Starting phenix.real_space_refine on Fri Aug 9 22:24:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlu_37632/08_2024/8wlu_37632.cif" } resolution = 2.87 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= 0.000 sd= 0.003 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 132 5.16 5 C 17355 2.51 5 N 4419 2.21 5 O 5532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 968": "OD1" <-> "OD2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A GLU 1055": "OE1" <-> "OE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "A PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1110": "OD1" <-> "OD2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 561": "OD1" <-> "OD2" Residue "C ASP 565": "OD1" <-> "OD2" Residue "C ASP 573": "OD1" <-> "OD2" Residue "C ASP 644": "OD1" <-> "OD2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 962": "OD1" <-> "OD2" Residue "C ASP 968": "OD1" <-> "OD2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C GLU 973": "OE1" <-> "OE2" Residue "C GLU 1075": "OE1" <-> "OE2" Residue "C PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "B PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 555": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B ASP 650": "OD1" <-> "OD2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B ASP 826": "OD1" <-> "OD2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1110": "OD1" <-> "OD2" Residue "B TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27438 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "C" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "B" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8604 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 58, 'TRANS': 1047} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: "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: 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: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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 Time building chain proxies: 14.59, per 1000 atoms: 0.53 Number of scatterers: 27438 At special positions: 0 Unit cell: (141.629, 146.021, 169.077, 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 132 16.00 O 5532 8.00 N 4419 7.00 C 17355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.02 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.04 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.04 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.02 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.02 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 590 " " NAG B1301 " - " ASN B 145 " " NAG B1302 " - " ASN B 590 " " NAG C1301 " - " ASN C 145 " " NAG C1302 " - " ASN C 590 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 110 " " NAG F 1 " - " ASN A 120 " " NAG G 1 " - " ASN A 159 " " NAG H 1 " - " ASN A 228 " " NAG I 1 " - " ASN A 270 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 603 " " NAG L 1 " - " ASN A 700 " " NAG M 1 " - " ASN A 784 " " NAG N 1 " - " ASN A1057 " " NAG O 1 " - " ASN A1081 " " NAG P 1 " - " ASN A1117 " " NAG Q 1 " - " ASN A 692 " " NAG R 1 " - " ASN A 319 " " NAG S 1 " - " ASN A 358 " " NAG T 1 " - " ASN C 66 " " NAG U 1 " - " ASN C 110 " " NAG V 1 " - " ASN C 120 " " NAG W 1 " - " ASN C 159 " " NAG X 1 " - " ASN C 228 " " NAG Y 1 " - " ASN C 270 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 603 " " NAG b 1 " - " ASN C 700 " " NAG c 1 " - " ASN C 784 " " NAG d 1 " - " ASN C1057 " " NAG e 1 " - " ASN C1081 " " NAG f 1 " - " ASN C1117 " " NAG g 1 " - " ASN C 692 " " NAG h 1 " - " ASN C 319 " " NAG i 1 " - " ASN C 358 " " NAG j 1 " - " ASN B 66 " " NAG k 1 " - " ASN B 110 " " NAG l 1 " - " ASN B 120 " " NAG m 1 " - " ASN B 159 " " NAG n 1 " - " ASN B 228 " " NAG o 1 " - " ASN B 270 " " NAG p 1 " - " ASN B 331 " " NAG q 1 " - " ASN B 603 " " NAG r 1 " - " ASN B 700 " " NAG s 1 " - " ASN B 784 " " NAG t 1 " - " ASN B1057 " " NAG u 1 " - " ASN B1081 " " NAG v 1 " - " ASN B1117 " " NAG w 1 " - " ASN B 692 " " NAG x 1 " - " ASN B 319 " " NAG y 1 " - " ASN B 358 " Time building additional restraints: 12.32 Conformation dependent library (CDL) restraints added in 4.7 seconds 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6216 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 48 sheets defined 25.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.653A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.693A pdb=" N ASN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.477A pdb=" N ARG A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.828A pdb=" N TYR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 729 through 740 removed outlier: 3.504A pdb=" N GLY A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.674A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.987A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 Processing helix chain 'A' and resid 928 through 948 Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.721A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.514A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 removed outlier: 4.781A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.399A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 617 through 625 removed outlier: 3.905A pdb=" N TYR C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 729 through 740 removed outlier: 3.531A pdb=" N GLY C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.638A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 839 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 893 Processing helix chain 'C' and resid 895 through 902 removed outlier: 3.982A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 Processing helix chain 'C' and resid 949 through 951 No H-bonds generated for 'chain 'C' and resid 949 through 951' Processing helix chain 'C' and resid 959 through 967 removed outlier: 3.667A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1015 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.541A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 removed outlier: 4.689A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.383A pdb=" N ARG B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.848A pdb=" N TYR B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.583A pdb=" N GLY B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 766 Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.653A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 893 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.000A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 948 Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 959 through 967 removed outlier: 3.650A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.746A pdb=" N SER A 65 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 252 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 181 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 60 removed outlier: 7.874A pdb=" N THR A 262 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 278 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET A 264 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 276 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 266 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.537A pdb=" N PHE A 139 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 140 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.416A pdb=" N GLY A 101 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 237 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 99 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 162 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN A 130 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS A 160 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLU A 132 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N PHE A 158 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.439A pdb=" N VAL A 582 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 316 removed outlier: 5.229A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.972A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.544A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.174A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.777A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.339A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA A1038 " --> pdb=" O GLY A1042 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1044 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A1046 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A1034 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1048 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.339A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A1059 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.382A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.584A pdb=" N SER C 686 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB8, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 4.295A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.736A pdb=" N SER C 65 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 252 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 52 through 60 removed outlier: 7.843A pdb=" N THR C 262 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP C 278 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET C 264 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 276 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS C 266 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.405A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 147 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.417A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR C 237 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 99 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C 119 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 299 through 303 removed outlier: 4.129A pdb=" N VAL C 582 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 313 through 316 removed outlier: 5.252A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.967A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.519A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AC9, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.180A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.316A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY C1042 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA C1038 " --> pdb=" O GLY C1042 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1044 " --> pdb=" O PRO C1036 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C1046 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C1034 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C1048 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.316A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR C1059 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.379A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 770 through 772 removed outlier: 3.607A pdb=" N SER B 686 " --> pdb=" O MET C 771 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AD6, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.303A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.758A pdb=" N SER B 65 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 252 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 181 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 52 through 60 removed outlier: 7.837A pdb=" N THR B 262 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASP B 278 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 264 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 276 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS B 266 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.502A pdb=" N PHE B 139 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 147 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.361A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 237 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 99 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 119 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 162 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN B 130 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 160 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU B 132 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE B 158 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 299 through 303 removed outlier: 4.436A pdb=" N VAL B 582 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 313 through 316 removed outlier: 5.216A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.964A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 382 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.547A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AE7, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.151A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 695 through 711 removed outlier: 6.623A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA B1038 " --> pdb=" O GLY B1042 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B1044 " --> pdb=" O PRO B1036 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B1046 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B1034 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B1048 " --> pdb=" O LEU B1032 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 695 through 711 removed outlier: 6.623A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B1059 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.439A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AF3, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.306A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3006 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.03 Time building geometry restraints manager: 13.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7455 1.33 - 1.45: 5988 1.45 - 1.58: 14439 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 28056 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C ASN C 722 " pdb=" O ASN C 722 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.49e+00 ... (remaining 28051 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.70: 468 104.70 - 112.04: 14432 112.04 - 119.37: 8714 119.37 - 126.70: 14287 126.70 - 134.03: 298 Bond angle restraints: 38199 Sorted by residual: angle pdb=" N GLY B 727 " pdb=" CA GLY B 727 " pdb=" C GLY B 727 " ideal model delta sigma weight residual 112.73 120.17 -7.44 1.20e+00 6.94e-01 3.85e+01 angle pdb=" N GLY C 727 " pdb=" CA GLY C 727 " pdb=" C GLY C 727 " ideal model delta sigma weight residual 112.73 120.12 -7.39 1.20e+00 6.94e-01 3.79e+01 angle pdb=" N GLY A 740 " pdb=" CA GLY A 740 " pdb=" C GLY A 740 " ideal model delta sigma weight residual 110.63 119.26 -8.63 1.43e+00 4.89e-01 3.64e+01 angle pdb=" N GLY B 740 " pdb=" CA GLY B 740 " pdb=" C GLY B 740 " ideal model delta sigma weight residual 110.63 118.98 -8.35 1.43e+00 4.89e-01 3.41e+01 angle pdb=" N GLY A 727 " pdb=" CA GLY A 727 " pdb=" C GLY A 727 " ideal model delta sigma weight residual 112.73 119.56 -6.83 1.20e+00 6.94e-01 3.23e+01 ... (remaining 38194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 16617 21.62 - 43.25: 1210 43.25 - 64.87: 253 64.87 - 86.49: 132 86.49 - 108.11: 73 Dihedral angle restraints: 18285 sinusoidal: 8619 harmonic: 9666 Sorted by residual: dihedral pdb=" CB CYS C 726 " pdb=" SG CYS C 726 " pdb=" SG CYS C 732 " pdb=" CB CYS C 732 " ideal model delta sinusoidal sigma weight residual -86.00 -27.99 -58.01 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS A 726 " pdb=" SG CYS A 726 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -29.35 -56.65 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS B 726 " pdb=" SG CYS B 726 " pdb=" SG CYS B 732 " pdb=" CB CYS B 732 " ideal model delta sinusoidal sigma weight residual -86.00 -32.17 -53.83 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 18282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4539 0.135 - 0.270: 95 0.270 - 0.404: 16 0.404 - 0.539: 0 0.539 - 0.674: 3 Chirality restraints: 4653 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 145 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 145 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 4650 not shown) Planarity restraints: 4863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 590 " -0.009 2.00e-02 2.50e+03 3.75e-02 1.76e+01 pdb=" CG ASN A 590 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 590 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN A 590 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 590 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" CG ASN A 590 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 590 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 590 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 968 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 969 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 969 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 969 " 0.037 5.00e-02 4.00e+02 ... (remaining 4860 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 89 2.51 - 3.11: 19923 3.11 - 3.71: 40017 3.71 - 4.30: 62404 4.30 - 4.90: 101687 Nonbonded interactions: 224120 Sorted by model distance: nonbonded pdb=" O GLY B 581 " pdb=" NE2 GLN B 600 " model vdw 1.919 3.120 nonbonded pdb=" O ASN B 427 " pdb=" OG SER B 431 " model vdw 2.087 3.040 nonbonded pdb=" O ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.222 3.040 nonbonded pdb=" NZ LYS A 298 " pdb=" OD1 ASP A 650 " model vdw 2.241 3.120 nonbonded pdb=" O3 NAG u 1 " pdb=" N2 NAG u 2 " model vdw 2.253 3.120 ... (remaining 224115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'c' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 76.640 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.260 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.005 0.063 28056 Z= 0.308 Angle : 0.818 8.633 38199 Z= 0.435 Chirality : 0.058 0.674 4653 Planarity : 0.005 0.068 4809 Dihedral : 18.008 108.114 11937 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.22 % Allowed : 17.19 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3312 helix: 1.82 (0.19), residues: 699 sheet: 0.25 (0.19), residues: 708 loop : -0.63 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 869 HIS 0.006 0.002 HIS B1047 PHE 0.017 0.002 PHE A 881 TYR 0.021 0.002 TYR C 368 ARG 0.014 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 57 residues processed: 238 average time/residue: 1.2269 time to fit residues: 348.3849 Evaluate side-chains 229 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1057 ASN Chi-restraints excluded: chain C residue 1098 ILE Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 797 LYS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 600 GLN A 948 GLN C 722 ASN C1089 GLN B 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28056 Z= 0.192 Angle : 0.608 10.142 38199 Z= 0.303 Chirality : 0.049 0.605 4653 Planarity : 0.004 0.065 4809 Dihedral : 12.318 70.679 6151 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.74 % Allowed : 16.04 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3312 helix: 2.21 (0.19), residues: 699 sheet: 0.20 (0.19), residues: 702 loop : -0.66 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 424 HIS 0.003 0.001 HIS A 38 PHE 0.011 0.001 PHE A 881 TYR 0.016 0.001 TYR A1050 ARG 0.006 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 184 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: A 319 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 759 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8251 (ttp80) REVERT: A 788 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 313 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: C 319 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8018 (p0) REVERT: C 723 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8983 (ttt) REVERT: C 1032 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9032 (mt) REVERT: B 416 ASP cc_start: 0.8211 (p0) cc_final: 0.7882 (p0) outliers start: 79 outliers final: 40 residues processed: 246 average time/residue: 1.1942 time to fit residues: 350.2585 Evaluate side-chains 222 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 267 optimal weight: 0.1980 chunk 297 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 302 GLN A 600 GLN A 672 GLN C 148 GLN C 550 GLN C1089 GLN B 196 HIS B 938 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28056 Z= 0.199 Angle : 0.580 10.205 38199 Z= 0.287 Chirality : 0.048 0.512 4653 Planarity : 0.004 0.062 4809 Dihedral : 8.222 59.558 6096 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.61 % Allowed : 15.31 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3312 helix: 2.33 (0.19), residues: 681 sheet: 0.13 (0.18), residues: 738 loop : -0.68 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS A 38 PHE 0.011 0.001 PHE C 90 TYR 0.020 0.001 TYR A1050 ARG 0.004 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 185 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: A 319 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7986 (p0) REVERT: A 759 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8153 (ttp80) REVERT: A 788 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 922 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 930 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: C 313 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: C 319 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8079 (p0) REVERT: C 723 MET cc_start: 0.9317 (mtp) cc_final: 0.9052 (ttt) REVERT: C 817 MET cc_start: 0.5695 (tmm) cc_final: 0.5105 (ppp) REVERT: C 1021 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8962 (mmtp) REVERT: B 172 ASP cc_start: 0.7338 (m-30) cc_final: 0.6209 (p0) REVERT: B 239 PHE cc_start: 0.8425 (m-80) cc_final: 0.8109 (m-80) REVERT: B 416 ASP cc_start: 0.8206 (p0) cc_final: 0.7895 (p0) REVERT: B 922 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8299 (m) REVERT: B 940 GLN cc_start: 0.8490 (tt0) cc_final: 0.8267 (tt0) outliers start: 104 outliers final: 47 residues processed: 259 average time/residue: 1.1902 time to fit residues: 367.7127 Evaluate side-chains 227 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 600 GLN A 985 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 GLN C 985 GLN C1089 GLN B 948 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28056 Z= 0.338 Angle : 0.632 9.812 38199 Z= 0.319 Chirality : 0.050 0.504 4653 Planarity : 0.005 0.068 4809 Dihedral : 7.253 56.296 6090 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.78 % Allowed : 15.38 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3312 helix: 1.86 (0.19), residues: 714 sheet: 0.30 (0.19), residues: 696 loop : -0.82 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.007 0.002 HIS A 38 PHE 0.013 0.002 PHE A 528 TYR 0.019 0.002 TYR A1050 ARG 0.006 0.001 ARG A 888 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 166 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: A 319 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 759 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8196 (ttp80) REVERT: A 922 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8153 (m) REVERT: C 172 ASP cc_start: 0.7113 (m-30) cc_final: 0.6119 (p0) REVERT: C 313 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: C 723 MET cc_start: 0.9331 (mtp) cc_final: 0.9003 (ttt) REVERT: C 904 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (mppt) REVERT: C 971 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: C 1021 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8804 (mppt) REVERT: B 239 PHE cc_start: 0.8569 (m-80) cc_final: 0.8355 (m-80) REVERT: B 416 ASP cc_start: 0.8198 (p0) cc_final: 0.7899 (p0) REVERT: B 600 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 680 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8553 (ptm) REVERT: B 922 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8314 (m) REVERT: B 940 GLN cc_start: 0.8497 (tt0) cc_final: 0.8272 (tt0) REVERT: B 1098 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8515 (mm) outliers start: 109 outliers final: 60 residues processed: 249 average time/residue: 1.2658 time to fit residues: 374.9860 Evaluate side-chains 235 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 164 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 904 LYS Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 971 GLU Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 286 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 600 GLN A 985 GLN C 985 GLN C1089 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28056 Z= 0.218 Angle : 0.565 10.219 38199 Z= 0.284 Chirality : 0.047 0.481 4653 Planarity : 0.004 0.065 4809 Dihedral : 6.617 56.200 6088 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.44 % Allowed : 16.15 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3312 helix: 2.03 (0.19), residues: 699 sheet: 0.21 (0.19), residues: 732 loop : -0.84 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS B 38 PHE 0.010 0.001 PHE C 90 TYR 0.018 0.001 TYR A1050 ARG 0.005 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 172 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 319 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 759 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8161 (ttp80) REVERT: A 788 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8503 (mt) REVERT: A 922 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8109 (m) REVERT: A 930 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8374 (mtpp) REVERT: A 933 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: C 723 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8913 (ttt) REVERT: C 933 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: C 962 ASP cc_start: 0.8620 (m-30) cc_final: 0.8415 (m-30) REVERT: C 1021 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8802 (mppt) REVERT: B 416 ASP cc_start: 0.8188 (p0) cc_final: 0.7915 (p0) REVERT: B 454 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8948 (ptp90) REVERT: B 922 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8273 (m) REVERT: B 940 GLN cc_start: 0.8515 (tt0) cc_final: 0.8286 (tt0) REVERT: B 1098 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8453 (mm) outliers start: 99 outliers final: 56 residues processed: 244 average time/residue: 1.3381 time to fit residues: 387.3617 Evaluate side-chains 234 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 166 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 476 TYR Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 963 ILE Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1110 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1090 ARG Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 187 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN A 985 GLN C 550 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1089 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28056 Z= 0.151 Angle : 0.528 10.069 38199 Z= 0.263 Chirality : 0.046 0.450 4653 Planarity : 0.004 0.062 4809 Dihedral : 6.095 56.930 6087 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.92 % Allowed : 16.67 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3312 helix: 2.31 (0.19), residues: 687 sheet: 0.25 (0.19), residues: 732 loop : -0.70 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.002 0.001 HIS A 38 PHE 0.010 0.001 PHE C 910 TYR 0.018 0.001 TYR A1050 ARG 0.005 0.000 ARG C 759 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 178 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: A 319 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8080 (p0) REVERT: A 759 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8014 (ttp80) REVERT: A 788 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 922 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8166 (m) REVERT: A 930 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: A 933 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: C 99 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 723 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8943 (ttt) REVERT: C 904 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8392 (mppt) REVERT: C 933 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: C 971 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: C 1021 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8823 (mppt) REVERT: B 416 ASP cc_start: 0.8139 (p0) cc_final: 0.7880 (p0) REVERT: B 922 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8214 (m) REVERT: B 940 GLN cc_start: 0.8584 (tt0) cc_final: 0.8321 (tt0) REVERT: B 1098 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (mm) outliers start: 84 outliers final: 47 residues processed: 236 average time/residue: 1.1964 time to fit residues: 339.6744 Evaluate side-chains 232 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 171 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 476 TYR Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 904 LYS Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 971 GLU Chi-restraints excluded: chain C residue 1021 LYS Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1075 GLU Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1098 ILE Chi-restraints excluded: chain B residue 1110 ASP Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 180 optimal weight: 0.0670 chunk 268 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: