Starting phenix.real_space_refine on Thu Mar 21 07:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq0_32078/03_2024/7vq0_32078.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.067 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 128 5.16 5 C 18712 2.51 5 N 4837 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29517 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8554 Classifications: {'peptide': 1093} Link IDs: {'PTRANS': 54, 'TRANS': 1038} Chain breaks: 6 Chain: "B" Number of atoms: 8524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8524 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 7 Chain: "C" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8540 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 5 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.08, per 1000 atoms: 0.51 Number of scatterers: 29517 At special positions: 0 Unit cell: (147.03, 153.12, 225.33, 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 128 16.00 O 5840 8.00 N 4837 7.00 C 18712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.02 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 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 15 " - pdb=" SG CYS C 136 " 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " 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=2, symmetry=0 Links applied ALPHA1-4 " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " 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 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 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1402 " - " ASN B 122 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C 709 " " NAG C1411 " - " ASN C1158 " " NAG H 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 616 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 616 " " 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 Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 5.6 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 58 sheets defined 23.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.523A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.536A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.559A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.567A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.740A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.567A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.871A pdb=" N ILE A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 835 " --> pdb=" O ALA A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.170A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.691A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.967A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.911A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.866A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.528A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.048A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.255A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.779A 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 619 through 623 removed outlier: 4.074A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.803A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.648A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.017A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.767A pdb=" N THR D 89 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.611A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.848A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 143 removed outlier: 4.906A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.899A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.623A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.693A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.519A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.300A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.257A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.784A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.268A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.915A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.997A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 140 removed outlier: 6.585A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.593A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.615A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.270A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.186A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.598A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.693A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.779A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.097A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.488A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.716A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.647A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.014A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.816A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.277A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.601A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 18 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D 81 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 20 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 77 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 36 through 39 removed outlier: 6.409A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.589A pdb=" N GLN E 5 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 67 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.839A pdb=" N VAL E 12 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 91 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 39 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 50 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 57 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.752A pdb=" N GLN F 5 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 23 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 20 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.892A pdb=" N THR F 110 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR F 92 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 2976 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: 12.50 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9341 1.34 - 1.47: 7674 1.47 - 1.59: 12980 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 30159 Sorted by residual: bond pdb=" C5 MAN O 3 " pdb=" O5 MAN O 3 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C5 MAN P 3 " pdb=" O5 MAN P 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C5 MAN e 3 " pdb=" O5 MAN e 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C5 MAN W 3 " pdb=" O5 MAN W 3 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" C5 MAN f 3 " pdb=" O5 MAN f 3 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 655 106.08 - 113.06: 16684 113.06 - 120.04: 9825 120.04 - 127.02: 13564 127.02 - 134.00: 270 Bond angle restraints: 40998 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.16 -4.46 1.22e+00 6.72e-01 1.33e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 121.64 -3.71 1.20e+00 6.94e-01 9.57e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.19 -3.49 1.22e+00 6.72e-01 8.20e+00 angle pdb=" C ASP E 53 " pdb=" CA ASP E 53 " pdb=" CB ASP E 53 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.79e+00 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 113.53 110.86 2.67 9.80e-01 1.04e+00 7.41e+00 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 17988 24.39 - 48.77: 925 48.77 - 73.16: 119 73.16 - 97.54: 64 97.54 - 121.93: 20 Dihedral angle restraints: 19116 sinusoidal: 8598 harmonic: 10518 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.03 76.03 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.41 -73.59 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.01 71.01 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 19113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4248 0.070 - 0.141: 608 0.141 - 0.211: 7 0.211 - 0.281: 2 0.281 - 0.352: 3 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4865 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 527 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.001 2.00e-02 2.50e+03 2.28e-02 6.52e+00 pdb=" CG ASN A 616 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO A 561 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.025 5.00e-02 4.00e+02 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 636 2.68 - 3.23: 27914 3.23 - 3.79: 45765 3.79 - 4.34: 61508 4.34 - 4.90: 101858 Nonbonded interactions: 237681 Sorted by model distance: nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.124 2.440 nonbonded pdb=" NH2 ARG A 34 " pdb=" OE2 GLU A 191 " model vdw 2.183 2.520 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.192 2.440 nonbonded pdb=" OG1 THR C 470 " pdb=" O TYR F 58 " model vdw 2.200 2.440 nonbonded pdb=" O SER A 937 " pdb=" OG1 THR A 941 " model vdw 2.204 2.440 ... (remaining 237676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 145 or resid 152 through 623 or resid 636 throu \ gh 836 or resid 854 through 1162 or resid 1401 through 1409)) selection = (chain 'B' and (resid 14 through 68 or resid 77 through 836 or resid 854 through \ 1162 or resid 1401 through 1409)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 145 or resid 152 through \ 177 or resid 185 through 1162 or resid 1401 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.540 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 80.420 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 30159 Z= 0.250 Angle : 0.594 8.303 40998 Z= 0.284 Chirality : 0.045 0.352 4868 Planarity : 0.003 0.068 5185 Dihedral : 15.233 121.930 12222 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % 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: -0.40 (0.14), residues: 3576 helix: 1.91 (0.20), residues: 741 sheet: -0.18 (0.19), residues: 752 loop : -1.14 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.006 0.001 HIS A 66 PHE 0.025 0.001 PHE A 168 TYR 0.019 0.001 TYR A 170 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 3.044 Fit side-chains REVERT: B 237 ARG cc_start: 0.7453 (mtp-110) cc_final: 0.7121 (ttp-110) REVERT: B 568 ASP cc_start: 0.7065 (t0) cc_final: 0.6783 (t0) REVERT: B 904 TYR cc_start: 0.7881 (m-10) cc_final: 0.7538 (m-10) REVERT: C 52 GLN cc_start: 0.7740 (pp30) cc_final: 0.7534 (pp30) REVERT: C 586 ASP cc_start: 0.8041 (m-30) cc_final: 0.7775 (m-30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.3984 time to fit residues: 180.8105 Evaluate side-chains 195 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 969 ASN A1010 GLN B 544 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 926 GLN B1106 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 30159 Z= 0.580 Angle : 0.733 10.605 40998 Z= 0.370 Chirality : 0.051 0.269 4868 Planarity : 0.005 0.049 5185 Dihedral : 10.661 108.547 5771 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 0.73 % Allowed : 8.79 % Favored : 90.48 % 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: -0.84 (0.14), residues: 3576 helix: 1.30 (0.19), residues: 742 sheet: -0.24 (0.18), residues: 791 loop : -1.44 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.008 0.002 HIS A1048 PHE 0.025 0.002 PHE C1148 TYR 0.023 0.002 TYR A 453 ARG 0.005 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 3.600 Fit side-chains REVERT: A 335 LEU cc_start: 0.8574 (tp) cc_final: 0.8327 (mm) REVERT: A 960 ASN cc_start: 0.8006 (m-40) cc_final: 0.7797 (t0) REVERT: B 904 TYR cc_start: 0.7952 (m-10) cc_final: 0.7743 (m-10) REVERT: E 81 MET cc_start: 0.0119 (tpt) cc_final: -0.0136 (tpt) outliers start: 23 outliers final: 16 residues processed: 228 average time/residue: 0.3924 time to fit residues: 148.6925 Evaluate side-chains 199 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 291 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN C 762 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30159 Z= 0.233 Angle : 0.568 9.205 40998 Z= 0.283 Chirality : 0.044 0.269 4868 Planarity : 0.004 0.046 5185 Dihedral : 9.514 108.696 5771 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 1.21 % Allowed : 11.69 % Favored : 87.10 % 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: -0.55 (0.14), residues: 3576 helix: 1.81 (0.19), residues: 743 sheet: -0.18 (0.18), residues: 780 loop : -1.32 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.006 0.001 HIS A 66 PHE 0.016 0.001 PHE A 168 TYR 0.020 0.001 TYR A 453 ARG 0.007 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 215 time to evaluate : 3.127 Fit side-chains REVERT: A 335 LEU cc_start: 0.8533 (tp) cc_final: 0.8292 (mm) REVERT: B 568 ASP cc_start: 0.6994 (t0) cc_final: 0.6784 (t0) REVERT: B 726 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 904 TYR cc_start: 0.7966 (m-10) cc_final: 0.7752 (m-10) REVERT: C 220 PHE cc_start: 0.7561 (t80) cc_final: 0.7146 (t80) REVERT: E 81 MET cc_start: 0.0024 (tpt) cc_final: -0.0280 (tpt) outliers start: 38 outliers final: 25 residues processed: 243 average time/residue: 0.3880 time to fit residues: 156.4745 Evaluate side-chains 214 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 0.0070 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 311 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 926 GLN B1106 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30159 Z= 0.223 Angle : 0.559 12.389 40998 Z= 0.275 Chirality : 0.043 0.263 4868 Planarity : 0.003 0.047 5185 Dihedral : 8.844 107.393 5771 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 1.78 % Allowed : 13.34 % Favored : 84.87 % 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: -0.48 (0.14), residues: 3576 helix: 1.94 (0.19), residues: 744 sheet: -0.17 (0.18), residues: 776 loop : -1.28 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.005 0.001 HIS A 66 PHE 0.014 0.001 PHE A 168 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 202 time to evaluate : 3.254 Fit side-chains revert: symmetry clash REVERT: B 237 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7483 (ttt-90) REVERT: B 726 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8566 (mp) REVERT: B 904 TYR cc_start: 0.7987 (m-10) cc_final: 0.7777 (m-10) REVERT: C 118 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7677 (tp) REVERT: C 220 PHE cc_start: 0.7567 (t80) cc_final: 0.7143 (t80) REVERT: E 81 MET cc_start: -0.0065 (tpt) cc_final: -0.0311 (tpt) outliers start: 56 outliers final: 32 residues processed: 244 average time/residue: 0.3740 time to fit residues: 153.7944 Evaluate side-chains 221 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 914 ASN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 30159 Z= 0.534 Angle : 0.696 9.483 40998 Z= 0.348 Chirality : 0.048 0.250 4868 Planarity : 0.004 0.047 5185 Dihedral : 9.184 106.408 5771 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.74 % Allowed : 14.55 % Favored : 82.71 % 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: -0.84 (0.14), residues: 3576 helix: 1.42 (0.19), residues: 739 sheet: -0.31 (0.18), residues: 803 loop : -1.47 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 64 HIS 0.008 0.001 HIS A1048 PHE 0.023 0.002 PHE C1148 TYR 0.021 0.002 TYR B1067 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 202 time to evaluate : 3.130 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 324 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: A 335 LEU cc_start: 0.8569 (tp) cc_final: 0.8336 (mm) REVERT: A 406 GLU cc_start: 0.8444 (mp0) cc_final: 0.8145 (mp0) REVERT: A 515 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6592 (p90) REVERT: A 1004 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 726 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 985 ASP cc_start: 0.7367 (p0) cc_final: 0.6973 (p0) REVERT: C 118 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7711 (tp) REVERT: E 81 MET cc_start: -0.0288 (tpt) cc_final: -0.0545 (tpt) outliers start: 86 outliers final: 61 residues processed: 269 average time/residue: 0.3826 time to fit residues: 172.5462 Evaluate side-chains 254 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 4.9990 chunk 313 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 613 GLN A 914 ASN A1010 GLN B 207 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30159 Z= 0.165 Angle : 0.553 9.189 40998 Z= 0.272 Chirality : 0.043 0.275 4868 Planarity : 0.003 0.049 5185 Dihedral : 8.277 106.246 5771 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 1.91 % Allowed : 16.15 % Favored : 81.94 % 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: -0.51 (0.14), residues: 3576 helix: 1.96 (0.19), residues: 741 sheet: -0.24 (0.18), residues: 762 loop : -1.29 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 64 HIS 0.003 0.001 HIS A 66 PHE 0.022 0.001 PHE B 643 TYR 0.017 0.001 TYR A 453 ARG 0.015 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (mt) REVERT: A 140 PHE cc_start: 0.5765 (p90) cc_final: 0.5512 (p90) REVERT: A 335 LEU cc_start: 0.8538 (tp) cc_final: 0.8303 (mm) REVERT: A 406 GLU cc_start: 0.8491 (mp0) cc_final: 0.8167 (mp0) REVERT: A 509 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6675 (mtt-85) REVERT: A 515 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.6294 (p90) REVERT: B 239 GLN cc_start: 0.7857 (tt0) cc_final: 0.7298 (tt0) REVERT: B 726 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8541 (mp) REVERT: C 118 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7656 (tp) REVERT: C 220 PHE cc_start: 0.7553 (t80) cc_final: 0.7224 (t80) REVERT: C 537 LYS cc_start: 0.8517 (mmpt) cc_final: 0.8292 (mtmm) REVERT: E 81 MET cc_start: -0.0254 (tpt) cc_final: -0.0764 (tpp) outliers start: 60 outliers final: 35 residues processed: 268 average time/residue: 0.3652 time to fit residues: 164.5532 Evaluate side-chains 246 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 293 optimal weight: 0.0060 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 914 ASN A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30159 Z= 0.223 Angle : 0.552 9.240 40998 Z= 0.272 Chirality : 0.043 0.262 4868 Planarity : 0.003 0.049 5185 Dihedral : 7.845 105.432 5771 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 1.97 % Allowed : 17.10 % Favored : 80.92 % 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: -0.47 (0.14), residues: 3576 helix: 1.98 (0.19), residues: 744 sheet: -0.26 (0.18), residues: 771 loop : -1.25 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.001 PHE A 342 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 3.301 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (mt) REVERT: A 140 PHE cc_start: 0.5806 (p90) cc_final: 0.5540 (p90) REVERT: A 324 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 335 LEU cc_start: 0.8538 (tp) cc_final: 0.8299 (mm) REVERT: A 406 GLU cc_start: 0.8548 (mp0) cc_final: 0.8206 (mp0) REVERT: A 509 ARG cc_start: 0.6990 (mtt90) cc_final: 0.6696 (mtt-85) REVERT: A 515 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.6349 (p90) REVERT: B 239 GLN cc_start: 0.7846 (tt0) cc_final: 0.7262 (tt0) REVERT: B 726 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8559 (mp) REVERT: C 118 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7640 (tp) REVERT: C 220 PHE cc_start: 0.7616 (t80) cc_final: 0.7269 (t80) REVERT: C 537 LYS cc_start: 0.8496 (mmpt) cc_final: 0.8277 (mtmm) REVERT: E 81 MET cc_start: -0.0330 (tpt) cc_final: -0.0772 (tpp) outliers start: 62 outliers final: 45 residues processed: 254 average time/residue: 0.3717 time to fit residues: 159.6123 Evaluate side-chains 251 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30159 Z= 0.180 Angle : 0.536 11.963 40998 Z= 0.264 Chirality : 0.043 0.268 4868 Planarity : 0.003 0.049 5185 Dihedral : 7.504 104.589 5771 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Rotamer: Outliers : 1.78 % Allowed : 17.55 % Favored : 80.67 % 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: -0.39 (0.14), residues: 3576 helix: 2.16 (0.19), residues: 733 sheet: -0.25 (0.18), residues: 777 loop : -1.20 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.003 0.000 HIS A 49 PHE 0.020 0.001 PHE B 565 TYR 0.017 0.001 TYR A 423 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 218 time to evaluate : 3.255 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 140 PHE cc_start: 0.5799 (p90) cc_final: 0.5537 (p90) REVERT: A 338 PHE cc_start: 0.8417 (m-10) cc_final: 0.8186 (m-80) REVERT: A 406 GLU cc_start: 0.8559 (mp0) cc_final: 0.8304 (mp0) REVERT: A 509 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6786 (mtt-85) REVERT: A 515 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.6446 (p90) REVERT: B 239 GLN cc_start: 0.7826 (tt0) cc_final: 0.7246 (tt0) REVERT: B 726 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8547 (mp) REVERT: C 118 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7608 (tp) REVERT: C 220 PHE cc_start: 0.7595 (t80) cc_final: 0.7258 (t80) REVERT: D 36 TRP cc_start: 0.2451 (m100) cc_final: 0.2219 (m100) outliers start: 56 outliers final: 45 residues processed: 261 average time/residue: 0.3664 time to fit residues: 160.3750 Evaluate side-chains 250 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 292 optimal weight: 0.0060 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30159 Z= 0.246 Angle : 0.556 11.077 40998 Z= 0.274 Chirality : 0.043 0.260 4868 Planarity : 0.003 0.048 5185 Dihedral : 7.453 104.244 5771 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 1.88 % Allowed : 17.32 % Favored : 80.80 % 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: -0.43 (0.14), residues: 3576 helix: 2.06 (0.19), residues: 739 sheet: -0.19 (0.18), residues: 793 loop : -1.26 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.020 0.001 PHE B 565 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 3.357 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8564 (mt) REVERT: A 140 PHE cc_start: 0.5740 (p90) cc_final: 0.5481 (p90) REVERT: A 324 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 338 PHE cc_start: 0.8456 (m-10) cc_final: 0.8183 (m-80) REVERT: A 406 GLU cc_start: 0.8537 (mp0) cc_final: 0.8311 (mp0) REVERT: A 509 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6759 (mtt-85) REVERT: A 515 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.6399 (p90) REVERT: B 239 GLN cc_start: 0.7827 (tt0) cc_final: 0.7245 (tt0) REVERT: B 726 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 118 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7588 (tp) REVERT: C 220 PHE cc_start: 0.7624 (t80) cc_final: 0.7287 (t80) REVERT: D 36 TRP cc_start: 0.2450 (m100) cc_final: 0.2231 (m100) REVERT: E 81 MET cc_start: -0.0712 (tpp) cc_final: -0.0972 (tpp) outliers start: 59 outliers final: 48 residues processed: 244 average time/residue: 0.3677 time to fit residues: 151.6100 Evaluate side-chains 248 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 2.9990 chunk 341 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 237 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30159 Z= 0.276 Angle : 0.572 10.801 40998 Z= 0.282 Chirality : 0.044 0.260 4868 Planarity : 0.004 0.049 5185 Dihedral : 7.431 103.482 5771 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.06 % Favored : 94.83 % Rotamer: Outliers : 1.75 % Allowed : 17.52 % Favored : 80.73 % 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: -0.49 (0.14), residues: 3576 helix: 1.94 (0.19), residues: 745 sheet: -0.23 (0.18), residues: 809 loop : -1.28 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE B 565 TYR 0.021 0.001 TYR A 423 ARG 0.004 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 202 time to evaluate : 3.476 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 140 PHE cc_start: 0.5723 (p90) cc_final: 0.5462 (p90) REVERT: A 324 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 338 PHE cc_start: 0.8451 (m-10) cc_final: 0.8244 (m-80) REVERT: A 406 GLU cc_start: 0.8522 (mp0) cc_final: 0.8259 (mp0) REVERT: A 509 ARG cc_start: 0.7017 (mtt90) cc_final: 0.6571 (mtt-85) REVERT: A 515 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6416 (p90) REVERT: B 239 GLN cc_start: 0.7805 (tt0) cc_final: 0.7216 (tt0) REVERT: B 326 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7068 (tt) REVERT: B 726 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 118 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7603 (tp) REVERT: C 220 PHE cc_start: 0.7602 (t80) cc_final: 0.7280 (t80) REVERT: D 36 TRP cc_start: 0.2513 (m100) cc_final: 0.2301 (m100) REVERT: E 81 MET cc_start: -0.0773 (tpp) cc_final: -0.1101 (tpp) outliers start: 55 outliers final: 48 residues processed: 242 average time/residue: 0.3720 time to fit residues: 151.6835 Evaluate side-chains 252 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 87 optimal weight: 0.0570 chunk 263 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 286 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 969 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN B 926 GLN C 360 ASN C1010 GLN C1011 GLN D 39 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.207883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136403 restraints weight = 42299.275| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.13 r_work: 0.3493 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30159 Z= 0.130 Angle : 0.519 10.807 40998 Z= 0.256 Chirality : 0.042 0.281 4868 Planarity : 0.003 0.049 5185 Dihedral : 6.811 103.114 5771 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 1.27 % Allowed : 18.06 % Favored : 80.67 % 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: -0.25 (0.14), residues: 3576 helix: 2.23 (0.19), residues: 742 sheet: -0.10 (0.18), residues: 764 loop : -1.13 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.001 PHE B 565 TYR 0.015 0.001 TYR A 453 ARG 0.004 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.24 seconds wall clock time: 115 minutes 11.34 seconds (6911.34 seconds total)