Starting phenix.real_space_refine on Tue Feb 20 02:28:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg6_23312/02_2024/7lg6_23312.pdb" } resolution = 3.28 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= 0.010 sd= 0.097 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 147 5.16 5 C 16638 2.51 5 N 4443 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "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 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "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 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 30": "OD1" <-> "OD2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26550 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "E" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "O" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "Q" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3552 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "P" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 965 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 116} Chain: "R" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1160 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" 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: "7" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "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 Time building chain proxies: 13.48, per 1000 atoms: 0.51 Number of scatterers: 26550 At special positions: 0 Unit cell: (159.65, 150.38, 157.59, 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 147 16.00 O 5322 8.00 N 4443 7.00 C 16638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS G 561 " distance=2.01 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS I 561 " distance=2.01 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN W 4 " - " MAN W 5 " " MAN X 4 " - " MAN X 5 " " MAN k 4 " - " MAN k 5 " " MAN l 4 " - " MAN l 5 " " MAN y 4 " - " MAN y 5 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA k 3 " - " MAN k 6 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA y 3 " - " MAN y 6 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 7 1 " - " FUC 7 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG f 1 " - " FUC f 2 " " NAG t 1 " - " FUC t 2 " NAG-ASN " NAG 0 1 " - " ASN F 295 " " NAG 1 1 " - " ASN F 332 " " NAG 2 1 " - " ASN F 386 " " NAG 3 1 " - " ASN F 392 " " NAG 4 1 " - " ASN F 448 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 363 " " NAG 7 1 " - " ASN I 611 " " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 137 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 197 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 137 " " NAG F 601 " - " ASN F 197 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 137 " " NAG G 701 " - " ASN G 618 " " NAG G 702 " - " ASN G 637 " " NAG I 701 " - " ASN I 618 " " NAG I 702 " - " ASN I 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 160 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 295 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 448 " " NAG d 1 " - " ASN A 301 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN B 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 156 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 276 " " NAG m 1 " - " ASN E 295 " " NAG n 1 " - " ASN E 332 " " NAG o 1 " - " ASN E 386 " " NAG p 1 " - " ASN E 392 " " NAG q 1 " - " ASN E 448 " " NAG r 1 " - " ASN E 301 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN G 611 " " NAG u 1 " - " ASN F 88 " " NAG v 1 " - " ASN F 156 " " NAG w 1 " - " ASN F 160 " " NAG x 1 " - " ASN F 234 " " NAG y 1 " - " ASN F 262 " " NAG z 1 " - " ASN F 276 " Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 4.3 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 57 sheets defined 18.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.026A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.026A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.952A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 553 Processing helix chain 'G' and resid 561 through 568 removed outlier: 4.050A pdb=" N LEU G 565 " --> pdb=" O CYS G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 4.381A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 633 Processing helix chain 'G' and resid 635 through 637 No H-bonds generated for 'chain 'G' and resid 635 through 637' Processing helix chain 'G' and resid 638 through 658 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.027A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 336 through 354 removed outlier: 5.865A pdb=" N LEU F 342 " --> pdb=" O TRP F 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.953A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.952A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 553 Processing helix chain 'I' and resid 561 through 568 removed outlier: 4.049A pdb=" N LEU I 565 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.382A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 633 Processing helix chain 'I' and resid 635 through 637 No H-bonds generated for 'chain 'I' and resid 635 through 637' Processing helix chain 'I' and resid 638 through 658 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 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 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 82B" --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP C 35 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 50 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.021A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 56 through 59 removed outlier: 6.789A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 5.470A pdb=" N ILE Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 82B" --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP J 35 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.339A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.020A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AE6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE7, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AE8, first strand: chain 'F' and resid 201 through 203 Processing sheet with id=AE9, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.897A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.606A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'P' and resid 56 through 59 removed outlier: 6.788A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE P 34 " --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'R' and resid 10 through 13 removed outlier: 5.471A pdb=" N ILE R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR R 49 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.371A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 5.800A pdb=" N GLU K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 82B" --> pdb=" O GLU K 16 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.444A pdb=" N TRP K 35 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 1047 hydrogen bonds defined for protein. 2691 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: 11.57 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5481 1.32 - 1.47: 9946 1.47 - 1.61: 11456 1.61 - 1.76: 54 1.76 - 1.91: 168 Bond restraints: 27105 Sorted by residual: bond pdb=" NE ARG D 3 " pdb=" CZ ARG D 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG M 3 " pdb=" CZ ARG M 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE ARG N 3 " pdb=" CZ ARG N 3 " ideal model delta sigma weight residual 1.326 1.397 -0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" CB ASP R 91 " pdb=" CG ASP R 91 " ideal model delta sigma weight residual 1.516 1.367 0.149 2.50e-02 1.60e+03 3.53e+01 bond pdb=" CB ASP Q 91 " pdb=" CG ASP Q 91 " ideal model delta sigma weight residual 1.516 1.368 0.148 2.50e-02 1.60e+03 3.52e+01 ... (remaining 27100 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.86: 1336 106.86 - 114.65: 15751 114.65 - 122.44: 15573 122.44 - 130.23: 3997 130.23 - 138.02: 165 Bond angle restraints: 36822 Sorted by residual: angle pdb=" C TRP P 72C" pdb=" N ARG P 72D" pdb=" CA ARG P 72D" ideal model delta sigma weight residual 120.28 134.76 -14.48 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP O 72C" pdb=" N ARG O 72D" pdb=" CA ARG O 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" C TRP H 72C" pdb=" N ARG H 72D" pdb=" CA ARG H 72D" ideal model delta sigma weight residual 120.28 134.75 -14.47 1.34e+00 5.57e-01 1.17e+02 angle pdb=" N SER G 613 " pdb=" CA SER G 613 " pdb=" C SER G 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 angle pdb=" N SER I 613 " pdb=" CA SER I 613 " pdb=" C SER I 613 " ideal model delta sigma weight residual 114.62 102.94 11.68 1.14e+00 7.69e-01 1.05e+02 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 17288 21.21 - 42.41: 403 42.41 - 63.62: 105 63.62 - 84.83: 84 84.83 - 106.03: 39 Dihedral angle restraints: 17919 sinusoidal: 8859 harmonic: 9060 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.63 -43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 136.62 -43.62 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 17916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2885 0.101 - 0.203: 1042 0.203 - 0.304: 340 0.304 - 0.406: 159 0.406 - 0.507: 77 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 ... (remaining 4500 not shown) Planarity restraints: 4563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.98e+01 pdb=" CG ASN E 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG E 603 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 133 " 0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN F 133 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN F 133 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN F 133 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 603 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " -0.068 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN A 133 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.084 2.00e-02 2.50e+03 ... (remaining 4560 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 11239 2.92 - 3.41: 22833 3.41 - 3.91: 44050 3.91 - 4.40: 50557 4.40 - 4.90: 81424 Nonbonded interactions: 210103 Sorted by model distance: nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.421 2.520 nonbonded pdb=" NZ LYS F 46 " pdb=" OD2 ASP I 632 " model vdw 2.421 2.520 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP G 632 " model vdw 2.421 2.520 nonbonded pdb=" N GLY F 431 " pdb=" O GLY F 431 " model vdw 2.423 2.496 nonbonded pdb=" N GLY A 431 " pdb=" O GLY A 431 " model vdw 2.423 2.496 ... (remaining 210098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 1) selection = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '3' and resid 1) selection = (chain '4' and resid 1) selection = (chain '5' and resid 1) selection = (chain '6' and resid 1) selection = (chain '7' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'u' and resid 1) selection = (chain 'w' and resid 1) selection = (chain 'x' and resid 1) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'h' selection = chain 'v' } ncs_group { reference = chain 'W' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain 'X' selection = chain 'l' selection = chain 'z' } 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 individual isotropic 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.690 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 70.810 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.023 0.149 27105 Z= 1.463 Angle : 1.794 14.479 36822 Z= 1.158 Chirality : 0.140 0.507 4503 Planarity : 0.009 0.038 4503 Dihedral : 12.385 106.035 11949 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.57 % Favored : 95.75 % Rotamer: Outliers : 0.33 % Allowed : 0.76 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.39 (0.15), residues: 3105 helix: -0.80 (0.23), residues: 477 sheet: 0.93 (0.16), residues: 1116 loop : 0.24 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.011 TRP F 479 HIS 0.015 0.003 HIS E 374 PHE 0.034 0.006 PHE N 98 TYR 0.048 0.009 TYR F 177 ARG 0.007 0.001 ARG F 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 637 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mtp85) REVERT: B 632 ASP cc_start: 0.8843 (t70) cc_final: 0.8601 (t0) REVERT: G 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8591 (t0) REVERT: I 632 ASP cc_start: 0.8851 (t70) cc_final: 0.8579 (t0) outliers start: 9 outliers final: 3 residues processed: 646 average time/residue: 0.4706 time to fit residues: 452.5822 Evaluate side-chains 355 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 351 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain P residue 72 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 280 optimal weight: 0.6980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 10 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 39 GLN E 195 ASN O 10 GLN Q 37 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN F 195 ASN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27105 Z= 0.212 Angle : 0.728 9.323 36822 Z= 0.381 Chirality : 0.047 0.315 4503 Planarity : 0.004 0.040 4503 Dihedral : 9.720 84.068 6182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.99 % Favored : 95.33 % Rotamer: Outliers : 2.18 % Allowed : 6.91 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.49 (0.15), residues: 3105 helix: 0.58 (0.26), residues: 459 sheet: 1.09 (0.15), residues: 1119 loop : -0.28 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 96 HIS 0.006 0.001 HIS M 89 PHE 0.015 0.002 PHE E 383 TYR 0.021 0.002 TYR F 318 ARG 0.006 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 421 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7566 (tpt) cc_final: 0.7208 (mmm) REVERT: H 46 GLU cc_start: 0.6952 (tp30) cc_final: 0.6537 (tt0) REVERT: B 632 ASP cc_start: 0.8629 (t70) cc_final: 0.8269 (t0) REVERT: D 90 GLN cc_start: 0.7917 (tp40) cc_final: 0.7717 (tp40) REVERT: C 13 ARG cc_start: 0.6722 (mtt-85) cc_final: 0.6441 (mpp-170) REVERT: E 133 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: I 632 ASP cc_start: 0.8660 (t70) cc_final: 0.8420 (t0) outliers start: 60 outliers final: 32 residues processed: 452 average time/residue: 0.3992 time to fit residues: 280.4752 Evaluate side-chains 369 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 336 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 72 ARG Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 637 ASN Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 0.4980 chunk 278 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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** D 92 ASN C 77 GLN E 195 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN J 77 GLN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27105 Z= 0.257 Angle : 0.645 7.040 36822 Z= 0.336 Chirality : 0.046 0.309 4503 Planarity : 0.004 0.042 4503 Dihedral : 8.303 76.559 6182 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.22 % Favored : 94.30 % Rotamer: Outliers : 2.22 % Allowed : 8.44 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.34 (0.15), residues: 3105 helix: 0.65 (0.26), residues: 459 sheet: 1.03 (0.15), residues: 1107 loop : -0.47 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 96 HIS 0.007 0.001 HIS F 105 PHE 0.021 0.002 PHE K 78 TYR 0.017 0.002 TYR Q 86 ARG 0.006 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 377 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 93 TYR cc_start: 0.6531 (m-10) cc_final: 0.6263 (m-10) REVERT: B 632 ASP cc_start: 0.8746 (t70) cc_final: 0.8386 (t0) REVERT: C 13 ARG cc_start: 0.6768 (mtt-85) cc_final: 0.6264 (mpp-170) REVERT: C 37 ILE cc_start: 0.8332 (mm) cc_final: 0.7967 (tt) REVERT: J 82 ASN cc_start: 0.6453 (p0) cc_final: 0.6252 (p0) REVERT: I 632 ASP cc_start: 0.8715 (t70) cc_final: 0.8420 (t0) outliers start: 61 outliers final: 45 residues processed: 409 average time/residue: 0.3809 time to fit residues: 243.0435 Evaluate side-chains 383 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 338 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 188 optimal weight: 0.0020 chunk 282 optimal weight: 0.0030 chunk 298 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN Q 89 GLN M 92 ASN F 195 ASN R 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27105 Z= 0.153 Angle : 0.589 8.506 36822 Z= 0.300 Chirality : 0.044 0.307 4503 Planarity : 0.004 0.045 4503 Dihedral : 7.239 68.615 6168 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.86 % Favored : 94.75 % Rotamer: Outliers : 1.97 % Allowed : 9.93 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.35 (0.15), residues: 3105 helix: 0.73 (0.26), residues: 480 sheet: 1.08 (0.16), residues: 1080 loop : -0.52 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 96 HIS 0.005 0.001 HIS E 72 PHE 0.029 0.001 PHE C 78 TYR 0.014 0.001 TYR L 87 ARG 0.006 0.000 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 381 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6927 (tp30) cc_final: 0.6365 (tt0) REVERT: B 632 ASP cc_start: 0.8672 (t70) cc_final: 0.8353 (t0) REVERT: D 79 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7583 (tt0) REVERT: D 81 GLU cc_start: 0.7520 (pm20) cc_final: 0.7015 (pm20) REVERT: C 13 ARG cc_start: 0.6441 (mtt-85) cc_final: 0.6189 (mmt90) REVERT: E 150 MET cc_start: 0.8425 (mmm) cc_final: 0.7803 (mmt) REVERT: J 82 ASN cc_start: 0.6454 (p0) cc_final: 0.6168 (p0) REVERT: F 133 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: F 416 LEU cc_start: 0.8620 (mt) cc_final: 0.8420 (mt) REVERT: R 86 TYR cc_start: 0.7260 (m-80) cc_final: 0.7052 (m-80) REVERT: I 632 ASP cc_start: 0.8604 (t70) cc_final: 0.8307 (t0) outliers start: 54 outliers final: 37 residues processed: 409 average time/residue: 0.3976 time to fit residues: 253.0354 Evaluate side-chains 370 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 332 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 553 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN C 77 GLN E 195 ASN M 92 ASN N 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27105 Z= 0.288 Angle : 0.632 10.481 36822 Z= 0.319 Chirality : 0.046 0.308 4503 Planarity : 0.004 0.052 4503 Dihedral : 6.953 65.414 6168 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.64 % Favored : 93.98 % Rotamer: Outliers : 2.47 % Allowed : 10.23 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.20 (0.15), residues: 3105 helix: 0.63 (0.26), residues: 477 sheet: 1.07 (0.16), residues: 1086 loop : -0.71 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 96 HIS 0.007 0.001 HIS F 105 PHE 0.019 0.002 PHE K 78 TYR 0.017 0.001 TYR J 50 ARG 0.007 0.000 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 343 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8878 (t70) cc_final: 0.8521 (t0) REVERT: C 13 ARG cc_start: 0.6718 (mtt-85) cc_final: 0.6433 (mmt90) REVERT: E 150 MET cc_start: 0.8461 (mmm) cc_final: 0.7841 (mmt) REVERT: M 81 GLU cc_start: 0.7927 (pm20) cc_final: 0.7602 (pm20) REVERT: J 4 LEU cc_start: 0.8318 (mm) cc_final: 0.8055 (mp) REVERT: J 82 ASN cc_start: 0.6635 (p0) cc_final: 0.6353 (p0) REVERT: F 133 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: F 150 MET cc_start: 0.8259 (mmm) cc_final: 0.7763 (mmm) REVERT: F 416 LEU cc_start: 0.8761 (mt) cc_final: 0.8550 (mt) REVERT: I 632 ASP cc_start: 0.8712 (t70) cc_final: 0.8442 (t0) REVERT: K 45 LEU cc_start: 0.8040 (mt) cc_final: 0.7812 (mt) outliers start: 68 outliers final: 57 residues processed: 379 average time/residue: 0.3811 time to fit residues: 227.0273 Evaluate side-chains 378 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 553 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 298 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 chunk 156 optimal weight: 2.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN G 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27105 Z= 0.272 Angle : 0.625 10.955 36822 Z= 0.314 Chirality : 0.045 0.304 4503 Planarity : 0.004 0.046 4503 Dihedral : 6.655 59.967 6168 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.48 % Favored : 94.20 % Rotamer: Outliers : 2.62 % Allowed : 10.59 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.10 (0.15), residues: 3105 helix: 0.62 (0.26), residues: 477 sheet: 1.00 (0.16), residues: 1110 loop : -0.83 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 96 HIS 0.006 0.001 HIS F 105 PHE 0.019 0.002 PHE H 63 TYR 0.015 0.001 TYR J 50 ARG 0.008 0.000 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 343 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: B 632 ASP cc_start: 0.8901 (t70) cc_final: 0.8516 (t0) REVERT: C 13 ARG cc_start: 0.6779 (mtt-85) cc_final: 0.6505 (mmt90) REVERT: E 133 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7984 (m-40) REVERT: E 150 MET cc_start: 0.8368 (mmm) cc_final: 0.7766 (mmt) REVERT: J 82 ASN cc_start: 0.6698 (p0) cc_final: 0.6455 (p0) REVERT: F 133 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: F 150 MET cc_start: 0.8234 (mmm) cc_final: 0.7774 (mmm) REVERT: F 416 LEU cc_start: 0.8788 (mt) cc_final: 0.8587 (mt) REVERT: I 632 ASP cc_start: 0.8764 (t70) cc_final: 0.8469 (t0) REVERT: N 39 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7858 (ptpt) outliers start: 72 outliers final: 59 residues processed: 383 average time/residue: 0.3857 time to fit residues: 231.6574 Evaluate side-chains 387 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 325 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 553 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27105 Z= 0.290 Angle : 0.632 9.720 36822 Z= 0.317 Chirality : 0.045 0.303 4503 Planarity : 0.004 0.047 4503 Dihedral : 6.447 53.342 6168 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 2.62 % Allowed : 11.21 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.03 (0.15), residues: 3105 helix: 0.56 (0.25), residues: 477 sheet: 1.01 (0.16), residues: 1107 loop : -0.92 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 96 HIS 0.006 0.001 HIS F 105 PHE 0.016 0.002 PHE H 63 TYR 0.015 0.001 TYR J 50 ARG 0.008 0.000 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 334 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7694 (m-40) REVERT: H 77 THR cc_start: 0.8917 (p) cc_final: 0.8672 (m) REVERT: B 632 ASP cc_start: 0.8932 (t70) cc_final: 0.8550 (t0) REVERT: C 13 ARG cc_start: 0.6859 (mtt-85) cc_final: 0.6554 (mmt90) REVERT: E 150 MET cc_start: 0.8349 (mmm) cc_final: 0.7799 (mmt) REVERT: M 4 MET cc_start: 0.6266 (pmm) cc_final: 0.5857 (mtm) REVERT: J 82 ASN cc_start: 0.6760 (p0) cc_final: 0.6509 (p0) REVERT: F 133 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7768 (m-40) REVERT: F 150 MET cc_start: 0.8209 (mmm) cc_final: 0.7772 (mmm) REVERT: I 632 ASP cc_start: 0.8800 (t70) cc_final: 0.8486 (t0) REVERT: N 39 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7922 (ptpt) REVERT: K 52 ASN cc_start: 0.8658 (t0) cc_final: 0.8285 (t0) outliers start: 72 outliers final: 62 residues processed: 382 average time/residue: 0.3901 time to fit residues: 232.7905 Evaluate side-chains 385 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 321 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 562 GLN Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 553 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 189 optimal weight: 0.5980 chunk 202 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN G 563 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27105 Z= 0.379 Angle : 0.673 9.331 36822 Z= 0.337 Chirality : 0.046 0.304 4503 Planarity : 0.004 0.047 4503 Dihedral : 6.493 59.984 6168 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.47 % Favored : 93.14 % Rotamer: Outliers : 2.84 % Allowed : 11.14 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.13 (0.15), residues: 3105 helix: 0.40 (0.25), residues: 477 sheet: 0.93 (0.16), residues: 1107 loop : -1.04 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 96 HIS 0.007 0.001 HIS E 105 PHE 0.016 0.002 PHE H 63 TYR 0.017 0.002 TYR J 50 ARG 0.008 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 331 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7727 (m-40) REVERT: H 57 MET cc_start: 0.8757 (ttp) cc_final: 0.8481 (ttm) REVERT: B 632 ASP cc_start: 0.8969 (t70) cc_final: 0.8593 (t0) REVERT: C 13 ARG cc_start: 0.6880 (mtt-85) cc_final: 0.6576 (mmt90) REVERT: E 133 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: E 150 MET cc_start: 0.8369 (mmm) cc_final: 0.7865 (mmt) REVERT: M 4 MET cc_start: 0.6359 (pmm) cc_final: 0.5956 (mtm) REVERT: F 133 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7728 (m-40) REVERT: F 150 MET cc_start: 0.8201 (mmm) cc_final: 0.7777 (mmm) REVERT: I 632 ASP cc_start: 0.8797 (t70) cc_final: 0.8445 (t0) REVERT: K 52 ASN cc_start: 0.8747 (t0) cc_final: 0.8321 (t0) outliers start: 78 outliers final: 67 residues processed: 381 average time/residue: 0.3949 time to fit residues: 235.0323 Evaluate side-chains 384 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 314 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 93 TYR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 562 GLN Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 474 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 553 SER Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 chunk 277 optimal weight: 0.0030 chunk 167 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 0.0770 chunk 262 optimal weight: 0.8980 chunk 276 optimal weight: 0.0170 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 105 HIS ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27105 Z= 0.144 Angle : 0.583 8.880 36822 Z= 0.292 Chirality : 0.043 0.302 4503 Planarity : 0.004 0.048 4503 Dihedral : 5.411 42.624 6168 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.64 % Favored : 94.14 % Rotamer: Outliers : 1.35 % Allowed : 12.99 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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 (0.16), residues: 3105 helix: 0.84 (0.26), residues: 480 sheet: 1.13 (0.16), residues: 1095 loop : -0.95 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 94 HIS 0.005 0.001 HIS M 89 PHE 0.017 0.001 PHE H 63 TYR 0.011 0.001 TYR J 50 ARG 0.008 0.000 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 357 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6902 (tp30) cc_final: 0.6305 (tt0) REVERT: H 77 THR cc_start: 0.8900 (p) cc_final: 0.8656 (m) REVERT: L 31 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7338 (mtm110) REVERT: B 632 ASP cc_start: 0.8875 (t70) cc_final: 0.8483 (t0) REVERT: C 13 ARG cc_start: 0.6850 (mtt-85) cc_final: 0.6556 (mmt90) REVERT: E 150 MET cc_start: 0.8329 (mmm) cc_final: 0.7853 (mmt) REVERT: Q 31 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7282 (mtm-85) REVERT: M 4 MET cc_start: 0.6348 (pmm) cc_final: 0.5888 (mtm) REVERT: F 150 MET cc_start: 0.8164 (mmm) cc_final: 0.7809 (mmm) REVERT: R 31 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7375 (mtm-85) REVERT: I 632 ASP cc_start: 0.8647 (t70) cc_final: 0.8334 (t0) REVERT: K 52 ASN cc_start: 0.8543 (t0) cc_final: 0.8133 (t0) outliers start: 37 outliers final: 28 residues processed: 378 average time/residue: 0.4085 time to fit residues: 238.6126 Evaluate side-chains 355 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 327 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 93 TYR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.6980 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27105 Z= 0.169 Angle : 0.586 9.175 36822 Z= 0.293 Chirality : 0.043 0.300 4503 Planarity : 0.004 0.051 4503 Dihedral : 5.132 35.249 6168 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.99 % Favored : 93.82 % Rotamer: Outliers : 1.09 % Allowed : 13.61 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.16 (0.16), residues: 3105 helix: 1.02 (0.26), residues: 477 sheet: 1.08 (0.16), residues: 1119 loop : -0.97 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP N 94 HIS 0.004 0.001 HIS A 105 PHE 0.016 0.001 PHE H 63 TYR 0.013 0.001 TYR J 50 ARG 0.009 0.000 ARG Q 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 333 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6959 (tp30) cc_final: 0.6429 (tt0) REVERT: H 77 THR cc_start: 0.8901 (p) cc_final: 0.8648 (m) REVERT: L 17 GLU cc_start: 0.8286 (mp0) cc_final: 0.8012 (mp0) REVERT: L 31 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7328 (mtm110) REVERT: B 632 ASP cc_start: 0.8890 (t70) cc_final: 0.8510 (t0) REVERT: C 13 ARG cc_start: 0.6856 (mtt-85) cc_final: 0.6554 (mmt90) REVERT: E 150 MET cc_start: 0.8337 (mmm) cc_final: 0.7876 (mmt) REVERT: Q 31 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7243 (mtm-85) REVERT: M 4 MET cc_start: 0.6390 (pmm) cc_final: 0.5939 (mtm) REVERT: F 150 MET cc_start: 0.8135 (mmm) cc_final: 0.7741 (mmm) REVERT: R 31 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7349 (mtm-85) REVERT: I 530 MET cc_start: 0.8809 (mmm) cc_final: 0.7388 (mtt) REVERT: I 632 ASP cc_start: 0.8755 (t70) cc_final: 0.8379 (t0) REVERT: K 52 ASN cc_start: 0.8517 (t0) cc_final: 0.8102 (t0) outliers start: 30 outliers final: 27 residues processed: 351 average time/residue: 0.4189 time to fit residues: 226.9419 Evaluate side-chains 354 residues out of total 2751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 327 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ASP Chi-restraints excluded: chain Q residue 93 TYR Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 328 GLN H 53 ASN L 1 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073422 restraints weight = 51658.882| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.31 r_work: 0.2841 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27105 Z= 0.283 Angle : 0.629 8.334 36822 Z= 0.314 Chirality : 0.045 0.299 4503 Planarity : 0.004 0.053 4503 Dihedral : 5.254 32.951 6168 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 1.24 % Allowed : 13.79 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 0.01 (0.15), residues: 3105 helix: 0.85 (0.26), residues: 477 sheet: 0.98 (0.16), residues: 1119 loop : -1.05 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 94 HIS 0.009 0.001 HIS F 105 PHE 0.016 0.002 PHE C 78 TYR 0.016 0.001 TYR K 50 ARG 0.009 0.000 ARG Q 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5884.90 seconds wall clock time: 108 minutes 0.09 seconds (6480.09 seconds total)