Starting phenix.real_space_refine on Fri Mar 6 04:01:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krq_23010/03_2026/7krq_23010.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 120 5.16 5 C 17643 2.51 5 N 4479 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27819 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "B" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "C" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "V" 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: "W" 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: "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: 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: "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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "g" 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: "h" 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: "i" 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: "j" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.29, per 1000 atoms: 0.23 Number of scatterers: 27819 At special positions: 0 Unit cell: (146.85, 149.325, 196.35, 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 120 16.00 O 5577 8.00 N 4479 7.00 C 17643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.28 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.90 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 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=2.72 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.61 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.56 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.38 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.37 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.61 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.58 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.66 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.37 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.54 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.47 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.56 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.62 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.88 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.91 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.59 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.73 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.35 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.44 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.05 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG 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 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 343 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6294 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 51 sheets defined 27.6% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.854A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.962A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.572A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.979A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (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 618 through 624 removed outlier: 3.596A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.849A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.721A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.513A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.779A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 4.202A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.701A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.554A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.719A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.110A 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 removed outlier: 3.716A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 982 removed outlier: 3.524A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.848A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1160 removed outlier: 3.967A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.516A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.876A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.959A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.610A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.504A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.851A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.634A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.497A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.772A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.933A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 847' Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.660A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.532A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.716A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.102A 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: 3.731A 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 982 removed outlier: 3.507A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.850A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 removed outlier: 3.937A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.945A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.601A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.961A 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 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.552A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.849A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (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 removed outlier: 3.772A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.523A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.774A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.630A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.580A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.099A 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: 3.763A 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 982 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.852A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 removed outlier: 3.950A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.258A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.258A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.991A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.772A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.863A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.468A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.763A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.568A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.722A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.217A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.000A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.964A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.821A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.983A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.560A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.248A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.248A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.443A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.961A 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: 12.855A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.424A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.748A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.533A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.728A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.898A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.202A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.959A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.496A 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 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.792A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.415A 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: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A 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: 4.395A 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: 4.534A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.261A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.261A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.464A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.863A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.460A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.688A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.932A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.726A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.856A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.218A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.819A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.952A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3063 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: 6.82 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6187 1.33 - 1.46: 6639 1.46 - 1.58: 15452 1.58 - 1.71: 3 1.71 - 1.83: 150 Bond restraints: 28431 Sorted by residual: bond pdb=" N ILE B 624 " pdb=" CA ILE B 624 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.25e-02 6.40e+03 1.85e+01 bond pdb=" N ILE C 624 " pdb=" CA ILE C 624 " ideal model delta sigma weight residual 1.459 1.512 -0.053 1.25e-02 6.40e+03 1.78e+01 bond pdb=" C4 NAG S 2 " pdb=" O4 NAG S 2 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C4 NAG d 2 " pdb=" O4 NAG d 2 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C4 NAG H 2 " pdb=" O4 NAG H 2 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 28426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 31177 2.29 - 4.57: 6951 4.57 - 6.86: 504 6.86 - 9.15: 41 9.15 - 11.43: 9 Bond angle restraints: 38682 Sorted by residual: angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 112.87 121.88 -9.01 1.20e+00 6.94e-01 5.64e+01 angle pdb=" N ASP A 848 " pdb=" CA ASP A 848 " pdb=" C ASP A 848 " ideal model delta sigma weight residual 107.49 118.92 -11.43 1.74e+00 3.30e-01 4.32e+01 angle pdb=" N ASP B 848 " pdb=" CA ASP B 848 " pdb=" C ASP B 848 " ideal model delta sigma weight residual 107.49 118.90 -11.41 1.74e+00 3.30e-01 4.30e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 112.34 120.77 -8.43 1.30e+00 5.92e-01 4.20e+01 angle pdb=" CA ASP A 586 " pdb=" CB ASP A 586 " pdb=" CG ASP A 586 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.86e+01 ... (remaining 38677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.16: 17408 25.16 - 50.32: 714 50.32 - 75.49: 173 75.49 - 100.65: 35 100.65 - 125.81: 63 Dihedral angle restraints: 18393 sinusoidal: 8601 harmonic: 9792 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 -179.75 -87.25 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.71 -84.71 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -167.46 81.46 1 1.00e+01 1.00e-02 8.17e+01 ... (remaining 18390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 4634 0.271 - 0.542: 53 0.542 - 0.813: 4 0.813 - 1.084: 6 1.084 - 1.355: 7 Chirality restraints: 4704 Sorted by residual: chirality pdb=" C1 MAN U 3 " pdb=" O4 NAG U 2 " pdb=" C2 MAN U 3 " pdb=" O5 MAN U 3 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-02 2.50e+03 5.23e+01 chirality pdb=" C1 MAN R 3 " pdb=" O4 NAG R 2 " pdb=" C2 MAN R 3 " pdb=" O5 MAN R 3 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-02 2.50e+03 4.87e+01 chirality pdb=" C1 MAN G 3 " pdb=" O4 NAG G 2 " pdb=" C2 MAN G 3 " pdb=" O5 MAN G 3 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-02 2.50e+03 4.76e+01 ... (remaining 4701 not shown) Planarity restraints: 4899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " 0.143 2.00e-02 2.50e+03 1.54e-01 2.95e+02 pdb=" CG ASN C 717 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " -0.244 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.133 2.00e-02 2.50e+03 1.47e-01 2.71e+02 pdb=" CG ASN B 717 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.238 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.135 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN C1074 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG h 1 " 0.168 2.00e-02 2.50e+03 ... (remaining 4896 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 53 2.48 - 3.09: 17974 3.09 - 3.69: 39945 3.69 - 4.30: 62848 4.30 - 4.90: 102335 Nonbonded interactions: 223155 Sorted by model distance: nonbonded pdb=" O ILE A 624 " pdb=" N ALA A 626 " model vdw 1.879 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.030 3.120 nonbonded pdb=" O TYR C 756 " pdb=" CD2 PHE C 759 " model vdw 2.032 3.340 nonbonded pdb=" OD1 ASN B 122 " pdb=" O ASN B 125 " model vdw 2.074 3.040 nonbonded pdb=" OD1 ASN C 122 " pdb=" O ASN C 125 " model vdw 2.075 3.040 ... (remaining 223150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' 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 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' 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: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 27.540 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.021 0.884 28587 Z= 1.124 Angle : 2.043 52.203 39105 Z= 1.248 Chirality : 0.116 1.355 4704 Planarity : 0.012 0.134 4845 Dihedral : 16.459 125.810 11964 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.84 % Allowed : 5.90 % Favored : 93.26 % Rotamer: Outliers : 3.18 % Allowed : 4.13 % Favored : 92.69 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.13), residues: 3339 helix: -1.81 (0.15), residues: 723 sheet: 0.43 (0.19), residues: 666 loop : -1.54 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.104 0.019 TYR C 837 PHE 0.096 0.013 PHE A 898 TRP 0.076 0.016 TRP C 886 HIS 0.012 0.004 HIS A1159 Details of bonding type rmsd covalent geometry : bond 0.01353 (28431) covalent geometry : angle 1.78385 (38682) SS BOND : bond 0.39292 ( 45) SS BOND : angle 15.19985 ( 90) hydrogen bonds : bond 0.16604 ( 1095) hydrogen bonds : angle 8.84371 ( 3063) link_ALPHA1-4 : bond 0.02783 ( 21) link_ALPHA1-4 : angle 4.03613 ( 63) link_BETA1-4 : bond 0.00923 ( 33) link_BETA1-4 : angle 1.85781 ( 99) link_BETA1-6 : bond 0.02003 ( 3) link_BETA1-6 : angle 2.75020 ( 9) link_NAG-ASN : bond 0.12531 ( 54) link_NAG-ASN : angle 10.50846 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 591 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 PRO cc_start: 0.7945 (Cg_endo) cc_final: 0.7353 (Cg_exo) REVERT: A 844 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.5232 (mt) REVERT: A 1125 ASN cc_start: 0.7927 (p0) cc_final: 0.7587 (p0) REVERT: B 844 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5320 (tt) REVERT: C 337 PRO cc_start: 0.7879 (Cg_endo) cc_final: 0.7299 (Cg_exo) REVERT: C 402 ILE cc_start: 0.7731 (pt) cc_final: 0.7497 (pt) REVERT: C 775 ASP cc_start: 0.8487 (m-30) cc_final: 0.8255 (m-30) REVERT: C 1125 ASN cc_start: 0.7862 (p0) cc_final: 0.7637 (p0) outliers start: 93 outliers final: 15 residues processed: 668 average time/residue: 0.2059 time to fit residues: 207.7075 Evaluate side-chains 293 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 474 GLN A 784 GLN A 836 GLN A 919 ASN A 954 GLN B 474 GLN B 613 GLN B 762 GLN B 836 GLN B 919 ASN B 954 GLN C 613 GLN C 764 ASN C 907 ASN C 919 ASN C 954 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.114546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079009 restraints weight = 68593.330| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.41 r_work: 0.3084 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28587 Z= 0.166 Angle : 0.818 13.641 39105 Z= 0.401 Chirality : 0.049 0.289 4704 Planarity : 0.005 0.088 4845 Dihedral : 13.441 110.563 5977 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.20 % Favored : 96.56 % Rotamer: Outliers : 2.90 % Allowed : 9.53 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3339 helix: 0.66 (0.19), residues: 735 sheet: 0.18 (0.18), residues: 768 loop : -1.20 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 567 TYR 0.025 0.002 TYR C 636 PHE 0.030 0.002 PHE B 79 TRP 0.022 0.002 TRP B 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00363 (28431) covalent geometry : angle 0.77663 (38682) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.94146 ( 90) hydrogen bonds : bond 0.04660 ( 1095) hydrogen bonds : angle 6.38738 ( 3063) link_ALPHA1-4 : bond 0.01392 ( 21) link_ALPHA1-4 : angle 2.79216 ( 63) link_BETA1-4 : bond 0.00479 ( 33) link_BETA1-4 : angle 1.80030 ( 99) link_BETA1-6 : bond 0.01562 ( 3) link_BETA1-6 : angle 2.01839 ( 9) link_NAG-ASN : bond 0.00585 ( 54) link_NAG-ASN : angle 3.19318 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 308 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7396 (mtm) cc_final: 0.7099 (pmm) REVERT: A 177 MET cc_start: 0.6948 (ppp) cc_final: 0.6120 (ptm) REVERT: A 205 SER cc_start: 0.8931 (p) cc_final: 0.8700 (t) REVERT: A 229 LEU cc_start: 0.8824 (mt) cc_final: 0.8430 (mp) REVERT: A 740 MET cc_start: 0.9224 (tpp) cc_final: 0.8992 (tpp) REVERT: B 21 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6720 (ttm-80) REVERT: B 133 PHE cc_start: 0.8327 (m-80) cc_final: 0.8012 (m-80) REVERT: B 153 MET cc_start: 0.7534 (mtm) cc_final: 0.7297 (pmm) REVERT: B 205 SER cc_start: 0.8923 (p) cc_final: 0.8693 (t) REVERT: B 229 LEU cc_start: 0.8796 (mt) cc_final: 0.8385 (mp) REVERT: B 351 TYR cc_start: 0.8421 (p90) cc_final: 0.8084 (p90) REVERT: B 740 MET cc_start: 0.9206 (tpp) cc_final: 0.8948 (tpp) REVERT: B 849 LEU cc_start: 0.8719 (mm) cc_final: 0.8428 (mm) REVERT: C 168 PHE cc_start: 0.7846 (t80) cc_final: 0.7458 (t80) REVERT: C 205 SER cc_start: 0.8968 (p) cc_final: 0.8556 (t) REVERT: C 351 TYR cc_start: 0.8418 (p90) cc_final: 0.8045 (p90) REVERT: C 402 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (pt) REVERT: C 751 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8730 (t0) REVERT: C 979 ASP cc_start: 0.8785 (m-30) cc_final: 0.8530 (t0) outliers start: 85 outliers final: 32 residues processed: 365 average time/residue: 0.1529 time to fit residues: 94.9577 Evaluate side-chains 256 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 272 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 314 GLN B 207 HIS B 580 GLN C 17 ASN C 314 GLN C 580 GLN C 613 GLN C 764 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.105644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068260 restraints weight = 68900.694| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.36 r_work: 0.2855 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.139 28587 Z= 0.394 Angle : 0.878 9.416 39105 Z= 0.431 Chirality : 0.052 0.248 4704 Planarity : 0.005 0.084 4845 Dihedral : 12.564 112.383 5958 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.85 % Favored : 94.94 % Rotamer: Outliers : 3.04 % Allowed : 12.30 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3339 helix: 0.54 (0.18), residues: 783 sheet: 0.02 (0.17), residues: 795 loop : -1.27 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1107 TYR 0.054 0.003 TYR B 636 PHE 0.031 0.002 PHE B 79 TRP 0.034 0.003 TRP B 633 HIS 0.011 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00907 (28431) covalent geometry : angle 0.84960 (38682) SS BOND : bond 0.00564 ( 45) SS BOND : angle 1.80237 ( 90) hydrogen bonds : bond 0.05241 ( 1095) hydrogen bonds : angle 6.21843 ( 3063) link_ALPHA1-4 : bond 0.01737 ( 21) link_ALPHA1-4 : angle 2.82657 ( 63) link_BETA1-4 : bond 0.00411 ( 33) link_BETA1-4 : angle 1.48557 ( 99) link_BETA1-6 : bond 0.01439 ( 3) link_BETA1-6 : angle 2.31921 ( 9) link_NAG-ASN : bond 0.00592 ( 54) link_NAG-ASN : angle 2.69289 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 228 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7565 (t0) cc_final: 0.7304 (p0) REVERT: A 177 MET cc_start: 0.7278 (ppp) cc_final: 0.6501 (ptm) REVERT: A 191 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8100 (tt0) REVERT: A 205 SER cc_start: 0.9100 (p) cc_final: 0.8829 (t) REVERT: A 239 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8166 (mm-40) REVERT: A 314 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: A 402 ILE cc_start: 0.8710 (tp) cc_final: 0.8429 (tp) REVERT: A 633 TRP cc_start: 0.8298 (p-90) cc_final: 0.7640 (p-90) REVERT: A 636 TYR cc_start: 0.7072 (m-80) cc_final: 0.6861 (m-80) REVERT: A 740 MET cc_start: 0.9249 (tpp) cc_final: 0.9033 (tpp) REVERT: A 918 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: B 21 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7059 (ttm-80) REVERT: B 133 PHE cc_start: 0.8378 (m-80) cc_final: 0.8166 (m-80) REVERT: B 153 MET cc_start: 0.7594 (mtm) cc_final: 0.7269 (pmm) REVERT: B 191 GLU cc_start: 0.8678 (mt-10) cc_final: 0.7912 (tt0) REVERT: B 205 SER cc_start: 0.9058 (p) cc_final: 0.8730 (t) REVERT: B 402 ILE cc_start: 0.8586 (tp) cc_final: 0.8338 (tp) REVERT: B 912 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8849 (p) REVERT: C 168 PHE cc_start: 0.7945 (t80) cc_final: 0.7682 (t80) REVERT: C 191 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8095 (tt0) REVERT: C 481 ASN cc_start: 0.8216 (m-40) cc_final: 0.7637 (t0) REVERT: C 740 MET cc_start: 0.9223 (tpp) cc_final: 0.8929 (ttt) REVERT: C 979 ASP cc_start: 0.8792 (m-30) cc_final: 0.8488 (t0) outliers start: 89 outliers final: 36 residues processed: 295 average time/residue: 0.1514 time to fit residues: 77.2557 Evaluate side-chains 231 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 136 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 277 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 287 optimal weight: 0.2980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 580 GLN B 125 ASN B 211 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.070120 restraints weight = 67700.050| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.36 r_work: 0.2907 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 28587 Z= 0.181 Angle : 0.720 9.776 39105 Z= 0.347 Chirality : 0.046 0.211 4704 Planarity : 0.004 0.083 4845 Dihedral : 11.682 107.625 5953 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.20 % Rotamer: Outliers : 2.66 % Allowed : 13.08 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3339 helix: 1.27 (0.19), residues: 747 sheet: 0.04 (0.17), residues: 765 loop : -1.06 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 158 TYR 0.024 0.002 TYR C1138 PHE 0.026 0.001 PHE B 79 TRP 0.016 0.001 TRP A 633 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00409 (28431) covalent geometry : angle 0.69156 (38682) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.56337 ( 90) hydrogen bonds : bond 0.04237 ( 1095) hydrogen bonds : angle 5.86901 ( 3063) link_ALPHA1-4 : bond 0.01638 ( 21) link_ALPHA1-4 : angle 2.81541 ( 63) link_BETA1-4 : bond 0.00330 ( 33) link_BETA1-4 : angle 1.31378 ( 99) link_BETA1-6 : bond 0.01562 ( 3) link_BETA1-6 : angle 2.49524 ( 9) link_NAG-ASN : bond 0.00358 ( 54) link_NAG-ASN : angle 2.26245 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7420 (t0) cc_final: 0.7201 (p0) REVERT: A 153 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7327 (pmm) REVERT: A 168 PHE cc_start: 0.7975 (t80) cc_final: 0.7771 (t80) REVERT: A 177 MET cc_start: 0.7391 (ppp) cc_final: 0.6558 (ptm) REVERT: A 191 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8118 (tt0) REVERT: A 205 SER cc_start: 0.9020 (p) cc_final: 0.8787 (t) REVERT: A 239 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8198 (mm-40) REVERT: A 314 GLN cc_start: 0.8408 (tp40) cc_final: 0.8142 (tt0) REVERT: A 402 ILE cc_start: 0.8665 (tp) cc_final: 0.8361 (tp) REVERT: A 633 TRP cc_start: 0.8208 (p-90) cc_final: 0.7268 (p-90) REVERT: B 21 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7115 (ttm-80) REVERT: B 102 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7397 (mmm-85) REVERT: B 153 MET cc_start: 0.7597 (mtm) cc_final: 0.7341 (pmm) REVERT: B 191 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7850 (tt0) REVERT: B 402 ILE cc_start: 0.8564 (tp) cc_final: 0.8296 (tp) REVERT: B 820 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8544 (t0) REVERT: B 912 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 979 ASP cc_start: 0.8858 (m-30) cc_final: 0.8461 (t0) REVERT: C 168 PHE cc_start: 0.7955 (t80) cc_final: 0.7590 (t80) REVERT: C 191 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8029 (tt0) REVERT: C 298 GLU cc_start: 0.8764 (tt0) cc_final: 0.8562 (tt0) REVERT: C 481 ASN cc_start: 0.8176 (m-40) cc_final: 0.7591 (t0) REVERT: C 740 MET cc_start: 0.9139 (tpp) cc_final: 0.8832 (ttt) REVERT: C 755 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8265 (mp10) outliers start: 78 outliers final: 47 residues processed: 259 average time/residue: 0.1537 time to fit residues: 69.1195 Evaluate side-chains 243 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 148 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 314 GLN C 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071105 restraints weight = 68329.496| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.41 r_work: 0.2923 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28587 Z= 0.148 Angle : 0.685 9.862 39105 Z= 0.327 Chirality : 0.045 0.228 4704 Planarity : 0.004 0.080 4845 Dihedral : 10.816 105.249 5953 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.17 % Rotamer: Outliers : 2.73 % Allowed : 13.32 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3339 helix: 1.49 (0.19), residues: 750 sheet: 0.17 (0.17), residues: 768 loop : -1.00 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.024 0.001 TYR B 636 PHE 0.025 0.001 PHE B 79 TRP 0.012 0.001 TRP A 633 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00328 (28431) covalent geometry : angle 0.65652 (38682) SS BOND : bond 0.00549 ( 45) SS BOND : angle 1.25594 ( 90) hydrogen bonds : bond 0.03880 ( 1095) hydrogen bonds : angle 5.67502 ( 3063) link_ALPHA1-4 : bond 0.01652 ( 21) link_ALPHA1-4 : angle 3.11011 ( 63) link_BETA1-4 : bond 0.00334 ( 33) link_BETA1-4 : angle 1.15922 ( 99) link_BETA1-6 : bond 0.01778 ( 3) link_BETA1-6 : angle 2.43724 ( 9) link_NAG-ASN : bond 0.00323 ( 54) link_NAG-ASN : angle 2.10673 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8055 (t80) cc_final: 0.7822 (t80) REVERT: A 175 PHE cc_start: 0.8692 (p90) cc_final: 0.8114 (p90) REVERT: A 177 MET cc_start: 0.7400 (ppp) cc_final: 0.6728 (ptp) REVERT: A 191 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8086 (tt0) REVERT: A 205 SER cc_start: 0.8921 (p) cc_final: 0.8700 (t) REVERT: A 239 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8297 (mm-40) REVERT: B 102 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7411 (mmm-85) REVERT: B 191 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7879 (tt0) REVERT: B 402 ILE cc_start: 0.8456 (tp) cc_final: 0.8217 (tp) REVERT: B 820 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8444 (t0) REVERT: B 979 ASP cc_start: 0.8870 (m-30) cc_final: 0.8513 (t0) REVERT: C 178 ASP cc_start: 0.8480 (m-30) cc_final: 0.8143 (p0) REVERT: C 191 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8017 (tt0) REVERT: C 481 ASN cc_start: 0.8181 (m-40) cc_final: 0.7575 (t0) REVERT: C 755 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8244 (mp10) outliers start: 80 outliers final: 48 residues processed: 270 average time/residue: 0.1518 time to fit residues: 70.6003 Evaluate side-chains 243 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 61 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 211 ASN B 314 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068335 restraints weight = 68503.195| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.28 r_work: 0.2842 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 28587 Z= 0.249 Angle : 0.733 9.893 39105 Z= 0.351 Chirality : 0.046 0.204 4704 Planarity : 0.004 0.075 4845 Dihedral : 10.243 106.016 5951 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 3.18 % Allowed : 13.25 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3339 helix: 1.40 (0.19), residues: 753 sheet: 0.01 (0.18), residues: 765 loop : -0.96 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 158 TYR 0.020 0.002 TYR C 904 PHE 0.028 0.002 PHE C 133 TRP 0.010 0.001 TRP A 633 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00571 (28431) covalent geometry : angle 0.70723 (38682) SS BOND : bond 0.00606 ( 45) SS BOND : angle 1.40197 ( 90) hydrogen bonds : bond 0.04297 ( 1095) hydrogen bonds : angle 5.72254 ( 3063) link_ALPHA1-4 : bond 0.01766 ( 21) link_ALPHA1-4 : angle 2.93333 ( 63) link_BETA1-4 : bond 0.00345 ( 33) link_BETA1-4 : angle 1.24333 ( 99) link_BETA1-6 : bond 0.01833 ( 3) link_BETA1-6 : angle 2.44793 ( 9) link_NAG-ASN : bond 0.00383 ( 54) link_NAG-ASN : angle 2.14410 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 197 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8034 (t80) cc_final: 0.7814 (t80) REVERT: A 177 MET cc_start: 0.7590 (ppp) cc_final: 0.6842 (ppp) REVERT: A 239 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: B 102 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7645 (mmm-85) REVERT: B 191 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 314 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: B 850 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8880 (mm) REVERT: C 178 ASP cc_start: 0.8499 (m-30) cc_final: 0.8143 (p0) REVERT: C 191 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8016 (tt0) REVERT: C 481 ASN cc_start: 0.8174 (m-40) cc_final: 0.7575 (t0) REVERT: C 740 MET cc_start: 0.9142 (tpp) cc_final: 0.8896 (ttt) REVERT: C 755 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: C 850 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8904 (mm) outliers start: 93 outliers final: 61 residues processed: 271 average time/residue: 0.1460 time to fit residues: 69.4280 Evaluate side-chains 251 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 318 optimal weight: 1.9990 chunk 269 optimal weight: 0.0770 chunk 257 optimal weight: 0.0170 chunk 274 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 332 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 613 GLN C 115 GLN C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070728 restraints weight = 67833.299| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.28 r_work: 0.2898 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28587 Z= 0.133 Angle : 0.670 10.442 39105 Z= 0.318 Chirality : 0.044 0.249 4704 Planarity : 0.004 0.075 4845 Dihedral : 9.459 103.541 5951 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.29 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 14.17 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3339 helix: 1.68 (0.20), residues: 738 sheet: 0.11 (0.18), residues: 768 loop : -0.89 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 158 TYR 0.019 0.001 TYR C1138 PHE 0.027 0.001 PHE A 133 TRP 0.007 0.001 TRP A 633 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00289 (28431) covalent geometry : angle 0.64514 (38682) SS BOND : bond 0.00342 ( 45) SS BOND : angle 1.12050 ( 90) hydrogen bonds : bond 0.03647 ( 1095) hydrogen bonds : angle 5.50889 ( 3063) link_ALPHA1-4 : bond 0.01787 ( 21) link_ALPHA1-4 : angle 2.99210 ( 63) link_BETA1-4 : bond 0.00368 ( 33) link_BETA1-4 : angle 1.13993 ( 99) link_BETA1-6 : bond 0.01951 ( 3) link_BETA1-6 : angle 2.11153 ( 9) link_NAG-ASN : bond 0.00280 ( 54) link_NAG-ASN : angle 1.89958 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8223 (mt0) cc_final: 0.8008 (mm-40) REVERT: A 175 PHE cc_start: 0.8570 (p90) cc_final: 0.7882 (p90) REVERT: A 191 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8069 (tt0) REVERT: A 239 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8291 (mm-40) REVERT: B 102 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7614 (mmm-85) REVERT: B 158 ARG cc_start: 0.7416 (mmt-90) cc_final: 0.6897 (tpp-160) REVERT: B 191 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 441 LEU cc_start: 0.8725 (mt) cc_final: 0.8376 (tp) REVERT: C 131 CYS cc_start: 0.5062 (OUTLIER) cc_final: 0.4322 (m) REVERT: C 178 ASP cc_start: 0.8458 (m-30) cc_final: 0.8149 (p0) REVERT: C 191 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8017 (tt0) REVERT: C 481 ASN cc_start: 0.8177 (m-40) cc_final: 0.7553 (t0) REVERT: C 740 MET cc_start: 0.9051 (tpp) cc_final: 0.8804 (ttt) REVERT: C 755 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: C 850 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8813 (mm) outliers start: 70 outliers final: 47 residues processed: 263 average time/residue: 0.1474 time to fit residues: 66.7133 Evaluate side-chains 227 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 266 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 300 optimal weight: 0.0040 chunk 16 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 314 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069281 restraints weight = 68757.469| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.31 r_work: 0.2874 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 28587 Z= 0.185 Angle : 0.699 11.503 39105 Z= 0.332 Chirality : 0.045 0.304 4704 Planarity : 0.004 0.072 4845 Dihedral : 8.832 102.780 5951 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Rotamer: Outliers : 2.49 % Allowed : 14.45 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3339 helix: 1.70 (0.19), residues: 741 sheet: 0.09 (0.18), residues: 768 loop : -0.92 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.018 0.001 TYR C 904 PHE 0.021 0.001 PHE C 400 TRP 0.009 0.001 TRP A 633 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00421 (28431) covalent geometry : angle 0.67284 (38682) SS BOND : bond 0.00531 ( 45) SS BOND : angle 1.45474 ( 90) hydrogen bonds : bond 0.03839 ( 1095) hydrogen bonds : angle 5.53868 ( 3063) link_ALPHA1-4 : bond 0.01880 ( 21) link_ALPHA1-4 : angle 3.10074 ( 63) link_BETA1-4 : bond 0.00336 ( 33) link_BETA1-4 : angle 1.14663 ( 99) link_BETA1-6 : bond 0.01888 ( 3) link_BETA1-6 : angle 2.19705 ( 9) link_NAG-ASN : bond 0.00304 ( 54) link_NAG-ASN : angle 1.99228 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 184 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8245 (mt0) cc_final: 0.8018 (mm-40) REVERT: A 153 MET cc_start: 0.7735 (mtm) cc_final: 0.7523 (mpp) REVERT: A 158 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7118 (mmt-90) REVERT: A 177 MET cc_start: 0.7810 (ppp) cc_final: 0.6624 (ptm) REVERT: A 185 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7729 (p0) REVERT: A 239 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: A 441 LEU cc_start: 0.8814 (mt) cc_final: 0.8439 (tp) REVERT: B 102 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7723 (mmm-85) REVERT: B 158 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.6958 (tpp-160) REVERT: B 191 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 314 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: B 441 LEU cc_start: 0.8794 (mt) cc_final: 0.8429 (tp) REVERT: B 850 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 1092 GLU cc_start: 0.8240 (pm20) cc_final: 0.7977 (pm20) REVERT: C 178 ASP cc_start: 0.8478 (m-30) cc_final: 0.8149 (p0) REVERT: C 191 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8003 (tt0) REVERT: C 441 LEU cc_start: 0.8794 (mt) cc_final: 0.8472 (tp) REVERT: C 481 ASN cc_start: 0.8210 (m-40) cc_final: 0.7595 (t0) REVERT: C 740 MET cc_start: 0.9102 (tpp) cc_final: 0.8837 (ttt) REVERT: C 755 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: C 850 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8818 (mm) REVERT: C 1092 GLU cc_start: 0.8101 (pm20) cc_final: 0.7879 (pm20) outliers start: 73 outliers final: 54 residues processed: 245 average time/residue: 0.1448 time to fit residues: 61.5239 Evaluate side-chains 237 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 40 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 147 optimal weight: 0.0670 chunk 76 optimal weight: 0.0270 chunk 287 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.107362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070910 restraints weight = 68488.286| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.32 r_work: 0.2903 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28587 Z= 0.130 Angle : 0.674 10.655 39105 Z= 0.320 Chirality : 0.045 0.391 4704 Planarity : 0.004 0.082 4845 Dihedral : 8.028 100.803 5951 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 1.95 % Allowed : 15.10 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3339 helix: 1.82 (0.19), residues: 741 sheet: 0.09 (0.18), residues: 753 loop : -0.90 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.018 0.001 TYR C1138 PHE 0.030 0.001 PHE B 133 TRP 0.008 0.001 TRP A 633 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00282 (28431) covalent geometry : angle 0.64612 (38682) SS BOND : bond 0.00367 ( 45) SS BOND : angle 1.51225 ( 90) hydrogen bonds : bond 0.03551 ( 1095) hydrogen bonds : angle 5.46293 ( 3063) link_ALPHA1-4 : bond 0.01843 ( 21) link_ALPHA1-4 : angle 3.23547 ( 63) link_BETA1-4 : bond 0.00372 ( 33) link_BETA1-4 : angle 1.13614 ( 99) link_BETA1-6 : bond 0.01978 ( 3) link_BETA1-6 : angle 2.01594 ( 9) link_NAG-ASN : bond 0.00297 ( 54) link_NAG-ASN : angle 1.89204 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7465 (mmt-90) cc_final: 0.6884 (mmm-85) REVERT: A 177 MET cc_start: 0.7722 (ppp) cc_final: 0.6507 (ptm) REVERT: A 185 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7759 (p0) REVERT: A 239 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: A 265 TYR cc_start: 0.7870 (p90) cc_final: 0.7483 (p90) REVERT: A 441 LEU cc_start: 0.8852 (mt) cc_final: 0.8460 (tp) REVERT: A 850 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8820 (mm) REVERT: B 102 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7673 (mmm-85) REVERT: B 158 ARG cc_start: 0.7453 (mmt-90) cc_final: 0.7016 (tpp-160) REVERT: B 191 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 441 LEU cc_start: 0.8815 (mt) cc_final: 0.8441 (tp) REVERT: B 850 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 1092 GLU cc_start: 0.8231 (pm20) cc_final: 0.7975 (pm20) REVERT: C 137 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8327 (m-40) REVERT: C 178 ASP cc_start: 0.8430 (m-30) cc_final: 0.8131 (p0) REVERT: C 191 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8020 (tt0) REVERT: C 298 GLU cc_start: 0.8663 (tt0) cc_final: 0.8326 (mt-10) REVERT: C 441 LEU cc_start: 0.8829 (mt) cc_final: 0.8483 (tp) REVERT: C 481 ASN cc_start: 0.8124 (m-40) cc_final: 0.7492 (t0) REVERT: C 740 MET cc_start: 0.9028 (tpp) cc_final: 0.8768 (ttt) REVERT: C 755 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: C 850 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8758 (mm) REVERT: C 1072 GLU cc_start: 0.8542 (pm20) cc_final: 0.8292 (pm20) REVERT: C 1092 GLU cc_start: 0.8071 (pm20) cc_final: 0.7842 (pm20) outliers start: 57 outliers final: 42 residues processed: 240 average time/residue: 0.1477 time to fit residues: 61.3230 Evaluate side-chains 227 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 331 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 322 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070982 restraints weight = 68362.228| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.29 r_work: 0.2902 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 28587 Z= 0.162 Angle : 0.772 59.199 39105 Z= 0.400 Chirality : 0.045 0.447 4704 Planarity : 0.004 0.085 4845 Dihedral : 8.015 100.771 5951 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.14 % Rotamer: Outliers : 2.19 % Allowed : 15.10 % Favored : 82.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3339 helix: 1.82 (0.19), residues: 741 sheet: 0.10 (0.18), residues: 753 loop : -0.90 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.017 0.001 TYR C1138 PHE 0.021 0.001 PHE C 400 TRP 0.020 0.001 TRP A 633 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00351 (28431) covalent geometry : angle 0.74861 (38682) SS BOND : bond 0.00438 ( 45) SS BOND : angle 1.45090 ( 90) hydrogen bonds : bond 0.03556 ( 1095) hydrogen bonds : angle 5.46295 ( 3063) link_ALPHA1-4 : bond 0.01780 ( 21) link_ALPHA1-4 : angle 3.24300 ( 63) link_BETA1-4 : bond 0.00395 ( 33) link_BETA1-4 : angle 1.15422 ( 99) link_BETA1-6 : bond 0.01910 ( 3) link_BETA1-6 : angle 2.01021 ( 9) link_NAG-ASN : bond 0.00296 ( 54) link_NAG-ASN : angle 1.89283 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7464 (mmt-90) cc_final: 0.6879 (mmm-85) REVERT: A 177 MET cc_start: 0.7717 (ppp) cc_final: 0.6509 (ptm) REVERT: A 185 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 239 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8300 (mm-40) REVERT: A 441 LEU cc_start: 0.8853 (mt) cc_final: 0.8461 (tp) REVERT: B 102 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7679 (mmm-85) REVERT: B 158 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.7017 (tpp-160) REVERT: B 191 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 441 LEU cc_start: 0.8818 (mt) cc_final: 0.8441 (tp) REVERT: B 850 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 1092 GLU cc_start: 0.8212 (pm20) cc_final: 0.7957 (pm20) REVERT: C 178 ASP cc_start: 0.8438 (m-30) cc_final: 0.8133 (p0) REVERT: C 191 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8013 (tt0) REVERT: C 298 GLU cc_start: 0.8667 (tt0) cc_final: 0.8367 (mt-10) REVERT: C 441 LEU cc_start: 0.8842 (mt) cc_final: 0.8495 (tp) REVERT: C 481 ASN cc_start: 0.8126 (m-40) cc_final: 0.7495 (t0) REVERT: C 740 MET cc_start: 0.9032 (tpp) cc_final: 0.8771 (ttt) REVERT: C 755 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: C 850 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8759 (mm) REVERT: C 1072 GLU cc_start: 0.8564 (pm20) cc_final: 0.8310 (pm20) REVERT: C 1092 GLU cc_start: 0.8064 (pm20) cc_final: 0.7834 (pm20) outliers start: 64 outliers final: 54 residues processed: 233 average time/residue: 0.1498 time to fit residues: 60.2699 Evaluate side-chains 235 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 237 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070681 restraints weight = 67784.618| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.27 r_work: 0.2909 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 28587 Z= 0.202 Angle : 0.853 59.199 39105 Z= 0.462 Chirality : 0.049 1.252 4704 Planarity : 0.004 0.086 4845 Dihedral : 8.024 100.780 5951 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 2.19 % Allowed : 15.03 % Favored : 82.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3339 helix: 1.79 (0.19), residues: 741 sheet: 0.11 (0.18), residues: 753 loop : -0.91 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.016 0.001 TYR A1067 PHE 0.021 0.001 PHE C 400 TRP 0.017 0.001 TRP A 633 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00434 (28431) covalent geometry : angle 0.83327 (38682) SS BOND : bond 0.00414 ( 45) SS BOND : angle 1.44475 ( 90) hydrogen bonds : bond 0.03594 ( 1095) hydrogen bonds : angle 5.46197 ( 3063) link_ALPHA1-4 : bond 0.01970 ( 21) link_ALPHA1-4 : angle 3.25191 ( 63) link_BETA1-4 : bond 0.00389 ( 33) link_BETA1-4 : angle 1.14682 ( 99) link_BETA1-6 : bond 0.02072 ( 3) link_BETA1-6 : angle 2.03146 ( 9) link_NAG-ASN : bond 0.00302 ( 54) link_NAG-ASN : angle 1.89080 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6691.16 seconds wall clock time: 115 minutes 24.72 seconds (6924.72 seconds total)