Starting phenix.real_space_refine on Fri Aug 9 06:43:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eaz_31047/08_2024/7eaz_31047.cif" } resolution = 3.5 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= -0.001 sd= 0.043 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 105 5.16 5 C 15861 2.51 5 N 4038 2.21 5 O 4952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24956 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7901 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 7 Chain: "B" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7964 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 51, 'TRANS': 968} Chain breaks: 7 Chain: "C" Number of atoms: 7949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7949 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 51, 'TRANS': 966} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 14.69, per 1000 atoms: 0.59 Number of scatterers: 24956 At special positions: 0 Unit cell: (139.7, 143, 194.7, 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 105 16.00 O 4952 8.00 N 4038 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 343 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG B2002 " - " ASN B 122 " " NAG B2004 " - " ASN B 603 " " NAG B2005 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 331 " " NAG b 1 " - " ASN C 343 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 709 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 4.4 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 26.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.548A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.491A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.122A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.554A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.680A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 removed outlier: 4.162A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.360A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.551A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.601A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.861A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.671A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.632A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.644A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.540A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.562A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.756A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.505A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.555A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.561A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.186A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.734A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.825A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.517A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.657A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.744A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.658A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.716A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.799A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.589A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.053A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.331A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.056A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.779A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.792A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.224A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.584A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.797A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.586A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.546A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.554A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.629A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.587A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.163A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.767A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.930A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 4.273A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.269A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.728A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.609A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.448A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.563A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.719A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 328 removed outlier: 4.991A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.825A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.859A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.570A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.775A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 4.054A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.635A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.946A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.569A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.615A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.206A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.549A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2460 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: 12.85 Time building geometry restraints manager: 11.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7850 1.35 - 1.47: 6582 1.47 - 1.59: 10938 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25499 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG C2001 " pdb=" O5 NAG C2001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 ... (remaining 25494 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.96: 771 106.96 - 114.08: 14904 114.08 - 121.20: 11920 121.20 - 128.33: 7006 128.33 - 135.45: 103 Bond angle restraints: 34704 Sorted by residual: angle pdb=" CA GLY A 219 " pdb=" C GLY A 219 " pdb=" N PHE A 220 " ideal model delta sigma weight residual 114.23 117.09 -2.86 8.80e-01 1.29e+00 1.06e+01 angle pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" C LEU A 984 " ideal model delta sigma weight residual 109.18 113.73 -4.55 1.42e+00 4.96e-01 1.03e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.58 -3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 121.53 -7.13 2.30e+00 1.89e-01 9.62e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.33 -3.63 1.22e+00 6.72e-01 8.86e+00 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 15132 23.48 - 46.96: 871 46.96 - 70.44: 130 70.44 - 93.92: 64 93.92 - 117.40: 23 Dihedral angle restraints: 16220 sinusoidal: 7346 harmonic: 8874 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -169.35 83.35 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 175.53 -82.53 1 1.00e+01 1.00e-02 8.35e+01 ... (remaining 16217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4175 0.197 - 0.394: 10 0.394 - 0.591: 2 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 4188 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C1 NAG A2006 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A2006 " pdb=" O5 NAG A2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 4185 not shown) Planarity restraints: 4423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO A 986 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 987 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 97 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS B 97 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS B 97 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 98 " -0.010 2.00e-02 2.50e+03 ... (remaining 4420 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 703 2.70 - 3.25: 24013 3.25 - 3.80: 36379 3.80 - 4.35: 44833 4.35 - 4.90: 76877 Nonbonded interactions: 182805 Sorted by model distance: nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.146 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.203 3.040 ... (remaining 182800 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' and (resid 27 through 1146 or resid 2001 through 2005)) selection = (chain 'B' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) } ncs_group { reference = chain 'D' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 73.130 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.004 0.047 25499 Z= 0.262 Angle : 0.667 10.447 34704 Z= 0.332 Chirality : 0.051 0.985 4188 Planarity : 0.004 0.063 4378 Dihedral : 15.474 117.398 10400 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.15 (0.15), residues: 3003 helix: 1.56 (0.21), residues: 648 sheet: -0.48 (0.20), residues: 674 loop : -1.91 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.003 0.001 HIS C 245 PHE 0.020 0.001 PHE A 823 TYR 0.013 0.001 TYR B1067 ARG 0.011 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.829 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.7917 (mtp) cc_final: 0.7693 (mtp) REVERT: B 190 ARG cc_start: 0.6136 (mtt90) cc_final: 0.5684 (ttt180) REVERT: B 740 MET cc_start: 0.8259 (tpt) cc_final: 0.7956 (tpt) REVERT: C 342 PHE cc_start: 0.6894 (t80) cc_final: 0.6217 (t80) REVERT: C 994 ASP cc_start: 0.7742 (m-30) cc_final: 0.7533 (m-30) REVERT: C 1019 ARG cc_start: 0.8404 (tpt170) cc_final: 0.8183 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3712 time to fit residues: 74.9162 Evaluate side-chains 90 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.5980 chunk 230 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 901 GLN B 919 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25499 Z= 0.200 Angle : 0.628 18.304 34704 Z= 0.305 Chirality : 0.047 0.677 4188 Planarity : 0.004 0.052 4378 Dihedral : 10.678 109.735 4978 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 0.45 % Allowed : 5.74 % Favored : 93.81 % 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: -1.02 (0.15), residues: 3003 helix: 1.59 (0.21), residues: 688 sheet: -0.37 (0.20), residues: 677 loop : -1.90 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.004 0.001 HIS B1064 PHE 0.025 0.001 PHE A 168 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8600 (tm-30) REVERT: B 578 ASP cc_start: 0.8095 (p0) cc_final: 0.7720 (p0) REVERT: B 740 MET cc_start: 0.8229 (tpt) cc_final: 0.7948 (tpt) REVERT: C 342 PHE cc_start: 0.7018 (t80) cc_final: 0.6331 (t80) REVERT: C 994 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) REVERT: C 1019 ARG cc_start: 0.8427 (tpt170) cc_final: 0.8213 (tpp-160) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 0.3248 time to fit residues: 60.9981 Evaluate side-chains 92 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.3980 chunk 85 optimal weight: 0.4980 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25499 Z= 0.158 Angle : 0.585 20.463 34704 Z= 0.282 Chirality : 0.046 0.633 4188 Planarity : 0.004 0.047 4378 Dihedral : 8.951 102.684 4978 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 0.71 % Allowed : 8.44 % Favored : 90.85 % 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: -0.82 (0.15), residues: 3003 helix: 1.80 (0.21), residues: 678 sheet: -0.16 (0.20), residues: 680 loop : -1.83 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.003 0.001 HIS B1064 PHE 0.010 0.001 PHE A 823 TYR 0.015 0.001 TYR B1067 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.8140 (t0) cc_final: 0.7919 (t0) REVERT: A 900 MET cc_start: 0.8010 (mtp) cc_final: 0.7767 (mtp) REVERT: B 552 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8184 (mt) REVERT: B 578 ASP cc_start: 0.8135 (p0) cc_final: 0.7790 (p0) REVERT: B 740 MET cc_start: 0.8150 (tpt) cc_final: 0.7804 (tpt) REVERT: C 338 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8712 (t80) REVERT: C 342 PHE cc_start: 0.7047 (t80) cc_final: 0.6343 (t80) REVERT: C 775 ASP cc_start: 0.8355 (m-30) cc_final: 0.8062 (m-30) REVERT: C 918 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6724 (mp0) outliers start: 19 outliers final: 9 residues processed: 124 average time/residue: 0.3296 time to fit residues: 70.1907 Evaluate side-chains 104 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 131 optimal weight: 0.3980 chunk 185 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 293 optimal weight: 0.0060 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25499 Z= 0.169 Angle : 0.581 21.032 34704 Z= 0.279 Chirality : 0.046 0.627 4188 Planarity : 0.004 0.046 4378 Dihedral : 8.233 95.398 4978 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.05 % Allowed : 10.69 % Favored : 88.26 % 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: -0.73 (0.15), residues: 3003 helix: 1.95 (0.21), residues: 667 sheet: -0.14 (0.20), residues: 691 loop : -1.76 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.003 0.001 HIS A1048 PHE 0.022 0.001 PHE A 238 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8720 (tpp) cc_final: 0.8364 (tpp) REVERT: A 1132 ILE cc_start: 0.8521 (pt) cc_final: 0.8277 (pt) REVERT: B 740 MET cc_start: 0.8171 (tpt) cc_final: 0.7792 (tpt) REVERT: C 342 PHE cc_start: 0.7116 (t80) cc_final: 0.6416 (t80) REVERT: C 918 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6779 (mp0) outliers start: 28 outliers final: 11 residues processed: 128 average time/residue: 0.3062 time to fit residues: 67.6779 Evaluate side-chains 100 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 0.0870 chunk 263 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 414 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25499 Z= 0.252 Angle : 0.613 21.543 34704 Z= 0.297 Chirality : 0.047 0.634 4188 Planarity : 0.004 0.045 4378 Dihedral : 8.092 93.873 4978 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.16 % Allowed : 12.00 % Favored : 86.84 % 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: -0.83 (0.15), residues: 3003 helix: 1.84 (0.21), residues: 677 sheet: -0.24 (0.19), residues: 700 loop : -1.83 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE B 168 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 578 ASP cc_start: 0.8378 (p0) cc_final: 0.7369 (p0) REVERT: B 740 MET cc_start: 0.8193 (tpt) cc_final: 0.7797 (tpt) REVERT: C 342 PHE cc_start: 0.7218 (t80) cc_final: 0.6464 (t80) REVERT: C 918 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6831 (mp0) outliers start: 31 outliers final: 19 residues processed: 122 average time/residue: 0.3171 time to fit residues: 66.0698 Evaluate side-chains 104 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 294 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25499 Z= 0.242 Angle : 0.614 21.884 34704 Z= 0.298 Chirality : 0.047 0.638 4188 Planarity : 0.004 0.043 4378 Dihedral : 7.945 92.522 4978 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 1.35 % Allowed : 13.05 % Favored : 85.60 % 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: -0.85 (0.15), residues: 3003 helix: 1.86 (0.21), residues: 671 sheet: -0.27 (0.20), residues: 698 loop : -1.84 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.004 0.001 HIS A1048 PHE 0.029 0.001 PHE C 238 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 740 MET cc_start: 0.8231 (tpt) cc_final: 0.7841 (tpt) REVERT: C 342 PHE cc_start: 0.7249 (t80) cc_final: 0.6442 (t80) REVERT: C 918 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6804 (mp0) outliers start: 36 outliers final: 25 residues processed: 118 average time/residue: 0.3259 time to fit residues: 65.6941 Evaluate side-chains 108 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.5980 chunk 33 optimal weight: 40.0000 chunk 167 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 239 GLN C 394 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25499 Z= 0.211 Angle : 0.605 22.070 34704 Z= 0.293 Chirality : 0.046 0.634 4188 Planarity : 0.004 0.044 4378 Dihedral : 7.793 91.427 4978 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 1.46 % Allowed : 13.69 % Favored : 84.85 % 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: -0.82 (0.15), residues: 3003 helix: 1.88 (0.21), residues: 671 sheet: -0.22 (0.20), residues: 692 loop : -1.82 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE C 238 TYR 0.015 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 1029 MET cc_start: 0.8975 (tmm) cc_final: 0.8224 (tmm) REVERT: A 1115 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 408 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: B 740 MET cc_start: 0.8224 (tpt) cc_final: 0.7826 (tpt) REVERT: C 342 PHE cc_start: 0.7280 (t80) cc_final: 0.6462 (t80) REVERT: C 918 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6757 (mp0) outliers start: 39 outliers final: 27 residues processed: 124 average time/residue: 0.3104 time to fit residues: 66.1548 Evaluate side-chains 113 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 199 optimal weight: 0.0030 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25499 Z= 0.241 Angle : 0.619 22.156 34704 Z= 0.300 Chirality : 0.047 0.636 4188 Planarity : 0.004 0.043 4378 Dihedral : 7.719 91.119 4978 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 1.54 % Allowed : 14.17 % Favored : 84.29 % 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: -0.86 (0.15), residues: 3003 helix: 1.80 (0.21), residues: 675 sheet: -0.25 (0.20), residues: 692 loop : -1.84 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 PHE 0.025 0.001 PHE C 238 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 84 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 1029 MET cc_start: 0.8985 (tmm) cc_final: 0.8217 (tmm) REVERT: A 1115 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 740 MET cc_start: 0.8254 (tpt) cc_final: 0.7864 (tpt) REVERT: C 342 PHE cc_start: 0.7296 (t80) cc_final: 0.6439 (t80) REVERT: C 918 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6768 (mp0) outliers start: 41 outliers final: 33 residues processed: 122 average time/residue: 0.3120 time to fit residues: 65.5747 Evaluate side-chains 119 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 256 optimal weight: 0.6980 chunk 273 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25499 Z= 0.172 Angle : 0.606 21.919 34704 Z= 0.292 Chirality : 0.046 0.627 4188 Planarity : 0.004 0.045 4378 Dihedral : 7.546 89.866 4978 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 1.42 % Allowed : 14.59 % Favored : 83.99 % 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: -0.74 (0.15), residues: 3003 helix: 1.90 (0.21), residues: 666 sheet: -0.15 (0.20), residues: 681 loop : -1.74 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.002 0.001 HIS A1048 PHE 0.028 0.001 PHE B 168 TYR 0.015 0.001 TYR C1067 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 1029 MET cc_start: 0.8973 (tmm) cc_final: 0.8261 (tmm) REVERT: A 1115 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 740 MET cc_start: 0.8161 (tpt) cc_final: 0.7767 (tpt) REVERT: C 342 PHE cc_start: 0.7305 (t80) cc_final: 0.6458 (t80) REVERT: C 918 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6672 (mp0) outliers start: 38 outliers final: 30 residues processed: 129 average time/residue: 0.3274 time to fit residues: 72.3553 Evaluate side-chains 121 residues out of total 2667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: