Starting phenix.real_space_refine on Sun Mar 17 07:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9x_29881/03_2024/8g9x_29881.pdb" } resolution = 4.46 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= 0.053 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 115 5.16 5 C 10610 2.51 5 N 2809 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "O ASP 659": "OD1" <-> "OD2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 78": "OD1" <-> "OD2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "P GLU 153": "OE1" <-> "OE2" Residue "P PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17036 Number of models: 1 Model: "" Number of chains: 53 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 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: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.12, per 1000 atoms: 0.54 Number of scatterers: 17036 At special positions: 0 Unit cell: (126.644, 149.182, 133.083, 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 115 16.00 O 3502 8.00 N 2809 7.00 C 10610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.02 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.02 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA a 3 " - " MAN a 4 " " BMA n 3 " - " MAN n 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 1 " - " ASN E 88 " " NAG B 701 " - " ASN B 637 " " NAG C 1 " - " ASN E 156 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 339 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 276 " " NAG F 1 " - " ASN E 160 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG G 604 " - " ASN G 276 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 301 " " NAG O 701 " - " ASN O 637 " " NAG P 601 " - " ASN P 133 " " NAG P 602 " - " ASN P 339 " " NAG P 603 " - " ASN P 355 " " NAG P 604 " - " ASN P 276 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 363 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 392 " " NAG U 1 " - " ASN E 448 " " NAG V 1 " - " ASN G 88 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN P 88 " " NAG j 1 " - " ASN P 156 " " NAG k 1 " - " ASN P 160 " " NAG l 1 " - " ASN P 197 " " NAG m 1 " - " ASN P 234 " " NAG n 1 " - " ASN P 262 " " NAG o 1 " - " ASN P 295 " " NAG p 1 " - " ASN P 301 " " NAG q 1 " - " ASN P 332 " " NAG r 1 " - " ASN P 363 " " NAG s 1 " - " ASN P 386 " " NAG t 1 " - " ASN P 392 " " NAG u 1 " - " ASN P 448 " Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 2.7 seconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 41 sheets defined 20.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.773A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.864A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.672A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.724A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.764A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.549A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 4.098A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.681A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.684A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.818A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.714A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.313A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.883A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.689A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.681A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.870A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.710A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.337A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.828A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.752A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.620A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.581A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.870A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.691A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 115 removed outlier: 3.729A pdb=" N MET P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.811A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.665A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.349A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.734A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 604 removed outlier: 3.739A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 604 removed outlier: 3.914A pdb=" N CYS D 604 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL P 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.793A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.768A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.843A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.843A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.673A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB5, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB6, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.676A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AB8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.906A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.906A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.757A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC7, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.657A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.644A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.016A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.574A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.666A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 86 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 91 through 93 removed outlier: 3.701A pdb=" N GLY P 237 " --> pdb=" O PHE P 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD7, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.725A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.725A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE3, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.746A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE5, first strand: chain 'P' and resid 375 through 378 468 hydrogen bonds defined for protein. 1209 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: 4.94 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5279 1.34 - 1.47: 4442 1.47 - 1.59: 7477 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 17352 Sorted by residual: bond pdb=" CG GLU O 584 " pdb=" CD GLU O 584 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.73e+00 bond pdb=" CG MET P 426 " pdb=" SD MET P 426 " ideal model delta sigma weight residual 1.803 1.747 0.056 2.50e-02 1.60e+03 5.00e+00 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 BMA t 3 " pdb=" C2 BMA t 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CG MET E 426 " pdb=" SD MET E 426 " ideal model delta sigma weight residual 1.803 1.752 0.051 2.50e-02 1.60e+03 4.17e+00 ... (remaining 17347 not shown) Histogram of bond angle deviations from ideal: 89.40 - 98.36: 10 98.36 - 107.32: 853 107.32 - 116.28: 11910 116.28 - 125.24: 10378 125.24 - 134.20: 397 Bond angle restraints: 23548 Sorted by residual: angle pdb=" CB MET E 95 " pdb=" CG MET E 95 " pdb=" SD MET E 95 " ideal model delta sigma weight residual 112.70 89.40 23.30 3.00e+00 1.11e-01 6.03e+01 angle pdb=" N GLY E 152 " pdb=" CA GLY E 152 " pdb=" C GLY E 152 " ideal model delta sigma weight residual 113.18 98.92 14.26 2.37e+00 1.78e-01 3.62e+01 angle pdb=" N GLU O 657 " pdb=" CA GLU O 657 " pdb=" CB GLU O 657 " ideal model delta sigma weight residual 110.28 118.41 -8.13 1.55e+00 4.16e-01 2.75e+01 angle pdb=" CA MET E 95 " pdb=" CB MET E 95 " pdb=" CG MET E 95 " ideal model delta sigma weight residual 114.10 124.59 -10.49 2.00e+00 2.50e-01 2.75e+01 angle pdb=" C MET E 95 " pdb=" N TRP E 96 " pdb=" CA TRP E 96 " ideal model delta sigma weight residual 122.60 112.86 9.74 1.88e+00 2.83e-01 2.68e+01 ... (remaining 23543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 10675 21.91 - 43.83: 844 43.83 - 65.74: 158 65.74 - 87.65: 119 87.65 - 109.57: 63 Dihedral angle restraints: 11859 sinusoidal: 6158 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.08 68.08 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -154.06 68.06 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.75 65.75 1 1.00e+01 1.00e-02 5.66e+01 ... (remaining 11856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2542 0.095 - 0.190: 364 0.190 - 0.284: 53 0.284 - 0.379: 13 0.379 - 0.474: 3 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CB ILE G 284 " pdb=" CA ILE G 284 " pdb=" CG1 ILE G 284 " pdb=" CG2 ILE G 284 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE E 284 " pdb=" CA ILE E 284 " pdb=" CG1 ILE E 284 " pdb=" CG2 ILE E 284 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 2972 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " 0.041 2.00e-02 2.50e+03 3.83e-02 3.67e+01 pdb=" CG TRP G 427 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 427 " 0.032 2.00e-02 2.50e+03 3.81e-02 3.63e+01 pdb=" CG TRP P 427 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP P 427 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP P 427 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP P 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP P 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 427 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 427 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 427 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP P 427 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 427 " -0.040 2.00e-02 2.50e+03 3.75e-02 3.52e+01 pdb=" CG TRP E 427 " 0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP E 427 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP E 427 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 427 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 427 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 427 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 427 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 427 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 427 " 0.002 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1884 2.73 - 3.27: 17018 3.27 - 3.82: 28230 3.82 - 4.36: 32428 4.36 - 4.90: 55072 Nonbonded interactions: 134632 Sorted by model distance: nonbonded pdb=" OH TYR E 61 " pdb=" O CYS E 74 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR P 61 " pdb=" O CYS P 74 " model vdw 2.210 2.440 nonbonded pdb=" O LEU P 369 " pdb=" OG1 THR P 373 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASN G 302 " pdb=" OG1 THR G 320 " model vdw 2.243 2.440 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.252 2.440 ... (remaining 134627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'r' selection = chain 's' selection = chain 't' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'a' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.660 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.370 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 17352 Z= 0.511 Angle : 1.324 23.299 23548 Z= 0.691 Chirality : 0.072 0.474 2975 Planarity : 0.008 0.057 2855 Dihedral : 19.098 109.567 8065 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.98 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -4.84 (0.15), residues: 1949 helix: -4.56 (0.10), residues: 422 sheet: -2.76 (0.20), residues: 490 loop : -2.82 (0.16), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.005 TRP G 427 HIS 0.012 0.003 HIS E 105 PHE 0.038 0.004 PHE P 288 TYR 0.034 0.003 TYR D 643 ARG 0.021 0.001 ARG G 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.046 Fit side-chains REVERT: B 626 MET cc_start: 0.8308 (ppp) cc_final: 0.7858 (ppp) REVERT: D 530 MET cc_start: 0.9099 (mpp) cc_final: 0.8555 (mpp) REVERT: E 271 MET cc_start: 0.9402 (tpt) cc_final: 0.9201 (tpp) REVERT: G 271 MET cc_start: 0.9445 (tpt) cc_final: 0.9068 (tpp) REVERT: G 475 MET cc_start: 0.9392 (mmm) cc_final: 0.8570 (mmm) REVERT: P 271 MET cc_start: 0.9155 (tpt) cc_final: 0.8743 (tpp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2559 time to fit residues: 24.7990 Evaluate side-chains 50 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.0570 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN D 543 ASN E 103 GLN E 289 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 289 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 591 GLN P 103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17352 Z= 0.217 Angle : 0.739 16.007 23548 Z= 0.365 Chirality : 0.046 0.261 2975 Planarity : 0.005 0.037 2855 Dihedral : 14.412 75.465 4403 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.17), residues: 1949 helix: -2.53 (0.21), residues: 418 sheet: -2.21 (0.24), residues: 376 loop : -2.34 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 427 HIS 0.003 0.001 HIS P 374 PHE 0.014 0.002 PHE P 288 TYR 0.016 0.001 TYR O 638 ARG 0.003 0.000 ARG P 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.005 Fit side-chains REVERT: B 626 MET cc_start: 0.8508 (ppp) cc_final: 0.8284 (ppp) REVERT: D 530 MET cc_start: 0.8709 (mpp) cc_final: 0.8097 (mpp) REVERT: E 161 MET cc_start: 0.8825 (tmm) cc_final: 0.8527 (tmm) REVERT: E 271 MET cc_start: 0.9454 (tpt) cc_final: 0.9183 (tpp) REVERT: G 426 MET cc_start: 0.9457 (ppp) cc_final: 0.9226 (ppp) REVERT: P 271 MET cc_start: 0.9194 (tpt) cc_final: 0.8837 (tpp) REVERT: P 494 LEU cc_start: 0.9801 (pp) cc_final: 0.9599 (pp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2590 time to fit residues: 24.8154 Evaluate side-chains 47 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 289 ASN P 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17352 Z= 0.198 Angle : 0.692 14.966 23548 Z= 0.341 Chirality : 0.046 0.270 2975 Planarity : 0.004 0.039 2855 Dihedral : 11.288 59.909 4403 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 1949 helix: -1.59 (0.24), residues: 419 sheet: -1.97 (0.24), residues: 382 loop : -2.14 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 96 HIS 0.004 0.001 HIS G 374 PHE 0.021 0.002 PHE G 391 TYR 0.015 0.001 TYR O 638 ARG 0.003 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.588 Fit side-chains REVERT: B 626 MET cc_start: 0.8697 (ppp) cc_final: 0.8473 (ppp) REVERT: D 530 MET cc_start: 0.8480 (mpp) cc_final: 0.8051 (mpp) REVERT: G 271 MET cc_start: 0.9398 (tpt) cc_final: 0.9150 (tpp) REVERT: O 626 MET cc_start: 0.7767 (ppp) cc_final: 0.7390 (pmm) REVERT: P 100 MET cc_start: 0.9763 (ppp) cc_final: 0.9560 (ppp) REVERT: P 161 MET cc_start: 0.8698 (tmm) cc_final: 0.8389 (tmm) REVERT: P 271 MET cc_start: 0.9110 (tpt) cc_final: 0.8776 (tpp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2593 time to fit residues: 24.3315 Evaluate side-chains 47 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 92 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17352 Z= 0.190 Angle : 0.657 14.183 23548 Z= 0.324 Chirality : 0.044 0.262 2975 Planarity : 0.004 0.054 2855 Dihedral : 9.915 59.973 4403 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1949 helix: -1.17 (0.26), residues: 407 sheet: -1.67 (0.25), residues: 352 loop : -2.01 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 96 HIS 0.003 0.001 HIS P 85 PHE 0.013 0.001 PHE G 391 TYR 0.016 0.001 TYR O 643 ARG 0.003 0.000 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.186 Fit side-chains REVERT: B 626 MET cc_start: 0.8562 (ppp) cc_final: 0.8235 (ppp) REVERT: D 530 MET cc_start: 0.9028 (mpp) cc_final: 0.8202 (mpp) REVERT: D 626 MET cc_start: 0.9381 (pmm) cc_final: 0.9167 (pmm) REVERT: E 271 MET cc_start: 0.9496 (tpt) cc_final: 0.9181 (tpt) REVERT: G 271 MET cc_start: 0.9380 (tpt) cc_final: 0.9150 (tpp) REVERT: O 626 MET cc_start: 0.7850 (ppp) cc_final: 0.7637 (pmm) REVERT: P 271 MET cc_start: 0.9119 (tpt) cc_final: 0.8780 (tpp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2520 time to fit residues: 23.7086 Evaluate side-chains 46 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN G 478 ASN ** O 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 17352 Z= 0.425 Angle : 0.873 13.268 23548 Z= 0.435 Chirality : 0.046 0.251 2975 Planarity : 0.005 0.041 2855 Dihedral : 9.964 59.673 4403 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 1949 helix: -1.37 (0.25), residues: 384 sheet: -2.31 (0.21), residues: 471 loop : -1.59 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 45 HIS 0.009 0.002 HIS P 249 PHE 0.030 0.003 PHE G 391 TYR 0.019 0.002 TYR P 39 ARG 0.005 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 2.060 Fit side-chains REVERT: B 626 MET cc_start: 0.8919 (ppp) cc_final: 0.8661 (ppp) REVERT: D 530 MET cc_start: 0.9025 (mpp) cc_final: 0.8141 (mpp) REVERT: D 626 MET cc_start: 0.9490 (pmm) cc_final: 0.9043 (pmm) REVERT: E 271 MET cc_start: 0.9427 (tpt) cc_final: 0.9090 (tpt) REVERT: E 434 MET cc_start: 0.9321 (tpp) cc_final: 0.9106 (tpp) REVERT: O 626 MET cc_start: 0.8188 (ppp) cc_final: 0.7872 (pmm) REVERT: P 161 MET cc_start: 0.8743 (tmm) cc_final: 0.8352 (tmm) REVERT: P 271 MET cc_start: 0.9070 (tpt) cc_final: 0.8659 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2707 time to fit residues: 23.6092 Evaluate side-chains 42 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17352 Z= 0.289 Angle : 0.736 12.486 23548 Z= 0.367 Chirality : 0.045 0.261 2975 Planarity : 0.004 0.039 2855 Dihedral : 9.607 59.882 4403 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.18), residues: 1949 helix: -0.69 (0.27), residues: 355 sheet: -2.18 (0.22), residues: 471 loop : -1.60 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.005 0.001 HIS P 249 PHE 0.018 0.002 PHE G 391 TYR 0.017 0.002 TYR E 318 ARG 0.004 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.579 Fit side-chains REVERT: B 589 ASP cc_start: 0.9661 (m-30) cc_final: 0.9402 (p0) REVERT: B 626 MET cc_start: 0.8737 (ppp) cc_final: 0.8450 (ppp) REVERT: D 530 MET cc_start: 0.9046 (mpp) cc_final: 0.8349 (mpp) REVERT: D 626 MET cc_start: 0.9447 (pmm) cc_final: 0.9159 (pmm) REVERT: E 271 MET cc_start: 0.9451 (tpt) cc_final: 0.8818 (tmm) REVERT: P 100 MET cc_start: 0.9799 (ppp) cc_final: 0.9592 (ppp) REVERT: P 161 MET cc_start: 0.8726 (tmm) cc_final: 0.8209 (tmm) REVERT: P 271 MET cc_start: 0.9060 (tpt) cc_final: 0.8583 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2503 time to fit residues: 22.4046 Evaluate side-chains 43 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 0.0000 chunk 108 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17352 Z= 0.196 Angle : 0.662 12.773 23548 Z= 0.325 Chirality : 0.044 0.265 2975 Planarity : 0.004 0.040 2855 Dihedral : 9.129 59.266 4403 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.18), residues: 1949 helix: -0.30 (0.28), residues: 354 sheet: -1.91 (0.23), residues: 444 loop : -1.57 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 571 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE P 288 TYR 0.015 0.001 TYR O 638 ARG 0.005 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: B 589 ASP cc_start: 0.9650 (m-30) cc_final: 0.9385 (p0) REVERT: B 626 MET cc_start: 0.8819 (ppp) cc_final: 0.8444 (ppp) REVERT: D 530 MET cc_start: 0.9031 (mpp) cc_final: 0.8206 (mpp) REVERT: D 626 MET cc_start: 0.9448 (pmm) cc_final: 0.9058 (pmm) REVERT: E 271 MET cc_start: 0.9546 (tpt) cc_final: 0.9121 (tmm) REVERT: E 434 MET cc_start: 0.9346 (tpp) cc_final: 0.9050 (tpp) REVERT: P 161 MET cc_start: 0.8742 (tmm) cc_final: 0.8521 (tmm) REVERT: P 271 MET cc_start: 0.9052 (tpt) cc_final: 0.8567 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2543 time to fit residues: 22.9315 Evaluate side-chains 46 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 112 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17352 Z= 0.297 Angle : 0.742 13.293 23548 Z= 0.366 Chirality : 0.044 0.257 2975 Planarity : 0.004 0.045 2855 Dihedral : 9.122 59.775 4403 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.18), residues: 1949 helix: -0.35 (0.28), residues: 355 sheet: -2.11 (0.22), residues: 465 loop : -1.48 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 96 HIS 0.007 0.001 HIS P 249 PHE 0.018 0.002 PHE G 391 TYR 0.015 0.002 TYR E 39 ARG 0.008 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: B 626 MET cc_start: 0.8958 (ppp) cc_final: 0.8742 (ppp) REVERT: D 530 MET cc_start: 0.9097 (mpp) cc_final: 0.8148 (mpp) REVERT: D 626 MET cc_start: 0.9520 (pmm) cc_final: 0.9074 (pmm) REVERT: E 271 MET cc_start: 0.9508 (tpt) cc_final: 0.9037 (tmm) REVERT: E 434 MET cc_start: 0.9381 (tpp) cc_final: 0.9129 (tpp) REVERT: P 100 MET cc_start: 0.9746 (ppp) cc_final: 0.9533 (ppp) REVERT: P 161 MET cc_start: 0.8757 (tmm) cc_final: 0.8525 (tmm) REVERT: P 271 MET cc_start: 0.9047 (tpt) cc_final: 0.8597 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2528 time to fit residues: 22.8283 Evaluate side-chains 44 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17352 Z= 0.245 Angle : 0.694 13.619 23548 Z= 0.341 Chirality : 0.044 0.263 2975 Planarity : 0.004 0.043 2855 Dihedral : 8.998 59.356 4403 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.18), residues: 1949 helix: -0.16 (0.28), residues: 355 sheet: -2.07 (0.23), residues: 465 loop : -1.45 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 571 HIS 0.003 0.001 HIS P 249 PHE 0.015 0.002 PHE G 391 TYR 0.015 0.002 TYR O 638 ARG 0.006 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.039 Fit side-chains REVERT: B 626 MET cc_start: 0.9018 (ppp) cc_final: 0.8814 (ppp) REVERT: D 530 MET cc_start: 0.9091 (mpp) cc_final: 0.8251 (mpp) REVERT: D 626 MET cc_start: 0.9483 (pmm) cc_final: 0.9012 (pmm) REVERT: E 95 MET cc_start: 0.9691 (mmm) cc_final: 0.9322 (mmt) REVERT: E 271 MET cc_start: 0.9502 (tpt) cc_final: 0.9221 (tpp) REVERT: P 161 MET cc_start: 0.8791 (tmm) cc_final: 0.8517 (tmm) REVERT: P 271 MET cc_start: 0.9049 (tpt) cc_final: 0.8602 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2586 time to fit residues: 23.7200 Evaluate side-chains 43 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 9.9990 chunk 186 optimal weight: 0.0170 chunk 113 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 179 optimal weight: 0.0770 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 656 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17352 Z= 0.148 Angle : 0.648 14.615 23548 Z= 0.314 Chirality : 0.045 0.271 2975 Planarity : 0.004 0.040 2855 Dihedral : 8.596 59.696 4403 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 1949 helix: 0.04 (0.28), residues: 354 sheet: -1.37 (0.26), residues: 389 loop : -1.56 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 69 HIS 0.004 0.001 HIS G 105 PHE 0.010 0.001 PHE E 288 TYR 0.013 0.001 TYR L 50 ARG 0.006 0.000 ARG H 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 530 MET cc_start: 0.9065 (mpp) cc_final: 0.8212 (mpp) REVERT: D 626 MET cc_start: 0.9476 (pmm) cc_final: 0.9094 (pmm) REVERT: E 95 MET cc_start: 0.9741 (mmm) cc_final: 0.9457 (mmt) REVERT: E 271 MET cc_start: 0.9520 (tpt) cc_final: 0.9113 (tmm) REVERT: G 475 MET cc_start: 0.9496 (mmm) cc_final: 0.9105 (mmm) REVERT: P 95 MET cc_start: 0.9112 (ppp) cc_final: 0.8517 (ppp) REVERT: P 161 MET cc_start: 0.8845 (tmm) cc_final: 0.8570 (tmm) REVERT: P 271 MET cc_start: 0.9021 (tpt) cc_final: 0.8628 (tpp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2578 time to fit residues: 24.9149 Evaluate side-chains 47 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 656 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.020567 restraints weight = 307837.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.021206 restraints weight = 188126.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021677 restraints weight = 132813.141| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17352 Z= 0.241 Angle : 0.685 13.255 23548 Z= 0.335 Chirality : 0.044 0.260 2975 Planarity : 0.004 0.039 2855 Dihedral : 8.563 59.982 4403 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 1949 helix: 0.07 (0.29), residues: 354 sheet: -1.85 (0.24), residues: 428 loop : -1.41 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 69 HIS 0.005 0.001 HIS L 34 PHE 0.014 0.002 PHE G 391 TYR 0.017 0.001 TYR L 50 ARG 0.006 0.000 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.17 seconds wall clock time: 45 minutes 33.51 seconds (2733.51 seconds total)