Starting phenix.real_space_refine on Sun Jul 5 01:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.map" model { file = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bfu_7094/07_2026/6bfu_7094.cif" } resolution = 3.5 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= 0.005 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 129 5.16 5 C 15255 2.51 5 N 3864 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "C" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7442 Classifications: {'peptide': 964} Link IDs: {'PTRANS': 34, 'TRANS': 929} Chain breaks: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 chiralities: 8 Time building chain proxies: 5.71, per 1000 atoms: 0.23 Number of scatterers: 24480 At special positions: 0 Unit cell: (122.36, 125.02, 159.6, 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 129 16.00 O 5232 8.00 N 3864 7.00 C 15255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.05 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.01 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.04 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.08 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.01 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.05 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.01 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.04 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.08 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.05 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.01 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.04 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.01 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.04 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.08 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.01 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " " BMA i 3 " - " MAN i 5 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1099 " - " ASN A 99 " " NAG A1162 " - " ASN A 162 " " NAG A1169 " - " ASN A 169 " " NAG A1331 " - " ASN A 331 " " NAG A1505 " - " ASN A 505 " " NAG A1531 " - " ASN A 531 " " NAG A1945 " - " ASN A 945 " " NAG A1970 " - " ASN A 970 " " NAG B1099 " - " ASN B 99 " " NAG B1162 " - " ASN B 162 " " NAG B1169 " - " ASN B 169 " " NAG B1331 " - " ASN B 331 " " NAG B1505 " - " ASN B 505 " " NAG B1531 " - " ASN B 531 " " NAG B1945 " - " ASN B 945 " " NAG B1970 " - " ASN B 970 " " NAG C1099 " - " ASN C 99 " " NAG C1162 " - " ASN C 162 " " NAG C1169 " - " ASN C 169 " " NAG C1331 " - " ASN C 331 " " NAG C1505 " - " ASN C 505 " " NAG C1531 " - " ASN C 531 " " NAG C1945 " - " ASN C 945 " " NAG C1970 " - " ASN C 970 " " NAG D 1 " - " ASN A 74 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN A 251 " " NAG H 1 " - " ASN A 311 " " NAG I 1 " - " ASN A 472 " " NAG J 1 " - " ASN A 494 " " NAG K 1 " - " ASN A 526 " " NAG L 1 " - " ASN A 652 " " NAG M 1 " - " ASN A 661 " " NAG N 1 " - " ASN A 788 " " NAG O 1 " - " ASN A 914 " " NAG P 1 " - " ASN A1003 " " NAG Q 1 " - " ASN B 74 " " NAG R 1 " - " ASN B 184 " " NAG S 1 " - " ASN B 241 " " NAG T 1 " - " ASN B 251 " " NAG U 1 " - " ASN B 311 " " NAG V 1 " - " ASN B 472 " " NAG W 1 " - " ASN B 494 " " NAG X 1 " - " ASN B 526 " " NAG Y 1 " - " ASN B 652 " " NAG Z 1 " - " ASN B 661 " " NAG a 1 " - " ASN B 788 " " NAG b 1 " - " ASN B 914 " " NAG c 1 " - " ASN B1003 " " NAG d 1 " - " ASN C 74 " " NAG e 1 " - " ASN C 184 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 251 " " NAG h 1 " - " ASN C 311 " " NAG i 1 " - " ASN C 472 " " NAG j 1 " - " ASN C 494 " " NAG k 1 " - " ASN C 526 " " NAG l 1 " - " ASN C 652 " " NAG m 1 " - " ASN C 661 " " NAG n 1 " - " ASN C 788 " " NAG o 1 " - " ASN C 914 " " NAG p 1 " - " ASN C1003 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 28.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 901 removed outlier: 3.721A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.039A pdb=" N THR B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.808A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 706 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 901 removed outlier: 3.719A pdb=" N GLN B 860 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.560A pdb=" N VAL C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 504 through 508 removed outlier: 4.040A pdb=" N THR C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.806A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 695 through 701 Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 901 removed outlier: 3.720A pdb=" N GLN C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1012 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 3.542A pdb=" N LEU A 89 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN A 241 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 91 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 239 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 7.375A pdb=" N ASP A 244 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR A 259 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 246 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 257 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 248 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR A 183 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.595A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN A 293 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 4.692A pdb=" N SER A 373 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 409 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 377 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 407 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 379 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 405 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR A 924 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 930 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET A 932 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 920 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 934 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN A 592 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB8, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 91 removed outlier: 3.543A pdb=" N LEU B 89 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 241 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 91 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 239 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP B 244 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 259 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 246 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 257 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 248 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.532A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 183 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 293 through 297 removed outlier: 3.658A pdb=" N GLN B 293 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER B 373 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 409 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 377 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 407 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU B 379 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 405 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AC9, first strand: chain 'B' and resid 353 through 358 removed outlier: 7.246A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 587 removed outlier: 6.944A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY B 928 " --> pdb=" O THR B 924 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 924 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 930 " --> pdb=" O THR B 922 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 922 " --> pdb=" O PHE B 930 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET B 932 " --> pdb=" O SER B 920 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 920 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 934 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 592 through 595 removed outlier: 4.172A pdb=" N GLN B 592 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 643 through 644 removed outlier: 5.865A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AD6, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 91 removed outlier: 3.541A pdb=" N LEU C 89 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN C 241 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 91 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 239 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 95 through 96 removed outlier: 7.377A pdb=" N ASP C 244 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 259 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 246 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 257 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C 248 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.531A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR C 183 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.594A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 293 through 297 removed outlier: 3.659A pdb=" N GLN C 293 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 349 through 350 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.494A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 333 through 335 removed outlier: 4.691A pdb=" N SER C 373 " --> pdb=" O GLY C 411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 409 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 377 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C 407 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU C 379 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 405 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AE7, first strand: chain 'C' and resid 353 through 358 removed outlier: 7.247A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AE9, first strand: chain 'C' and resid 571 through 587 removed outlier: 6.946A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 928 " --> pdb=" O THR C 924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR C 924 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 930 " --> pdb=" O THR C 922 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR C 922 " --> pdb=" O PHE C 930 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 932 " --> pdb=" O SER C 920 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 920 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA C 934 " --> pdb=" O ILE C 918 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 592 through 595 removed outlier: 4.173A pdb=" N GLN C 592 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 991 through 994 Processing sheet with id=AF3, first strand: chain 'C' and resid 964 through 969 1078 hydrogen bonds defined for protein. 2874 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: 6.76 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5199 1.32 - 1.45: 6468 1.45 - 1.58: 12897 1.58 - 1.71: 144 1.71 - 1.83: 180 Bond restraints: 24888 Sorted by residual: bond pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 1.474 1.438 0.036 7.40e-03 1.83e+04 2.31e+01 bond pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.26e+01 bond pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta sigma weight residual 1.474 1.439 0.035 7.40e-03 1.83e+04 2.25e+01 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C2 NAG d 2 " pdb=" N2 NAG d 2 " ideal model delta sigma weight residual 1.439 1.353 0.086 2.00e-02 2.50e+03 1.87e+01 ... (remaining 24883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 33225 4.24 - 8.49: 711 8.49 - 12.73: 0 12.73 - 16.98: 0 16.98 - 21.22: 3 Bond angle restraints: 33939 Sorted by residual: angle pdb=" CD1 LEU B 453 " pdb=" CG LEU B 453 " pdb=" CD2 LEU B 453 " ideal model delta sigma weight residual 110.80 132.02 -21.22 2.20e+00 2.07e-01 9.31e+01 angle pdb=" CD1 LEU A 453 " pdb=" CG LEU A 453 " pdb=" CD2 LEU A 453 " ideal model delta sigma weight residual 110.80 131.99 -21.19 2.20e+00 2.07e-01 9.28e+01 angle pdb=" CD1 LEU C 453 " pdb=" CG LEU C 453 " pdb=" CD2 LEU C 453 " ideal model delta sigma weight residual 110.80 131.96 -21.16 2.20e+00 2.07e-01 9.25e+01 angle pdb=" C LYS B 338 " pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta sigma weight residual 119.32 127.75 -8.43 1.14e+00 7.69e-01 5.46e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.32 127.71 -8.39 1.14e+00 7.69e-01 5.42e+01 ... (remaining 33934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13112 17.51 - 35.01: 436 35.01 - 52.51: 108 52.51 - 70.02: 54 70.02 - 87.52: 12 Dihedral angle restraints: 13722 sinusoidal: 5223 harmonic: 8499 Sorted by residual: dihedral pdb=" CB CYS C 433 " pdb=" SG CYS C 433 " pdb=" SG CYS C 484 " pdb=" CB CYS C 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS A 433 " pdb=" SG CYS A 433 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.50 78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 433 " pdb=" SG CYS B 433 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -164.48 78.48 1 1.00e+01 1.00e-02 7.68e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 4244 0.153 - 0.306: 151 0.306 - 0.458: 123 0.458 - 0.611: 45 0.611 - 0.764: 3 Chirality restraints: 4566 Sorted by residual: chirality pdb=" C1 BMA m 3 " pdb=" O4 NAG m 2 " pdb=" C2 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 4563 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.064 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.064 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR B 114 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " -0.064 2.00e-02 2.50e+03 3.40e-02 2.32e+01 pdb=" CG TYR C 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " -0.051 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 90 2.58 - 3.16: 22370 3.16 - 3.74: 36760 3.74 - 4.32: 54914 4.32 - 4.90: 87383 Nonbonded interactions: 201517 Sorted by model distance: nonbonded pdb=" O ASN A 169 " pdb=" OD1 ASN A 169 " model vdw 2.005 3.040 nonbonded pdb=" O ASN B 169 " pdb=" OD1 ASN B 169 " model vdw 2.006 3.040 nonbonded pdb=" O ASN C 169 " pdb=" OD1 ASN C 169 " model vdw 2.007 3.040 nonbonded pdb=" O ASN B 914 " pdb=" OD1 ASN B 914 " model vdw 2.060 3.040 nonbonded pdb=" O ASN A 914 " pdb=" OD1 ASN A 914 " model vdw 2.060 3.040 ... (remaining 201512 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'o' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'T' selection = chain 'c' selection = chain 'g' selection = chain 'p' } ncs_group { reference = chain 'I' selection = chain 'V' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.540 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.019 0.086 25095 Z= 0.974 Angle : 1.413 21.223 34521 Z= 0.815 Chirality : 0.108 0.764 4566 Planarity : 0.006 0.034 4104 Dihedral : 10.659 87.523 8121 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 0.35 % Allowed : 0.94 % Favored : 98.70 % 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: 0.52 (0.16), residues: 2880 helix: 1.17 (0.19), residues: 693 sheet: 0.14 (0.18), residues: 675 loop : 0.18 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.064 0.006 TYR A 114 PHE 0.024 0.004 PHE A 460 TRP 0.008 0.003 TRP C 396 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.01842 / 0.97 (24888) covalent geometry : angle 1.39130 / 0.81 (33939) SS BOND : bond 0.01835 / 1.21 ( 39) SS BOND : angle 3.07283 / 2.25 ( 78) hydrogen bonds : bond 0.16328 / 10.96 ( 991) hydrogen bonds : angle 7.96012 / 5.53 ( 2874) link_ALPHA1-2 : bond 0.04011 / 2.32 ( 9) link_ALPHA1-2 : angle 1.46917 / 0.98 ( 27) link_ALPHA1-3 : bond 0.03458 / 2.17 ( 12) link_ALPHA1-3 : angle 1.20073 / 0.77 ( 36) link_ALPHA1-6 : bond 0.03131 / 1.92 ( 12) link_ALPHA1-6 : angle 2.06955 / 1.33 ( 36) link_BETA1-4 : bond 0.03634 / 2.50 ( 72) link_BETA1-4 : angle 2.65821 / 1.87 ( 216) link_NAG-ASN : bond 0.02263 / 1.55 ( 63) link_NAG-ASN : angle 1.98873 / 1.38 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 529 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: 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: symmetry clash REVERT: A 69 PHE cc_start: 0.7994 (m-80) cc_final: 0.7721 (m-80) REVERT: A 252 THR cc_start: 0.8447 (p) cc_final: 0.8124 (p) REVERT: A 621 ASN cc_start: 0.8192 (m-40) cc_final: 0.7989 (m110) REVERT: A 886 GLN cc_start: 0.8275 (mt0) cc_final: 0.8069 (mt0) REVERT: B 76 THR cc_start: 0.8874 (p) cc_final: 0.8617 (p) REVERT: B 770 VAL cc_start: 0.9263 (m) cc_final: 0.8898 (p) REVERT: C 76 THR cc_start: 0.9135 (p) cc_final: 0.8915 (p) REVERT: C 770 VAL cc_start: 0.9224 (m) cc_final: 0.8985 (p) outliers start: 9 outliers final: 7 residues processed: 538 average time/residue: 0.1764 time to fit residues: 150.0625 Evaluate side-chains 236 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 GLN A 712 GLN A 830 HIS A 895 GLN B 168 HIS B 712 GLN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS B 961 GLN C 168 HIS C 589 GLN C 712 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088340 restraints weight = 42001.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092430 restraints weight = 19379.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094977 restraints weight = 12460.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096490 restraints weight = 9636.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097380 restraints weight = 8298.120| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25095 Z= 0.180 Angle : 0.722 8.427 34521 Z= 0.356 Chirality : 0.045 0.165 4566 Planarity : 0.005 0.084 4104 Dihedral : 5.318 55.455 3131 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.69 % Allowed : 7.60 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.20 (0.16), residues: 2880 helix: 2.68 (0.20), residues: 669 sheet: 0.18 (0.19), residues: 669 loop : 0.33 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 292 TYR 0.012 0.001 TYR B 398 PHE 0.017 0.002 PHE A 930 TRP 0.006 0.001 TRP C 396 HIS 0.009 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (24888) covalent geometry : angle 0.67733 / 0.35 (33939) SS BOND : bond 0.00480 / 0.30 ( 39) SS BOND : angle 0.87665 / 0.60 ( 78) hydrogen bonds : bond 0.05360 / 3.61 ( 991) hydrogen bonds : angle 5.71969 / 3.98 ( 2874) link_ALPHA1-2 : bond 0.00360 / 0.21 ( 9) link_ALPHA1-2 : angle 1.35791 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00711 / 0.44 ( 12) link_ALPHA1-3 : angle 1.22380 / 0.84 ( 36) link_ALPHA1-6 : bond 0.00537 / 0.33 ( 12) link_ALPHA1-6 : angle 1.65666 / 1.15 ( 36) link_BETA1-4 : bond 0.01201 / 0.80 ( 72) link_BETA1-4 : angle 2.74024 / 1.90 ( 216) link_NAG-ASN : bond 0.00280 / 0.18 ( 63) link_NAG-ASN : angle 1.67598 / 1.19 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.922 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: A 69 PHE cc_start: 0.8695 (m-80) cc_final: 0.8265 (m-80) REVERT: A 191 LEU cc_start: 0.9147 (tp) cc_final: 0.8944 (tp) REVERT: A 292 ARG cc_start: 0.7791 (mpt180) cc_final: 0.7251 (mmt-90) REVERT: A 607 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8619 (mpp80) REVERT: A 640 MET cc_start: 0.8846 (ttt) cc_final: 0.8580 (ttt) REVERT: A 884 MET cc_start: 0.8533 (mmt) cc_final: 0.7965 (mmt) REVERT: B 388 MET cc_start: 0.8529 (mtp) cc_final: 0.8299 (mtt) REVERT: B 1011 ASN cc_start: 0.8284 (t0) cc_final: 0.7980 (t0) REVERT: C 372 MET cc_start: 0.8203 (mtm) cc_final: 0.7907 (mtp) REVERT: C 388 MET cc_start: 0.8603 (mtp) cc_final: 0.8213 (mtt) REVERT: C 607 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8474 (mpp80) outliers start: 43 outliers final: 22 residues processed: 313 average time/residue: 0.1625 time to fit residues: 80.9486 Evaluate side-chains 220 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 621 ASN A 772 GLN B 808 ASN ** B 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083805 restraints weight = 42463.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.087687 restraints weight = 19949.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090102 restraints weight = 12988.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091550 restraints weight = 10151.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092403 restraints weight = 8793.770| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25095 Z= 0.244 Angle : 0.739 12.798 34521 Z= 0.354 Chirality : 0.047 0.498 4566 Planarity : 0.005 0.082 4104 Dihedral : 5.021 55.973 3119 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 8.78 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.05 (0.16), residues: 2880 helix: 2.82 (0.20), residues: 672 sheet: -0.02 (0.20), residues: 654 loop : 0.14 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.016 0.001 TYR B 259 PHE 0.020 0.002 PHE B 930 TRP 0.004 0.001 TRP A 396 HIS 0.008 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (24888) covalent geometry : angle 0.69616 / 0.35 (33939) SS BOND : bond 0.00464 / 0.33 ( 39) SS BOND : angle 1.06651 / 0.64 ( 78) hydrogen bonds : bond 0.04812 / 3.27 ( 991) hydrogen bonds : angle 5.32636 / 3.70 ( 2874) link_ALPHA1-2 : bond 0.00347 / 0.20 ( 9) link_ALPHA1-2 : angle 1.33888 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00600 / 0.36 ( 12) link_ALPHA1-3 : angle 1.31480 / 0.93 ( 36) link_ALPHA1-6 : bond 0.00454 / 0.27 ( 12) link_ALPHA1-6 : angle 1.38567 / 0.95 ( 36) link_BETA1-4 : bond 0.01064 / 0.71 ( 72) link_BETA1-4 : angle 2.59267 / 1.79 ( 216) link_NAG-ASN : bond 0.00803 / 0.45 ( 63) link_NAG-ASN : angle 1.88245 / 1.26 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.776 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 191 LEU cc_start: 0.9184 (tp) cc_final: 0.8948 (tp) REVERT: A 292 ARG cc_start: 0.7633 (mpt180) cc_final: 0.7317 (mmt-90) REVERT: A 607 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8653 (mpp80) REVERT: A 701 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8050 (ttp80) REVERT: A 727 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 884 MET cc_start: 0.8781 (mmt) cc_final: 0.8521 (mmt) REVERT: B 191 LEU cc_start: 0.9158 (tp) cc_final: 0.8569 (mp) REVERT: B 607 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8692 (mpp80) REVERT: B 701 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8191 (ttp80) REVERT: B 718 MET cc_start: 0.7404 (ptm) cc_final: 0.7103 (ptp) REVERT: B 1011 ASN cc_start: 0.8429 (t0) cc_final: 0.8104 (t0) REVERT: C 372 MET cc_start: 0.8313 (mtm) cc_final: 0.8027 (mtp) REVERT: C 607 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8224 (mpp80) REVERT: C 701 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8257 (ttp80) outliers start: 60 outliers final: 34 residues processed: 254 average time/residue: 0.1484 time to fit residues: 61.3617 Evaluate side-chains 205 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 842 ILE Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 270 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN A 627 HIS B 823 GLN C 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079323 restraints weight = 43173.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082968 restraints weight = 20855.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085289 restraints weight = 13649.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086707 restraints weight = 10653.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087542 restraints weight = 9207.493| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25095 Z= 0.150 Angle : 0.651 12.245 34521 Z= 0.313 Chirality : 0.044 0.311 4566 Planarity : 0.004 0.084 4104 Dihedral : 4.895 55.696 3119 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.81 % Allowed : 10.23 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.99 (0.16), residues: 2880 helix: 2.64 (0.20), residues: 693 sheet: -0.03 (0.20), residues: 669 loop : 0.13 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 84 TYR 0.010 0.001 TYR C 259 PHE 0.014 0.001 PHE A 930 TRP 0.004 0.001 TRP C 396 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (24888) covalent geometry : angle 0.60906 / 0.30 (33939) SS BOND : bond 0.00317 / 0.22 ( 39) SS BOND : angle 0.82024 / 0.59 ( 78) hydrogen bonds : bond 0.04271 / 2.93 ( 991) hydrogen bonds : angle 5.03009 / 3.50 ( 2874) link_ALPHA1-2 : bond 0.00350 / 0.20 ( 9) link_ALPHA1-2 : angle 1.35901 / 0.95 ( 27) link_ALPHA1-3 : bond 0.00572 / 0.34 ( 12) link_ALPHA1-3 : angle 1.33136 / 0.93 ( 36) link_ALPHA1-6 : bond 0.00492 / 0.30 ( 12) link_ALPHA1-6 : angle 1.34593 / 0.92 ( 36) link_BETA1-4 : bond 0.01070 / 0.72 ( 72) link_BETA1-4 : angle 2.43777 / 1.69 ( 216) link_NAG-ASN : bond 0.00505 / 0.33 ( 63) link_NAG-ASN : angle 1.67625 / 1.13 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9204 (tp) cc_final: 0.8935 (tp) REVERT: A 292 ARG cc_start: 0.7689 (mpt180) cc_final: 0.7383 (mmt-90) REVERT: A 607 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8296 (mpp80) REVERT: A 701 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7883 (ttp80) REVERT: A 703 MET cc_start: 0.9233 (tpp) cc_final: 0.8897 (tpp) REVERT: A 798 ASP cc_start: 0.7867 (t0) cc_final: 0.7663 (t0) REVERT: A 855 GLU cc_start: 0.6933 (mp0) cc_final: 0.6646 (mp0) REVERT: A 1011 ASN cc_start: 0.8432 (t0) cc_final: 0.8104 (t0) REVERT: B 607 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8547 (mpp80) REVERT: B 701 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8101 (ttp80) REVERT: B 718 MET cc_start: 0.7345 (ptm) cc_final: 0.7043 (ptp) REVERT: B 1011 ASN cc_start: 0.8495 (t0) cc_final: 0.8176 (t0) REVERT: C 372 MET cc_start: 0.8296 (mtm) cc_final: 0.8010 (mtp) REVERT: C 607 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8444 (mpp80) REVERT: C 701 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8128 (ttp80) REVERT: C 857 GLU cc_start: 0.8719 (tp30) cc_final: 0.8172 (tp30) REVERT: C 884 MET cc_start: 0.8962 (tpp) cc_final: 0.8667 (mmt) outliers start: 46 outliers final: 28 residues processed: 239 average time/residue: 0.1602 time to fit residues: 62.2161 Evaluate side-chains 202 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 904 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 32 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 185 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN B 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.079169 restraints weight = 43057.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082701 restraints weight = 21304.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084986 restraints weight = 14103.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086365 restraints weight = 11039.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087185 restraints weight = 9584.551| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25095 Z= 0.158 Angle : 0.639 10.631 34521 Z= 0.306 Chirality : 0.044 0.455 4566 Planarity : 0.004 0.085 4104 Dihedral : 4.816 55.899 3119 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.28 % Allowed : 10.59 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.90 (0.16), residues: 2880 helix: 2.55 (0.20), residues: 696 sheet: -0.11 (0.20), residues: 681 loop : 0.08 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 84 TYR 0.011 0.001 TYR A 222 PHE 0.013 0.001 PHE C 930 TRP 0.004 0.001 TRP A 973 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (24888) covalent geometry : angle 0.59615 / 0.30 (33939) SS BOND : bond 0.00310 / 0.21 ( 39) SS BOND : angle 0.84567 / 0.64 ( 78) hydrogen bonds : bond 0.04110 / 2.82 ( 991) hydrogen bonds : angle 4.93282 / 3.43 ( 2874) link_ALPHA1-2 : bond 0.00343 / 0.20 ( 9) link_ALPHA1-2 : angle 1.37300 / 0.96 ( 27) link_ALPHA1-3 : bond 0.00540 / 0.32 ( 12) link_ALPHA1-3 : angle 1.35879 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00476 / 0.29 ( 12) link_ALPHA1-6 : angle 1.34804 / 0.93 ( 36) link_BETA1-4 : bond 0.01069 / 0.72 ( 72) link_BETA1-4 : angle 2.43590 / 1.68 ( 216) link_NAG-ASN : bond 0.00481 / 0.31 ( 63) link_NAG-ASN : angle 1.66781 / 1.09 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9186 (tp) cc_final: 0.8910 (tp) REVERT: A 292 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7163 (mmt-90) REVERT: A 607 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8443 (mpp80) REVERT: A 701 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8021 (ttp80) REVERT: A 703 MET cc_start: 0.9205 (tpp) cc_final: 0.8834 (tpp) REVERT: A 884 MET cc_start: 0.8981 (tpp) cc_final: 0.8639 (mmt) REVERT: A 1011 ASN cc_start: 0.8394 (t0) cc_final: 0.8155 (t0) REVERT: B 191 LEU cc_start: 0.9176 (tp) cc_final: 0.8769 (mp) REVERT: B 607 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8821 (mmm-85) REVERT: B 701 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8177 (ttp80) REVERT: B 718 MET cc_start: 0.7220 (ptm) cc_final: 0.6922 (ptp) REVERT: B 884 MET cc_start: 0.8767 (mmp) cc_final: 0.8523 (tpt) REVERT: B 1011 ASN cc_start: 0.8465 (t0) cc_final: 0.8166 (t0) REVERT: C 372 MET cc_start: 0.8289 (mtm) cc_final: 0.8019 (mtp) REVERT: C 607 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8506 (mpp80) REVERT: C 622 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 701 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8236 (ttp80) REVERT: C 854 GLU cc_start: 0.7408 (pm20) cc_final: 0.7051 (pm20) REVERT: C 857 GLU cc_start: 0.8613 (tp30) cc_final: 0.8338 (tp30) REVERT: C 884 MET cc_start: 0.8994 (tpp) cc_final: 0.8703 (mmt) outliers start: 58 outliers final: 41 residues processed: 232 average time/residue: 0.1501 time to fit residues: 57.2348 Evaluate side-chains 205 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 40 optimal weight: 0.0870 chunk 269 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN B 627 HIS C 847 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078920 restraints weight = 43355.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082581 restraints weight = 20824.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084922 restraints weight = 13561.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086350 restraints weight = 10559.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087179 restraints weight = 9117.493| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25095 Z= 0.148 Angle : 0.625 10.539 34521 Z= 0.298 Chirality : 0.044 0.349 4566 Planarity : 0.004 0.083 4104 Dihedral : 4.761 55.919 3119 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 11.33 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.87 (0.16), residues: 2880 helix: 2.56 (0.20), residues: 696 sheet: -0.16 (0.21), residues: 636 loop : 0.05 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.011 0.001 TYR A 222 PHE 0.012 0.001 PHE C 206 TRP 0.004 0.001 TRP C 973 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (24888) covalent geometry : angle 0.58291 / 0.29 (33939) SS BOND : bond 0.00287 / 0.20 ( 39) SS BOND : angle 0.77102 / 0.59 ( 78) hydrogen bonds : bond 0.03958 / 2.72 ( 991) hydrogen bonds : angle 4.84316 / 3.37 ( 2874) link_ALPHA1-2 : bond 0.00349 / 0.20 ( 9) link_ALPHA1-2 : angle 1.36813 / 0.96 ( 27) link_ALPHA1-3 : bond 0.00533 / 0.32 ( 12) link_ALPHA1-3 : angle 1.35788 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00489 / 0.30 ( 12) link_ALPHA1-6 : angle 1.33465 / 0.92 ( 36) link_BETA1-4 : bond 0.01052 / 0.71 ( 72) link_BETA1-4 : angle 2.39716 / 1.65 ( 216) link_NAG-ASN : bond 0.00463 / 0.31 ( 63) link_NAG-ASN : angle 1.59838 / 1.10 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9167 (tp) cc_final: 0.8830 (tp) REVERT: A 292 ARG cc_start: 0.7739 (mpt180) cc_final: 0.7289 (mmt-90) REVERT: A 293 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: A 701 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7943 (ttp80) REVERT: A 703 MET cc_start: 0.9236 (tpp) cc_final: 0.8830 (tpp) REVERT: A 884 MET cc_start: 0.8988 (tpp) cc_final: 0.8644 (mmt) REVERT: B 607 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8808 (mmm-85) REVERT: B 701 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8115 (ttp80) REVERT: B 718 MET cc_start: 0.7215 (ptm) cc_final: 0.6908 (ptp) REVERT: B 780 GLU cc_start: 0.7886 (tp30) cc_final: 0.7204 (tp30) REVERT: B 987 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7939 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8547 (t0) cc_final: 0.8252 (t0) REVERT: C 59 PRO cc_start: 0.8199 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: C 372 MET cc_start: 0.8281 (mtm) cc_final: 0.8002 (mtp) REVERT: C 461 THR cc_start: 0.8904 (p) cc_final: 0.8702 (t) REVERT: C 607 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8640 (mpp80) REVERT: C 622 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8794 (mp) REVERT: C 701 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8226 (ttp80) REVERT: C 854 GLU cc_start: 0.7160 (pm20) cc_final: 0.6866 (pm20) REVERT: C 857 GLU cc_start: 0.8586 (tp30) cc_final: 0.8226 (tp30) REVERT: C 884 MET cc_start: 0.9006 (tpp) cc_final: 0.8701 (mmt) outliers start: 56 outliers final: 41 residues processed: 239 average time/residue: 0.1624 time to fit residues: 63.0291 Evaluate side-chains 209 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN A 824 GLN A1011 ASN B 823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.078744 restraints weight = 43178.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082248 restraints weight = 21396.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084442 restraints weight = 14169.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085826 restraints weight = 11175.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086630 restraints weight = 9681.147| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25095 Z= 0.165 Angle : 0.626 9.185 34521 Z= 0.301 Chirality : 0.044 0.323 4566 Planarity : 0.004 0.074 4104 Dihedral : 4.777 56.151 3119 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.36 % Allowed : 11.65 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.82 (0.16), residues: 2880 helix: 2.52 (0.20), residues: 693 sheet: -0.16 (0.20), residues: 636 loop : 0.02 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 943 TYR 0.011 0.001 TYR A 222 PHE 0.012 0.001 PHE C 930 TRP 0.006 0.001 TRP A 973 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (24888) covalent geometry : angle 0.58547 / 0.29 (33939) SS BOND : bond 0.00293 / 0.22 ( 39) SS BOND : angle 0.78858 / 0.60 ( 78) hydrogen bonds : bond 0.03946 / 2.70 ( 991) hydrogen bonds : angle 4.82137 / 3.35 ( 2874) link_ALPHA1-2 : bond 0.00351 / 0.20 ( 9) link_ALPHA1-2 : angle 1.36875 / 0.96 ( 27) link_ALPHA1-3 : bond 0.00508 / 0.30 ( 12) link_ALPHA1-3 : angle 1.38905 / 0.97 ( 36) link_ALPHA1-6 : bond 0.00464 / 0.28 ( 12) link_ALPHA1-6 : angle 1.35220 / 0.93 ( 36) link_BETA1-4 : bond 0.01020 / 0.69 ( 72) link_BETA1-4 : angle 2.40215 / 1.65 ( 216) link_NAG-ASN : bond 0.00454 / 0.30 ( 63) link_NAG-ASN : angle 1.51322 / 1.05 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9170 (tp) cc_final: 0.8863 (tp) REVERT: A 292 ARG cc_start: 0.7777 (mpt180) cc_final: 0.7280 (mmt-90) REVERT: A 316 MET cc_start: 0.8598 (mmm) cc_final: 0.8332 (mmm) REVERT: A 607 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8699 (mpp80) REVERT: A 701 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7966 (ttp80) REVERT: A 703 MET cc_start: 0.9179 (tpp) cc_final: 0.8735 (tpp) REVERT: A 936 LEU cc_start: 0.8774 (tt) cc_final: 0.8378 (mt) REVERT: B 104 MET cc_start: 0.8307 (mtm) cc_final: 0.7894 (mtt) REVERT: B 191 LEU cc_start: 0.9136 (tp) cc_final: 0.8862 (mp) REVERT: B 607 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8825 (mmm-85) REVERT: B 701 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8067 (ttp80) REVERT: B 718 MET cc_start: 0.7281 (ptm) cc_final: 0.6966 (ptp) REVERT: B 780 GLU cc_start: 0.7842 (tp30) cc_final: 0.7222 (tp30) REVERT: B 936 LEU cc_start: 0.9108 (tp) cc_final: 0.8881 (mt) REVERT: B 987 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8017 (ptm-80) REVERT: B 1011 ASN cc_start: 0.8514 (t0) cc_final: 0.8245 (t0) REVERT: C 372 MET cc_start: 0.8299 (mtm) cc_final: 0.7899 (mtp) REVERT: C 607 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8632 (mpp80) REVERT: C 622 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (mp) REVERT: C 701 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8262 (ttp80) REVERT: C 854 GLU cc_start: 0.7115 (pm20) cc_final: 0.6794 (pm20) REVERT: C 884 MET cc_start: 0.9016 (tpp) cc_final: 0.8705 (mmt) outliers start: 60 outliers final: 42 residues processed: 221 average time/residue: 0.1516 time to fit residues: 54.0933 Evaluate side-chains 208 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 202 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 263 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 225 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 ASN B 823 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.079437 restraints weight = 43204.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083006 restraints weight = 20535.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085321 restraints weight = 13316.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086739 restraints weight = 10335.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087492 restraints weight = 8908.136| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25095 Z= 0.136 Angle : 0.607 11.305 34521 Z= 0.292 Chirality : 0.043 0.270 4566 Planarity : 0.004 0.069 4104 Dihedral : 4.710 55.989 3119 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.09 % Allowed : 12.12 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.80 (0.16), residues: 2880 helix: 2.41 (0.20), residues: 711 sheet: -0.14 (0.21), residues: 627 loop : -0.01 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.010 0.001 TYR A 222 PHE 0.012 0.001 PHE C 206 TRP 0.005 0.001 TRP A 973 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24888) covalent geometry : angle 0.56717 / 0.28 (33939) SS BOND : bond 0.00280 / 0.19 ( 39) SS BOND : angle 0.79213 / 0.60 ( 78) hydrogen bonds : bond 0.03787 / 2.60 ( 991) hydrogen bonds : angle 4.75398 / 3.31 ( 2874) link_ALPHA1-2 : bond 0.00364 / 0.21 ( 9) link_ALPHA1-2 : angle 1.36440 / 0.96 ( 27) link_ALPHA1-3 : bond 0.00532 / 0.32 ( 12) link_ALPHA1-3 : angle 1.35816 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00511 / 0.31 ( 12) link_ALPHA1-6 : angle 1.31531 / 0.90 ( 36) link_BETA1-4 : bond 0.01040 / 0.70 ( 72) link_BETA1-4 : angle 2.34911 / 1.62 ( 216) link_NAG-ASN : bond 0.00352 / 0.23 ( 63) link_NAG-ASN : angle 1.40791 / 0.98 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.9138 (tp) cc_final: 0.8813 (tp) REVERT: A 292 ARG cc_start: 0.7871 (mpt180) cc_final: 0.7568 (mmt-90) REVERT: A 607 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8722 (mpp80) REVERT: A 701 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8072 (ttp80) REVERT: A 703 MET cc_start: 0.9205 (tpp) cc_final: 0.8727 (tpp) REVERT: A 884 MET cc_start: 0.9093 (tpp) cc_final: 0.8711 (mmt) REVERT: A 936 LEU cc_start: 0.8679 (tt) cc_final: 0.8344 (mt) REVERT: B 104 MET cc_start: 0.8291 (mtm) cc_final: 0.7888 (mtm) REVERT: B 607 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8825 (mmm-85) REVERT: B 701 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8017 (ttp80) REVERT: B 718 MET cc_start: 0.7280 (ptm) cc_final: 0.6962 (ptp) REVERT: B 780 GLU cc_start: 0.7926 (tp30) cc_final: 0.7326 (tp30) REVERT: B 987 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7945 (ptm-80) REVERT: C 99 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7676 (m-40) REVERT: C 372 MET cc_start: 0.8264 (mtm) cc_final: 0.7987 (mtp) REVERT: C 607 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8629 (mpp80) REVERT: C 622 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8780 (mp) REVERT: C 701 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8250 (ttp80) REVERT: C 740 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: C 854 GLU cc_start: 0.7080 (pm20) cc_final: 0.6848 (pm20) REVERT: C 884 MET cc_start: 0.9026 (tpp) cc_final: 0.8756 (mmt) outliers start: 53 outliers final: 38 residues processed: 221 average time/residue: 0.1592 time to fit residues: 56.8076 Evaluate side-chains 206 residues out of total 2541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 987 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5398 > 50: distance: 12 - 20: 5.027 distance: 21 - 22: 3.815 distance: 27 - 28: 5.740 distance: 27 - 220: 7.094 distance: 28 - 29: 10.736 distance: 28 - 31: 7.413 distance: 29 - 30: 15.913 distance: 29 - 35: 24.839 distance: 30 - 217: 21.927 distance: 31 - 32: 5.972 distance: 35 - 36: 21.580 distance: 36 - 37: 33.089 distance: 36 - 39: 7.631 distance: 37 - 38: 9.925 distance: 37 - 41: 32.149 distance: 39 - 40: 20.654 distance: 41 - 42: 21.447 distance: 41 - 203: 23.563 distance: 42 - 43: 3.462 distance: 42 - 45: 12.021 distance: 43 - 44: 23.257 distance: 43 - 49: 12.915 distance: 44 - 200: 20.604 distance: 45 - 46: 11.481 distance: 46 - 47: 7.470 distance: 47 - 48: 10.152 distance: 49 - 50: 4.145 distance: 50 - 51: 16.237 distance: 50 - 53: 4.553 distance: 51 - 52: 20.893 distance: 51 - 61: 22.315 distance: 53 - 54: 6.067 distance: 54 - 55: 5.042 distance: 54 - 56: 5.938 distance: 55 - 57: 3.014 distance: 61 - 62: 20.742 distance: 62 - 63: 26.193 distance: 62 - 65: 22.383 distance: 63 - 64: 28.028 distance: 63 - 69: 23.612 distance: 65 - 66: 25.722 distance: 66 - 67: 20.428 distance: 66 - 68: 18.647 distance: 69 - 70: 7.675 distance: 70 - 71: 23.427 distance: 70 - 73: 20.316 distance: 71 - 72: 18.326 distance: 71 - 77: 13.266 distance: 73 - 74: 8.036 distance: 74 - 75: 19.942 distance: 74 - 76: 6.418 distance: 77 - 78: 5.864 distance: 78 - 79: 9.014 distance: 78 - 81: 4.543 distance: 79 - 80: 5.180 distance: 79 - 84: 7.794 distance: 81 - 82: 8.614 distance: 82 - 83: 5.053 distance: 84 - 85: 4.908 distance: 86 - 90: 3.862 distance: 90 - 91: 5.723 distance: 91 - 94: 5.607 distance: 92 - 93: 12.640 distance: 92 - 99: 10.274 distance: 94 - 95: 4.414 distance: 95 - 96: 8.342 distance: 96 - 97: 3.009 distance: 96 - 98: 4.113