVERT: E 82 ASP cc_start: 0.6558 (p0) cc_final: 0.6290 (p0) REVERT: F 31 ASP cc_start: 0.8573 (p0) cc_final: 0.8259 (p0) REVERT: G 74 CYS cc_start: 0.7851 (m) cc_final: 0.7393 (m) REVERT: G 479 TRP cc_start: 0.8391 (m-10) cc_final: 0.7893 (m-90) REVERT: I 530 MET cc_start: 0.7236 (mmm) cc_final: 0.6453 (mmm) REVERT: I 629 MET cc_start: 0.8359 (mmm) cc_final: 0.7897 (mmm) REVERT: J 4 MET cc_start: 0.7490 (mmm) cc_final: 0.7055 (tpp) REVERT: J 42 GLN cc_start: 0.7512 (mp10) cc_final: 0.7148 (mp10) REVERT: J 63 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8475 (mmtt) REVERT: J 82 ASP cc_start: 0.6499 (p0) cc_final: 0.6035 (p0) outliers start: 79 outliers final: 61 residues processed: 362 average time/residue: 0.3042 time to fit residues: 172.4210 Evaluate side-chains 361 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 299 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.0980 chunk 128 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20853 Z= 0.261 Angle : 0.690 15.686 28353 Z= 0.341 Chirality : 0.045 0.242 3516 Planarity : 0.004 0.041 3465 Dihedral : 6.319 51.800 5019 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.00 % Allowed : 16.38 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.59 (0.17), residues: 2364 helix: 0.85 (0.28), residues: 354 sheet: 0.19 (0.19), residues: 729 loop : -1.10 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 36 HIS 0.003 0.001 HIS G 374 PHE 0.021 0.002 PHE H 47 TYR 0.019 0.002 TYR K 58 ARG 0.004 0.000 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 321 time to evaluate : 2.261 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: A 104 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8443 (ttm) REVERT: A 180 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 439 ILE cc_start: 0.8965 (pt) cc_final: 0.8655 (tp) REVERT: A 468 PHE cc_start: 0.8207 (m-80) cc_final: 0.7762 (m-10) REVERT: A 475 MET cc_start: 0.8180 (mmp) cc_final: 0.7861 (mmp) REVERT: A 479 TRP cc_start: 0.8240 (m-10) cc_final: 0.7802 (m-90) REVERT: B 530 MET cc_start: 0.7410 (mmm) cc_final: 0.6676 (mmm) REVERT: L 42 GLN cc_start: 0.7537 (mp10) cc_final: 0.7221 (mp-120) REVERT: L 75 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8485 (tp) REVERT: L 77 ASP cc_start: 0.7788 (t0) cc_final: 0.7471 (t0) REVERT: C 420 ILE cc_start: 0.9115 (mp) cc_final: 0.8840 (mt) REVERT: D 595 ILE cc_start: 0.9481 (tp) cc_final: 0.9264 (tp) REVERT: D 602 ILE cc_start: 0.9628 (tp) cc_final: 0.9340 (tp) REVERT: D 647 GLU cc_start: 0.8074 (tp30) cc_final: 0.7828 (tp30) REVERT: E 4 MET cc_start: 0.7571 (mmm) cc_final: 0.7097 (tpp) REVERT: E 82 ASP cc_start: 0.6588 (p0) cc_final: 0.6338 (p0) REVERT: F 6 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.5918 (mp0) REVERT: F 31 ASP cc_start: 0.8577 (p0) cc_final: 0.8147 (p0) REVERT: G 74 CYS cc_start: 0.7976 (m) cc_final: 0.7558 (m) REVERT: G 479 TRP cc_start: 0.8332 (m-10) cc_final: 0.7797 (m-90) REVERT: I 530 MET cc_start: 0.7102 (mmm) cc_final: 0.5880 (mmm) REVERT: I 629 MET cc_start: 0.8322 (mmm) cc_final: 0.7856 (mmm) REVERT: J 42 GLN cc_start: 0.7459 (mp10) cc_final: 0.7220 (mp10) REVERT: J 63 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8389 (mmtt) REVERT: J 82 ASP cc_start: 0.6523 (p0) cc_final: 0.6050 (p0) outliers start: 83 outliers final: 59 residues processed: 366 average time/residue: 0.3019 time to fit residues: 173.7345 Evaluate side-chains 357 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 294 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 608 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20853 Z= 0.189 Angle : 0.673 16.192 28353 Z= 0.332 Chirality : 0.045 0.215 3516 Planarity : 0.004 0.042 3465 Dihedral : 5.991 58.414 5019 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.75 % Allowed : 18.11 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.57 (0.17), residues: 2364 helix: 0.74 (0.27), residues: 360 sheet: 0.27 (0.19), residues: 720 loop : -1.09 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP H 36 HIS 0.006 0.001 HIS D 641 PHE 0.024 0.002 PHE H 47 TYR 0.025 0.001 TYR F 59 ARG 0.003 0.000 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 2.223 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: A 104 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8414 (ttm) REVERT: A 468 PHE cc_start: 0.7995 (m-80) cc_final: 0.7610 (m-10) REVERT: A 475 MET cc_start: 0.8180 (mmp) cc_final: 0.7799 (mmp) REVERT: A 479 TRP cc_start: 0.8165 (m-10) cc_final: 0.7686 (m-90) REVERT: B 530 MET cc_start: 0.7285 (mmm) cc_final: 0.6583 (mmm) REVERT: B 586 TYR cc_start: 0.9134 (t80) cc_final: 0.8916 (t80) REVERT: L 42 GLN cc_start: 0.7380 (mp10) cc_final: 0.7159 (mp10) REVERT: L 77 ASP cc_start: 0.7792 (t0) cc_final: 0.7510 (t0) REVERT: H 13 GLN cc_start: 0.8396 (pp30) cc_final: 0.8177 (pp30) REVERT: C 74 CYS cc_start: 0.7801 (m) cc_final: 0.7597 (m) REVERT: C 420 ILE cc_start: 0.9079 (mp) cc_final: 0.8833 (mt) REVERT: C 479 TRP cc_start: 0.8317 (m-10) cc_final: 0.8025 (m-90) REVERT: D 584 GLU cc_start: 0.8946 (tp30) cc_final: 0.8076 (tm-30) REVERT: D 595 ILE cc_start: 0.9468 (tp) cc_final: 0.9189 (tp) REVERT: D 602 ILE cc_start: 0.9606 (tp) cc_final: 0.9357 (tp) REVERT: E 4 MET cc_start: 0.7538 (mmm) cc_final: 0.7272 (tpp) REVERT: E 82 ASP cc_start: 0.6618 (p0) cc_final: 0.6317 (p0) REVERT: F 6 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.5849 (mp0) REVERT: F 31 ASP cc_start: 0.8598 (p0) cc_final: 0.8127 (p0) REVERT: F 32 TYR cc_start: 0.8521 (m-80) cc_final: 0.8086 (m-10) REVERT: G 74 CYS cc_start: 0.7958 (m) cc_final: 0.7572 (m) REVERT: G 479 TRP cc_start: 0.8271 (m-10) cc_final: 0.7751 (m-90) REVERT: I 530 MET cc_start: 0.6965 (mmm) cc_final: 0.5854 (mmm) REVERT: I 602 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9237 (tp) REVERT: I 629 MET cc_start: 0.8303 (mmm) cc_final: 0.7876 (mmm) REVERT: J 63 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8463 (mmtt) REVERT: J 82 ASP cc_start: 0.6502 (p0) cc_final: 0.6046 (p0) REVERT: K 6 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5235 (mp0) REVERT: K 31 ASP cc_start: 0.8144 (p0) cc_final: 0.7848 (p0) outliers start: 57 outliers final: 47 residues processed: 357 average time/residue: 0.3027 time to fit residues: 168.9040 Evaluate side-chains 357 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 662 GLU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20853 Z= 0.327 Angle : 0.711 15.969 28353 Z= 0.352 Chirality : 0.046 0.237 3516 Planarity : 0.004 0.039 3465 Dihedral : 6.237 55.368 5019 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.28 % Allowed : 17.68 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.66 (0.17), residues: 2364 helix: 0.70 (0.28), residues: 360 sheet: 0.23 (0.19), residues: 732 loop : -1.19 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 36 HIS 0.005 0.001 HIS G 374 PHE 0.029 0.002 PHE H 47 TYR 0.051 0.002 TYR K 32 ARG 0.006 0.001 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 299 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8501 (ttm) REVERT: A 180 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7617 (t0) REVERT: A 423 ILE cc_start: 0.9431 (mt) cc_final: 0.9224 (mt) REVERT: A 439 ILE cc_start: 0.8891 (pt) cc_final: 0.8614 (tp) REVERT: A 468 PHE cc_start: 0.8201 (m-80) cc_final: 0.7777 (m-10) REVERT: A 479 TRP cc_start: 0.8252 (m-10) cc_final: 0.7818 (m-90) REVERT: B 530 MET cc_start: 0.7522 (mmm) cc_final: 0.6821 (mmm) REVERT: L 42 GLN cc_start: 0.7392 (mp10) cc_final: 0.7116 (mp-120) REVERT: L 77 ASP cc_start: 0.7890 (t0) cc_final: 0.7632 (t0) REVERT: C 74 CYS cc_start: 0.7916 (m) cc_final: 0.7694 (m) REVERT: C 154 MET cc_start: 0.8449 (mmm) cc_final: 0.8075 (mmp) REVERT: C 420 ILE cc_start: 0.9015 (mp) cc_final: 0.8749 (mt) REVERT: D 584 GLU cc_start: 0.8924 (tp30) cc_final: 0.8100 (tm-30) REVERT: D 595 ILE cc_start: 0.9500 (tp) cc_final: 0.9247 (tp) REVERT: D 602 ILE cc_start: 0.9648 (tp) cc_final: 0.9407 (tp) REVERT: E 4 MET cc_start: 0.7807 (mmm) cc_final: 0.7501 (tpp) REVERT: E 82 ASP cc_start: 0.6599 (p0) cc_final: 0.6328 (p0) REVERT: F 31 ASP cc_start: 0.8610 (p0) cc_final: 0.8140 (p0) REVERT: F 81 MET cc_start: 0.7438 (ttm) cc_final: 0.7216 (mtt) REVERT: G 74 CYS cc_start: 0.7935 (m) cc_final: 0.7600 (m) REVERT: G 104 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8314 (ttm) REVERT: G 479 TRP cc_start: 0.8387 (m-10) cc_final: 0.7952 (m-90) REVERT: I 530 MET cc_start: 0.7217 (mmm) cc_final: 0.6093 (mmm) REVERT: I 602 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9286 (tp) REVERT: I 629 MET cc_start: 0.8384 (mmm) cc_final: 0.7980 (mmm) REVERT: I 655 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8679 (mmtt) REVERT: J 63 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8458 (mmtt) REVERT: J 82 ASP cc_start: 0.6577 (p0) cc_final: 0.6085 (p0) outliers start: 68 outliers final: 57 residues processed: 337 average time/residue: 0.2895 time to fit residues: 154.2551 Evaluate side-chains 352 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 291 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 662 GLU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 236 optimal weight: 0.2980 chunk 217 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 330 HIS A 425 ASN A 478 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20853 Z= 0.186 Angle : 0.686 15.953 28353 Z= 0.338 Chirality : 0.045 0.344 3516 Planarity : 0.004 0.046 3465 Dihedral : 5.788 46.000 5019 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.89 % Allowed : 18.40 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.62 (0.17), residues: 2364 helix: 0.65 (0.27), residues: 360 sheet: 0.27 (0.19), residues: 717 loop : -1.13 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP K 36 HIS 0.006 0.001 HIS B 641 PHE 0.033 0.002 PHE H 47 TYR 0.036 0.001 TYR K 32 ARG 0.005 0.000 ARG B 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 322 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8438 (ttm) REVERT: A 180 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7683 (t0) REVERT: A 439 ILE cc_start: 0.8798 (pt) cc_final: 0.8512 (tp) REVERT: A 468 PHE cc_start: 0.8078 (m-80) cc_final: 0.7631 (m-10) REVERT: A 479 TRP cc_start: 0.8061 (m-10) cc_final: 0.7662 (m-90) REVERT: B 530 MET cc_start: 0.7258 (mmm) cc_final: 0.6433 (mmm) REVERT: B 586 TYR cc_start: 0.9127 (t80) cc_final: 0.8927 (t80) REVERT: L 77 ASP cc_start: 0.7841 (t0) cc_final: 0.7568 (t0) REVERT: H 13 GLN cc_start: 0.8412 (pp30) cc_final: 0.8200 (pp30) REVERT: C 74 CYS cc_start: 0.7921 (m) cc_final: 0.7611 (m) REVERT: C 154 MET cc_start: 0.8366 (mmm) cc_final: 0.7699 (mmp) REVERT: C 420 ILE cc_start: 0.8980 (mp) cc_final: 0.8723 (mt) REVERT: D 584 GLU cc_start: 0.8891 (tp30) cc_final: 0.8078 (tm-30) REVERT: D 595 ILE cc_start: 0.9469 (tp) cc_final: 0.9222 (tp) REVERT: D 602 ILE cc_start: 0.9627 (tp) cc_final: 0.9394 (tp) REVERT: D 629 MET cc_start: 0.8434 (mmm) cc_final: 0.7328 (mmm) REVERT: E 4 MET cc_start: 0.7692 (mmm) cc_final: 0.7454 (tpp) REVERT: E 82 ASP cc_start: 0.6378 (p0) cc_final: 0.6085 (p0) REVERT: F 6 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: F 31 ASP cc_start: 0.8566 (p0) cc_final: 0.8072 (p0) REVERT: F 32 TYR cc_start: 0.8445 (m-80) cc_final: 0.8108 (m-10) REVERT: F 81 MET cc_start: 0.7515 (ttm) cc_final: 0.7241 (mtt) REVERT: G 74 CYS cc_start: 0.7932 (m) cc_final: 0.7536 (m) REVERT: G 479 TRP cc_start: 0.8238 (m-10) cc_final: 0.7731 (m-90) REVERT: I 530 MET cc_start: 0.7060 (mmm) cc_final: 0.5829 (mmm) REVERT: I 595 ILE cc_start: 0.9479 (tp) cc_final: 0.8893 (tp) REVERT: I 629 MET cc_start: 0.8315 (mmm) cc_final: 0.7947 (mmm) REVERT: I 647 GLU cc_start: 0.8043 (tp30) cc_final: 0.7497 (tp30) REVERT: J 63 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8514 (mmtt) REVERT: J 82 ASP cc_start: 0.6486 (p0) cc_final: 0.6014 (p0) REVERT: K 6 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5126 (mp0) outliers start: 60 outliers final: 49 residues processed: 354 average time/residue: 0.2975 time to fit residues: 165.5116 Evaluate side-chains 355 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 302 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 402 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 648 VAL Chi-restraints excluded: chain I residue 662 GLU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071392 restraints weight = 52949.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074093 restraints weight = 30390.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075931 restraints weight = 21269.530| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20853 Z= 0.206 Angle : 0.683 15.679 28353 Z= 0.337 Chirality : 0.045 0.225 3516 Planarity : 0.004 0.046 3465 Dihedral : 5.608 45.798 5019 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.79 % Allowed : 18.64 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.60 (0.17), residues: 2364 helix: 0.69 (0.27), residues: 360 sheet: 0.28 (0.19), residues: 717 loop : -1.12 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP K 36 HIS 0.003 0.001 HIS A 374 PHE 0.033 0.002 PHE H 47 TYR 0.027 0.001 TYR H 32 ARG 0.004 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.49 seconds wall clock time: 76 minutes 47.44 seconds (4607.44 seconds total)