Starting phenix.real_space_refine on Sun Mar 17 08:15:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9y_29882/03_2024/8g9y_29882.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.053 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 10664 2.51 5 N 2809 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 659": "OD1" <-> "OD2" Residue "D ASP 589": "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 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" 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 "E PHE 468": "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 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 ASP 167": "OD1" <-> "OD2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G TYR 318": "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 "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "O ASP 659": "OD1" <-> "OD2" Residue "O ASP 664": "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 ASP 167": "OD1" <-> "OD2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 217": "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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17135 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 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: 11.12, per 1000 atoms: 0.65 Number of scatterers: 17135 At special positions: 0 Unit cell: (132.01, 129.863, 134.156, 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 3547 8.00 N 2809 7.00 C 10664 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=2.04 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=2.04 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=2.07 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 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=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA f 3 " - " MAN f 5 " " BMA s 3 " - " MAN s 5 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " NAG-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: 9.01 Conformation dependent library (CDL) restraints added in 2.9 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: 38 helices and 42 sheets defined 20.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.065A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.548A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.659A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.854A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.586A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.689A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.721A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.531A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.834A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.685A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.274A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.917A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.658A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.594A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.873A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.738A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.320A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.909A 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 'H' and resid 98 through 100B removed outlier: 4.248A pdb=" N SER H 100B" --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.584A pdb=" N PHE L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.994A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.526A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.602A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.705A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.605A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.879A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 354 removed outlier: 3.597A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 351 " --> pdb=" O LYS P 347 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.257A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 3.801A 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 609 removed outlier: 8.570A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL G 36 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.989A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 499 removed outlier: 3.805A pdb=" N VAL E 38 " --> pdb=" O CYS O 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS O 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.547A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.553A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) 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 159 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 202 through 203 removed outlier: 6.865A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.804A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.715A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AB6, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AB7, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AC1, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC2, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 287 " --> pdb=" O MET G 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 260 through 261 removed outlier: 3.635A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.810A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AC8, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 94 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.976A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 33 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 49 " --> pdb=" O GLN L 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.505A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL P 242 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 86 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AD9, first strand: chain 'P' and resid 181 through 184 removed outlier: 4.636A pdb=" N GLU P 190 " --> pdb=" O ILE P 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.854A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 273 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.899A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AE4, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.820A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AE6, first strand: chain 'P' and resid 375 through 378 457 hydrogen bonds defined for protein. 1179 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: 5.95 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 5307 1.35 - 1.49: 4824 1.49 - 1.63: 7166 1.63 - 1.77: 17 1.77 - 1.91: 137 Bond restraints: 17451 Sorted by residual: bond pdb=" CB CYS E 205 " pdb=" SG CYS E 205 " ideal model delta sigma weight residual 1.808 1.700 0.108 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " ideal model delta sigma weight residual 1.808 1.909 -0.101 3.30e-02 9.18e+02 9.32e+00 bond pdb=" CG MET O 530 " pdb=" SD MET O 530 " ideal model delta sigma weight residual 1.803 1.739 0.064 2.50e-02 1.60e+03 6.57e+00 bond pdb=" CG LEU E 116 " pdb=" CD2 LEU E 116 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" C1 NAG s 2 " pdb=" O5 NAG s 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 91.85 - 100.86: 31 100.86 - 109.86: 3732 109.86 - 118.87: 11161 118.87 - 127.88: 8576 127.88 - 136.89: 183 Bond angle restraints: 23683 Sorted by residual: angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C ASN G 295 " pdb=" CA ASN G 295 " pdb=" CB ASN G 295 " ideal model delta sigma weight residual 111.97 123.50 -11.53 1.99e+00 2.53e-01 3.36e+01 angle pdb=" C ASN P 332 " pdb=" CA ASN P 332 " pdb=" CB ASN P 332 " ideal model delta sigma weight residual 109.35 120.81 -11.46 1.98e+00 2.55e-01 3.35e+01 angle pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " pdb=" SG CYS E 433 " ideal model delta sigma weight residual 114.40 127.38 -12.98 2.30e+00 1.89e-01 3.18e+01 angle pdb=" N CYS E 433 " pdb=" CA CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sigma weight residual 111.21 102.01 9.20 1.67e+00 3.59e-01 3.04e+01 ... (remaining 23678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 10799 21.73 - 43.45: 872 43.45 - 65.17: 154 65.17 - 86.90: 128 86.90 - 108.62: 77 Dihedral angle restraints: 12030 sinusoidal: 6329 harmonic: 5701 Sorted by residual: dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 3.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -152.85 66.85 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 12027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2333 0.079 - 0.158: 552 0.158 - 0.237: 92 0.237 - 0.316: 33 0.316 - 0.395: 10 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA ASN G 295 " pdb=" N ASN G 295 " pdb=" C ASN G 295 " pdb=" CB ASN G 295 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+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 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 3017 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 295 " -0.005 2.00e-02 2.50e+03 5.37e-02 3.61e+01 pdb=" CG ASN G 295 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN G 295 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN G 295 " 0.063 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " -0.025 2.00e-02 2.50e+03 2.83e-02 2.00e+01 pdb=" CG TRP G 427 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 653 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C GLN B 653 " 0.073 2.00e-02 2.50e+03 pdb=" O GLN B 653 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 654 " -0.025 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1913 2.73 - 3.28: 16983 3.28 - 3.82: 27716 3.82 - 4.36: 31756 4.36 - 4.90: 53916 Nonbonded interactions: 132284 Sorted by model distance: nonbonded pdb=" O SER L 43 " pdb=" NH1 ARG L 45 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASN P 302 " pdb=" OG1 THR P 320 " model vdw 2.231 2.440 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASN G 302 " pdb=" OG1 THR G 320 " model vdw 2.255 2.440 nonbonded pdb=" O LEU G 369 " pdb=" OG1 THR G 373 " model vdw 2.255 2.440 ... (remaining 132279 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 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'q' selection = chain 'r' 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' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 's' } 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.700 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.090 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 0.108 17451 Z= 0.502 Angle : 1.336 20.593 23683 Z= 0.687 Chirality : 0.074 0.395 3020 Planarity : 0.008 0.058 2855 Dihedral : 19.158 108.624 8236 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.22 % 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: -4.83 (0.15), residues: 1949 helix: -4.60 (0.10), residues: 414 sheet: -2.87 (0.20), residues: 448 loop : -2.79 (0.15), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.004 TRP G 427 HIS 0.013 0.002 HIS E 105 PHE 0.025 0.003 PHE P 288 TYR 0.020 0.003 TYR L 36 ARG 0.021 0.001 ARG E 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 61 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9076 (mpp) cc_final: 0.8851 (mpp) REVERT: D 530 MET cc_start: 0.9175 (mmp) cc_final: 0.8492 (mmp) REVERT: D 535 MET cc_start: 0.9454 (mpp) cc_final: 0.9182 (mpp) REVERT: E 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8791 (ppp) REVERT: G 104 MET cc_start: 0.9213 (ppp) cc_final: 0.8958 (ppp) REVERT: H 3 MET cc_start: 0.8684 (tmm) cc_final: 0.8462 (tmm) REVERT: O 530 MET cc_start: 0.9157 (mmp) cc_final: 0.8727 (mmp) REVERT: O 535 MET cc_start: 0.9495 (mmp) cc_final: 0.9260 (mmp) REVERT: O 632 ASP cc_start: 0.9108 (m-30) cc_final: 0.8896 (m-30) REVERT: P 95 MET cc_start: 0.9649 (ptm) cc_final: 0.8002 (ppp) REVERT: P 434 MET cc_start: 0.9084 (tmm) cc_final: 0.8518 (tmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2695 time to fit residues: 26.7908 Evaluate side-chains 48 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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: 7.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 103 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17451 Z= 0.321 Angle : 0.817 13.643 23683 Z= 0.402 Chirality : 0.047 0.336 3020 Planarity : 0.005 0.035 2855 Dihedral : 14.355 70.836 4574 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -3.55 (0.17), residues: 1949 helix: -2.59 (0.20), residues: 414 sheet: -2.50 (0.21), residues: 472 loop : -2.16 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 631 HIS 0.006 0.002 HIS P 374 PHE 0.014 0.002 PHE E 176 TYR 0.016 0.002 TYR G 177 ARG 0.005 0.001 ARG L 45 *********************** 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 53 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.800 Fit side-chains REVERT: B 643 TYR cc_start: 0.9588 (m-80) cc_final: 0.9355 (m-80) REVERT: D 530 MET cc_start: 0.9184 (mmp) cc_final: 0.8725 (mmp) REVERT: D 535 MET cc_start: 0.9461 (mpp) cc_final: 0.9174 (mpp) REVERT: E 95 MET cc_start: 0.9232 (ppp) cc_final: 0.8882 (ppp) REVERT: E 100 MET cc_start: 0.8699 (ppp) cc_final: 0.8434 (ppp) REVERT: G 95 MET cc_start: 0.9467 (ppp) cc_final: 0.8371 (ppp) REVERT: G 475 MET cc_start: 0.9005 (tpt) cc_final: 0.8689 (tpt) REVERT: O 530 MET cc_start: 0.9175 (mmp) cc_final: 0.8434 (mmp) REVERT: O 535 MET cc_start: 0.9547 (mmp) cc_final: 0.9307 (mmp) REVERT: O 643 TYR cc_start: 0.9421 (m-80) cc_final: 0.8964 (m-80) REVERT: P 95 MET cc_start: 0.9676 (ptm) cc_final: 0.8245 (ppp) REVERT: P 434 MET cc_start: 0.9256 (tmm) cc_final: 0.8770 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2874 time to fit residues: 25.7614 Evaluate side-chains 47 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17451 Z= 0.315 Angle : 0.780 12.118 23683 Z= 0.386 Chirality : 0.047 0.324 3020 Planarity : 0.004 0.035 2855 Dihedral : 11.551 64.812 4574 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.39 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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 (0.18), residues: 1949 helix: -1.43 (0.25), residues: 389 sheet: -2.42 (0.20), residues: 507 loop : -1.88 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 571 HIS 0.006 0.002 HIS P 374 PHE 0.016 0.002 PHE G 391 TYR 0.016 0.002 TYR G 318 ARG 0.005 0.001 ARG G 273 *********************** 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 50 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8471 (ppp) cc_final: 0.8206 (ppp) REVERT: B 643 TYR cc_start: 0.9608 (m-80) cc_final: 0.9371 (m-80) REVERT: D 530 MET cc_start: 0.9277 (mmp) cc_final: 0.8887 (mmp) REVERT: E 95 MET cc_start: 0.9321 (ppp) cc_final: 0.9013 (ppp) REVERT: G 95 MET cc_start: 0.9488 (ppp) cc_final: 0.8240 (ppp) REVERT: G 271 MET cc_start: 0.8210 (mpp) cc_final: 0.7974 (mpp) REVERT: O 530 MET cc_start: 0.9179 (mmp) cc_final: 0.8620 (mmp) REVERT: O 643 TYR cc_start: 0.9490 (m-80) cc_final: 0.9071 (m-80) REVERT: P 95 MET cc_start: 0.9573 (ptm) cc_final: 0.8401 (ppp) REVERT: P 434 MET cc_start: 0.9354 (tmm) cc_final: 0.8862 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2618 time to fit residues: 22.2266 Evaluate side-chains 47 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17451 Z= 0.312 Angle : 0.752 11.965 23683 Z= 0.370 Chirality : 0.045 0.328 3020 Planarity : 0.004 0.038 2855 Dihedral : 10.426 59.890 4574 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -1.03 (0.25), residues: 391 sheet: -2.28 (0.22), residues: 447 loop : -1.78 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 571 HIS 0.006 0.001 HIS P 374 PHE 0.014 0.002 PHE G 176 TYR 0.014 0.002 TYR E 191 ARG 0.004 0.001 ARG P 273 *********************** 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 : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8485 (ppp) cc_final: 0.8252 (ppp) REVERT: B 643 TYR cc_start: 0.9622 (m-80) cc_final: 0.9390 (m-80) REVERT: D 530 MET cc_start: 0.9385 (mmp) cc_final: 0.8961 (mmp) REVERT: E 95 MET cc_start: 0.9447 (ppp) cc_final: 0.9057 (ppp) REVERT: G 95 MET cc_start: 0.9338 (ppp) cc_final: 0.8629 (ppp) REVERT: G 271 MET cc_start: 0.8242 (mpp) cc_final: 0.7953 (mpp) REVERT: L 76 ASN cc_start: 0.9237 (m110) cc_final: 0.8956 (p0) REVERT: O 530 MET cc_start: 0.9176 (mmp) cc_final: 0.8872 (mmp) REVERT: O 643 TYR cc_start: 0.9526 (m-80) cc_final: 0.9160 (m-80) REVERT: P 95 MET cc_start: 0.9592 (ptm) cc_final: 0.8510 (ppp) REVERT: P 434 MET cc_start: 0.9377 (tmm) cc_final: 0.8874 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2630 time to fit residues: 23.8313 Evaluate side-chains 49 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17451 Z= 0.250 Angle : 0.703 11.797 23683 Z= 0.345 Chirality : 0.045 0.330 3020 Planarity : 0.004 0.042 2855 Dihedral : 9.929 59.826 4574 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -2.33 (0.18), residues: 1949 helix: -0.60 (0.26), residues: 383 sheet: -1.99 (0.24), residues: 405 loop : -1.73 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 571 HIS 0.005 0.001 HIS P 66 PHE 0.011 0.001 PHE G 391 TYR 0.013 0.001 TYR G 318 ARG 0.004 0.001 ARG P 273 *********************** 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 53 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8413 (ppp) cc_final: 0.8068 (ppp) REVERT: D 530 MET cc_start: 0.9341 (mmp) cc_final: 0.9005 (mmp) REVERT: E 95 MET cc_start: 0.9460 (ppp) cc_final: 0.9044 (ppp) REVERT: G 95 MET cc_start: 0.9370 (ppp) cc_final: 0.8616 (ppp) REVERT: G 271 MET cc_start: 0.8228 (mpp) cc_final: 0.7953 (mpp) REVERT: H 3 MET cc_start: 0.9021 (tmm) cc_final: 0.8785 (tmm) REVERT: L 76 ASN cc_start: 0.9215 (m110) cc_final: 0.8945 (p0) REVERT: O 530 MET cc_start: 0.9230 (mmp) cc_final: 0.8856 (mmp) REVERT: O 535 MET cc_start: 0.9490 (mmp) cc_final: 0.9282 (mmp) REVERT: O 643 TYR cc_start: 0.9538 (m-80) cc_final: 0.9172 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2935 time to fit residues: 25.6676 Evaluate side-chains 48 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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: 6.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 0.0070 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 170 GLN ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 289 ASN P 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17451 Z= 0.334 Angle : 0.768 10.580 23683 Z= 0.378 Chirality : 0.045 0.325 3020 Planarity : 0.004 0.036 2855 Dihedral : 9.740 59.980 4574 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 1949 helix: -0.56 (0.26), residues: 372 sheet: -2.14 (0.22), residues: 468 loop : -1.50 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 571 HIS 0.006 0.001 HIS P 66 PHE 0.025 0.002 PHE E 391 TYR 0.015 0.002 TYR G 318 ARG 0.005 0.001 ARG G 178 *********************** 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 55 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8466 (ppp) cc_final: 0.8191 (ppp) REVERT: D 530 MET cc_start: 0.9411 (mmp) cc_final: 0.9056 (mmp) REVERT: E 95 MET cc_start: 0.9533 (ppp) cc_final: 0.9083 (ppp) REVERT: G 95 MET cc_start: 0.9429 (ppp) cc_final: 0.8709 (ppp) REVERT: G 161 MET cc_start: 0.9209 (tpt) cc_final: 0.8934 (tpp) REVERT: G 271 MET cc_start: 0.8151 (mpp) cc_final: 0.7941 (mpp) REVERT: H 3 MET cc_start: 0.8990 (tmm) cc_final: 0.8775 (tmm) REVERT: L 76 ASN cc_start: 0.9231 (m110) cc_final: 0.8963 (p0) REVERT: O 530 MET cc_start: 0.9229 (mmp) cc_final: 0.8942 (mmp) REVERT: O 643 TYR cc_start: 0.9548 (m-80) cc_final: 0.9200 (m-80) REVERT: P 95 MET cc_start: 0.9646 (ptm) cc_final: 0.9094 (tmm) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2697 time to fit residues: 25.4820 Evaluate side-chains 49 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.0270 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17451 Z= 0.147 Angle : 0.645 13.822 23683 Z= 0.311 Chirality : 0.045 0.336 3020 Planarity : 0.003 0.038 2855 Dihedral : 9.130 59.398 4574 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.18), residues: 1949 helix: -0.20 (0.27), residues: 380 sheet: -1.48 (0.25), residues: 399 loop : -1.58 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 571 HIS 0.004 0.001 HIS G 216 PHE 0.011 0.001 PHE G 288 TYR 0.010 0.001 TYR D 638 ARG 0.006 0.000 ARG E 480 *********************** 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 58 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8473 (ppp) cc_final: 0.8019 (ppp) REVERT: D 530 MET cc_start: 0.9293 (mmp) cc_final: 0.9067 (mmp) REVERT: E 95 MET cc_start: 0.9355 (ppp) cc_final: 0.8925 (ppp) REVERT: G 95 MET cc_start: 0.9393 (ppp) cc_final: 0.8668 (ppp) REVERT: H 3 MET cc_start: 0.8995 (tmm) cc_final: 0.8789 (tmm) REVERT: L 76 ASN cc_start: 0.9202 (m110) cc_final: 0.8931 (p0) REVERT: O 530 MET cc_start: 0.9277 (mmp) cc_final: 0.8842 (mmp) REVERT: O 535 MET cc_start: 0.9444 (mmp) cc_final: 0.9235 (mmp) REVERT: O 643 TYR cc_start: 0.9505 (m-80) cc_final: 0.9189 (m-80) REVERT: P 95 MET cc_start: 0.9569 (ptm) cc_final: 0.8538 (ppp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3244 time to fit residues: 29.2727 Evaluate side-chains 50 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17451 Z= 0.257 Angle : 0.689 12.244 23683 Z= 0.335 Chirality : 0.044 0.327 3020 Planarity : 0.004 0.037 2855 Dihedral : 9.051 59.645 4574 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1949 helix: -0.08 (0.27), residues: 368 sheet: -1.51 (0.24), residues: 423 loop : -1.43 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 427 HIS 0.004 0.001 HIS P 66 PHE 0.013 0.002 PHE E 391 TYR 0.011 0.001 TYR G 318 ARG 0.010 0.001 ARG L 24 *********************** 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 53 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8590 (ppp) cc_final: 0.8221 (ppp) REVERT: D 530 MET cc_start: 0.9380 (mmp) cc_final: 0.8940 (mmp) REVERT: E 95 MET cc_start: 0.9439 (ppp) cc_final: 0.8996 (ppp) REVERT: G 95 MET cc_start: 0.9341 (ppp) cc_final: 0.8775 (ppp) REVERT: L 76 ASN cc_start: 0.9205 (m110) cc_final: 0.8909 (p0) REVERT: O 530 MET cc_start: 0.9249 (mmp) cc_final: 0.8876 (mmp) REVERT: P 95 MET cc_start: 0.9646 (ptm) cc_final: 0.9104 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2814 time to fit residues: 24.6443 Evaluate side-chains 50 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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: 6.9990 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17451 Z= 0.249 Angle : 0.685 12.505 23683 Z= 0.333 Chirality : 0.044 0.327 3020 Planarity : 0.004 0.039 2855 Dihedral : 8.984 59.595 4574 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1949 helix: -0.07 (0.27), residues: 367 sheet: -1.48 (0.23), residues: 463 loop : -1.42 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 571 HIS 0.004 0.001 HIS P 66 PHE 0.012 0.001 PHE G 288 TYR 0.010 0.001 TYR G 318 ARG 0.007 0.001 ARG L 24 *********************** 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 53 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8494 (ppp) cc_final: 0.8205 (ppp) REVERT: D 530 MET cc_start: 0.9366 (mmp) cc_final: 0.8968 (mmp) REVERT: E 95 MET cc_start: 0.9453 (ppp) cc_final: 0.8950 (ppp) REVERT: G 95 MET cc_start: 0.9420 (ppp) cc_final: 0.8884 (ppp) REVERT: G 426 MET cc_start: 0.9530 (tmm) cc_final: 0.9312 (tmm) REVERT: H 3 MET cc_start: 0.9065 (tmm) cc_final: 0.8797 (tmm) REVERT: L 76 ASN cc_start: 0.9224 (m110) cc_final: 0.8936 (p0) REVERT: O 530 MET cc_start: 0.9264 (mmp) cc_final: 0.8891 (mmp) REVERT: P 95 MET cc_start: 0.9630 (ptm) cc_final: 0.9121 (tmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2920 time to fit residues: 25.0103 Evaluate side-chains 49 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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: 2.9990 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 88 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 155 optimal weight: 0.0060 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17451 Z= 0.143 Angle : 0.644 12.707 23683 Z= 0.309 Chirality : 0.045 0.327 3020 Planarity : 0.003 0.039 2855 Dihedral : 8.581 59.909 4574 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1949 helix: -0.07 (0.28), residues: 381 sheet: -1.03 (0.24), residues: 453 loop : -1.57 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 69 HIS 0.010 0.001 HIS G 374 PHE 0.019 0.001 PHE G 376 TYR 0.008 0.001 TYR L 50 ARG 0.004 0.000 ARG L 45 ********************** 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 56 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.9681 (ptp) cc_final: 0.9141 (tpt) REVERT: B 626 MET cc_start: 0.8313 (ppp) cc_final: 0.8075 (ppp) REVERT: D 530 MET cc_start: 0.9269 (mmp) cc_final: 0.8985 (mmp) REVERT: E 95 MET cc_start: 0.9406 (ppp) cc_final: 0.8761 (ppp) REVERT: G 95 MET cc_start: 0.9350 (ppp) cc_final: 0.8784 (ppp) REVERT: L 76 ASN cc_start: 0.9239 (m110) cc_final: 0.8964 (p0) REVERT: O 530 MET cc_start: 0.9316 (mmp) cc_final: 0.8924 (mmp) REVERT: O 643 TYR cc_start: 0.9524 (m-80) cc_final: 0.9181 (m-80) REVERT: P 95 MET cc_start: 0.9604 (ptm) cc_final: 0.8702 (ppp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3247 time to fit residues: 29.0630 Evaluate side-chains 49 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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: 2.9990 chunk 165 optimal weight: 0.0770 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.027833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.022447 restraints weight = 264610.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.023109 restraints weight = 154601.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.023567 restraints weight = 107909.887| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17451 Z= 0.156 Angle : 0.616 12.614 23683 Z= 0.297 Chirality : 0.043 0.322 3020 Planarity : 0.003 0.036 2855 Dihedral : 8.335 59.661 4574 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1949 helix: 0.17 (0.28), residues: 365 sheet: -1.16 (0.23), residues: 483 loop : -1.37 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 427 HIS 0.006 0.001 HIS G 374 PHE 0.013 0.001 PHE G 288 TYR 0.008 0.001 TYR L 50 ARG 0.008 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.15 seconds wall clock time: 45 minutes 43.18 seconds (2743.18 seconds total)