Starting phenix.real_space_refine on Wed Aug 27 02:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehl_48059/08_2025/9ehl_48059.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24471 atoms to isotropic. 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 153 5.16 5 C 16335 2.51 5 N 4392 2.21 5 O 5263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26143 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3532 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "B" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3532 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "C" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3532 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "I" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 801 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "N" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "O" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1047 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "R" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 3, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 3, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.79, per 1000 atoms: 0.26 Number of scatterers: 26143 At special positions: 0 Unit cell: (158.912, 143.936, 156.416, 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 153 16.00 O 5263 8.00 N 4392 7.00 C 16335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 " BMA a 4 " - " MAN a 5 " " BMA j 4 " - " MAN j 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-4 " NAG Z 2 " - " MAN Z 3 " ALPHA1-6 " BMA s 3 " - " MAN s 6 " BETA1-3 " BMA V 3 " - " BMA V 4 " " BMA a 3 " - " BMA a 4 " " BMA j 3 " - " BMA j 4 " " BMA m 3 " - " BMA m 4 " BETA1-4 " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " 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 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 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 p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " BETA1-6 " BMA a 3 " - " BMA a 6 " " BMA j 3 " - " BMA j 6 " NAG-ASN " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG B 601 " - " ASN B 339 " " NAG B 602 " - " ASN B 88 " " NAG B 603 " - " ASN B 133 " " NAG B 604 " - " ASN B 295 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 448 " " NAG B 607 " - " ASN B 234 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 160 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 363 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN B 156 " " NAG c 1 " - " ASN B 160 " " NAG d 1 " - " ASN B 262 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 363 " " NAG g 1 " - " ASN B 386 " " NAG h 1 " - " ASN B 197 " " NAG i 1 " - " ASN B 276 " " NAG j 1 " - " ASN B 332 " " NAG k 1 " - " ASN C 156 " " NAG l 1 " - " ASN C 160 " " NAG m 1 " - " ASN C 262 " " NAG n 1 " - " ASN C 276 " " NAG o 1 " - " ASN C 301 " " NAG p 1 " - " ASN C 363 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 197 " " NAG s 1 " - " ASN C 332 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 59 sheets defined 16.9% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.760A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 64 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.675A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.040A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.749A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.529A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 98 through 114 removed outlier: 4.412A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.649A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.725A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.580A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.538A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.537A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.618A pdb=" N ASN C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.561A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.594A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.834A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.671A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.508A pdb=" N SER D 534 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.624A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.559A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.720A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 removed outlier: 3.852A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.088A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.508A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 removed outlier: 3.595A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.687A pdb=" N ASP E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.528A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 536 removed outlier: 3.590A pdb=" N THR F 536 " --> pdb=" O ALA F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.628A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.694A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.516A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.524A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 664 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.610A pdb=" N GLY G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.591A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.387A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.019A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100C through 100G Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.332A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.599A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.633A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.671A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.668A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.539A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.534A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.519A pdb=" N ASN O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.527A pdb=" N ASP P 82 " --> pdb=" O GLU P 79 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 79 through 83' Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.633A pdb=" N ASP Q 82 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 79 through 83' Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.802A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.679A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.184A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 416 " --> pdb=" O CYS A 331 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.826A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.692A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.417A pdb=" N VAL E 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR E 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.140A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.633A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.541A pdb=" N VAL B 120 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 130 through 133 Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.916A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 374 through 377 removed outlier: 3.820A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.589A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'C' and resid 181 through 184 removed outlier: 4.694A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.680A pdb=" N ALA C 433 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.389A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.514A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.540A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.789A pdb=" N GLN G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.238A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.503A pdb=" N GLN I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.503A pdb=" N GLN I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG I 94 " --> pdb=" O VAL I 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.658A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP J 35 " --> pdb=" O MET J 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.658A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=AE1, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.514A pdb=" N VAL K 11 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.514A pdb=" N VAL K 11 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER K 90 " --> pdb=" O ALA K 97 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.936A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AE7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 58 through 59 removed outlier: 3.717A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR M 33 " --> pdb=" O ALA M 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 58 through 59 removed outlier: 3.717A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR M 33 " --> pdb=" O ALA M 95 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.536A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'N' and resid 67 through 72 Processing sheet with id=AF5, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.715A pdb=" N SER O 7 " --> pdb=" O THR O 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL O 20 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'O' and resid 58 through 59 removed outlier: 3.750A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR O 33 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 58 through 59 removed outlier: 3.750A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR O 33 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 9 through 11 removed outlier: 3.680A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 19 through 22 removed outlier: 3.641A pdb=" N THR P 74 " --> pdb=" O SER P 63 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 11 through 13 removed outlier: 5.783A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 19 through 21 Processing sheet with id=AG4, first strand: chain 'R' and resid 45 through 48 removed outlier: 5.870A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 62 through 63 831 hydrogen bonds defined for protein. 2103 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: 5.75 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8234 1.34 - 1.47: 6663 1.47 - 1.59: 11579 1.59 - 1.71: 0 1.71 - 1.83: 216 Bond restraints: 26692 Sorted by residual: bond pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 1.459 1.493 -0.034 9.10e-03 1.21e+04 1.43e+01 bond pdb=" N ILE R 66B" pdb=" CA ILE R 66B" ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.443 1.475 -0.032 8.60e-03 1.35e+04 1.38e+01 bond pdb=" N TYR J 49 " pdb=" CA TYR J 49 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 26687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 36067 4.12 - 8.25: 163 8.25 - 12.37: 9 12.37 - 16.49: 0 16.49 - 20.62: 1 Bond angle restraints: 36240 Sorted by residual: angle pdb=" N GLY I 100H" pdb=" CA GLY I 100H" pdb=" C GLY I 100H" ideal model delta sigma weight residual 110.69 122.28 -11.59 1.33e+00 5.65e-01 7.59e+01 angle pdb=" C2 NAG n 1 " pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 110.06 89.44 20.62 3.00e+00 1.11e-01 4.72e+01 angle pdb=" N ASN C 197 " pdb=" CA ASN C 197 " pdb=" C ASN C 197 " ideal model delta sigma weight residual 114.75 107.23 7.52 1.26e+00 6.30e-01 3.56e+01 angle pdb=" N ARG I 100G" pdb=" CA ARG I 100G" pdb=" C ARG I 100G" ideal model delta sigma weight residual 111.28 117.49 -6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" C SER I 100D" pdb=" N PRO I 100E" pdb=" CA PRO I 100E" ideal model delta sigma weight residual 120.89 127.62 -6.73 1.21e+00 6.83e-01 3.09e+01 ... (remaining 36235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 16120 23.64 - 47.29: 776 47.29 - 70.93: 158 70.93 - 94.57: 117 94.57 - 118.22: 159 Dihedral angle restraints: 17330 sinusoidal: 8270 harmonic: 9060 Sorted by residual: dihedral pdb=" CA GLY B 312 " pdb=" C GLY B 312 " pdb=" N PRO B 313 " pdb=" CA PRO B 313 " ideal model delta harmonic sigma weight residual 180.00 91.58 88.42 0 5.00e+00 4.00e-02 3.13e+02 dihedral pdb=" CA CYS B 196 " pdb=" C CYS B 196 " pdb=" N ASN B 197 " pdb=" CA ASN B 197 " ideal model delta harmonic sigma weight residual 180.00 127.44 52.56 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 -14.17 -71.83 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 17327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.937: 4328 0.937 - 1.874: 1 1.874 - 2.810: 0 2.810 - 3.747: 0 3.747 - 4.684: 4 Chirality restraints: 4333 Sorted by residual: chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 2.23 -4.63 2.00e-02 2.50e+03 5.35e+04 chirality pdb=" C1 MAN d 4 " pdb=" O3 BMA d 3 " pdb=" C2 MAN d 4 " pdb=" O5 MAN d 4 " both_signs ideal model delta sigma weight residual False 2.40 1.03 1.37 2.00e-02 2.50e+03 4.66e+03 ... (remaining 4330 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " -0.091 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 386 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " 0.521 2.00e-02 2.50e+03 pdb=" C1 NAG q 1 " -0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 603 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG A 603 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 603 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG A 603 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 603 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.340 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG U 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " 0.123 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 6 2.08 - 2.78: 5843 2.78 - 3.49: 35284 3.49 - 4.19: 64628 4.19 - 4.90: 108122 Nonbonded interactions: 213883 Sorted by model distance: nonbonded pdb=" CB PRO I 100E" pdb=" CD1 LEU L 32 " model vdw 1.374 3.860 nonbonded pdb=" OG SER I 100D" pdb=" C1 NAG n 1 " model vdw 1.521 3.470 nonbonded pdb=" O PRO I 100E" pdb=" CD1 LEU L 32 " model vdw 1.622 3.460 nonbonded pdb=" CA PRO I 100E" pdb=" CD1 LEU L 32 " model vdw 1.645 3.890 nonbonded pdb=" C PRO I 100E" pdb=" CD1 LEU L 32 " model vdw 1.735 3.690 ... (remaining 213878 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'l' selection = chain 'o' selection = chain 'q' } ncs_group { reference = (chain 'U' and resid 1 through 3) selection = (chain 'V' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'm' and resid 1 through 3) } ncs_group { reference = (chain 'a' and (resid 1 through 3 or resid 5)) selection = (chain 'j' and (resid 1 through 3 or resid 5)) selection = (chain 's' and (resid 1 through 3 or resid 5)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.250 Find NCS groups from input model: 0.680 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.006 0.049 26850 Z= 0.390 Angle : 0.994 23.214 36669 Z= 0.512 Chirality : 0.154 4.684 4333 Planarity : 0.020 0.366 4476 Dihedral : 19.715 118.217 11393 Min Nonbonded Distance : 1.374 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.74 % Allowed : 5.31 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -3.73 (0.13), residues: 3105 helix: -3.05 (0.20), residues: 399 sheet: -1.98 (0.15), residues: 977 loop : -2.67 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 298 TYR 0.013 0.001 TYR L 49 PHE 0.015 0.001 PHE B 317 TRP 0.016 0.001 TRP G 100F HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00588 (26692) covalent geometry : angle 0.83795 (36240) SS BOND : bond 0.00393 ( 45) SS BOND : angle 1.05900 ( 90) hydrogen bonds : bond 0.24267 ( 786) hydrogen bonds : angle 9.95916 ( 2103) link_ALPHA1-2 : bond 0.04544 ( 3) link_ALPHA1-2 : angle 7.27201 ( 9) link_ALPHA1-3 : bond 0.04540 ( 4) link_ALPHA1-3 : angle 6.88581 ( 12) link_ALPHA1-4 : bond 0.04353 ( 1) link_ALPHA1-4 : angle 7.53576 ( 3) link_ALPHA1-6 : bond 0.03752 ( 1) link_ALPHA1-6 : angle 2.58248 ( 3) link_BETA1-3 : bond 0.04602 ( 4) link_BETA1-3 : angle 4.42196 ( 12) link_BETA1-4 : bond 0.04567 ( 44) link_BETA1-4 : angle 7.39998 ( 132) link_BETA1-6 : bond 0.03729 ( 2) link_BETA1-6 : angle 4.28551 ( 6) link_NAG-ASN : bond 0.00822 ( 54) link_NAG-ASN : angle 3.43252 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 718 time to evaluate : 1.077 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6290 (t60) cc_final: 0.5691 (t60) REVERT: B 107 ASP cc_start: 0.8323 (t0) cc_final: 0.7994 (t0) REVERT: B 232 LYS cc_start: 0.7536 (mtpp) cc_final: 0.6916 (mptt) REVERT: B 352 HIS cc_start: 0.7794 (m170) cc_final: 0.7590 (m170) REVERT: C 251 ILE cc_start: 0.8336 (mt) cc_final: 0.8115 (tt) REVERT: C 280 ASN cc_start: 0.9208 (p0) cc_final: 0.8889 (p0) REVERT: C 434 MET cc_start: 0.9005 (ttp) cc_final: 0.8753 (ttt) REVERT: D 625 ASN cc_start: 0.6591 (m110) cc_final: 0.6187 (t0) REVERT: E 543 ASN cc_start: 0.8164 (t0) cc_final: 0.7504 (t0) REVERT: F 650 GLN cc_start: 0.7017 (mm110) cc_final: 0.6764 (mm110) REVERT: G 80 MET cc_start: 0.8416 (tmm) cc_final: 0.7625 (tmm) REVERT: G 108 LEU cc_start: 0.8322 (tt) cc_final: 0.8114 (tp) REVERT: H 13 LYS cc_start: 0.8398 (mttt) cc_final: 0.8141 (mmmt) REVERT: H 72 ASP cc_start: 0.8042 (t0) cc_final: 0.7727 (t0) REVERT: I 97 PHE cc_start: 0.7673 (m-80) cc_final: 0.7344 (m-80) REVERT: J 78 LEU cc_start: 0.6106 (mt) cc_final: 0.5709 (tp) REVERT: K 58 VAL cc_start: 0.4960 (OUTLIER) cc_final: 0.4111 (p) REVERT: K 60 ASN cc_start: 0.7823 (m-40) cc_final: 0.7374 (t0) REVERT: L 73 LEU cc_start: 0.7357 (tp) cc_final: 0.7056 (tp) REVERT: L 85 ASP cc_start: 0.7767 (m-30) cc_final: 0.6944 (t0) REVERT: M 3 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7865 (mm-40) REVERT: M 5 GLN cc_start: 0.7261 (tp40) cc_final: 0.6865 (tp-100) REVERT: M 50 TYR cc_start: 0.8122 (p90) cc_final: 0.7724 (p90) REVERT: M 91 TYR cc_start: 0.7202 (m-80) cc_final: 0.7000 (m-80) REVERT: N 50 TYR cc_start: 0.7741 (p90) cc_final: 0.7471 (p90) REVERT: N 59 TYR cc_start: 0.7474 (m-80) cc_final: 0.7113 (m-10) REVERT: N 80 LEU cc_start: 0.7901 (tp) cc_final: 0.7569 (tp) REVERT: O 51 ILE cc_start: 0.7129 (tp) cc_final: 0.6879 (tt) REVERT: O 78 LEU cc_start: 0.7162 (tt) cc_final: 0.6447 (mt) REVERT: O 91 TYR cc_start: 0.5612 (m-80) cc_final: 0.5388 (m-80) REVERT: O 103 TRP cc_start: 0.6505 (m100) cc_final: 0.6201 (m-10) REVERT: P 49 TYR cc_start: 0.8380 (p90) cc_final: 0.7414 (p90) REVERT: P 73 LEU cc_start: 0.8164 (tp) cc_final: 0.7129 (tp) REVERT: P 90 MET cc_start: 0.8188 (tpp) cc_final: 0.7781 (ttm) REVERT: Q 31 ARG cc_start: 0.6740 (ptt90) cc_final: 0.6447 (ptt-90) REVERT: Q 73 LEU cc_start: 0.8032 (tp) cc_final: 0.7597 (tp) REVERT: Q 87 TYR cc_start: 0.6674 (m-80) cc_final: 0.5740 (m-80) REVERT: R 62 PHE cc_start: 0.6592 (m-80) cc_final: 0.6311 (m-80) REVERT: R 65 THR cc_start: 0.7117 (t) cc_final: 0.6912 (t) REVERT: R 73 LEU cc_start: 0.8633 (tp) cc_final: 0.8397 (tp) REVERT: R 96 TRP cc_start: 0.7722 (m100) cc_final: 0.7139 (m100) outliers start: 20 outliers final: 7 residues processed: 732 average time/residue: 0.2246 time to fit residues: 241.9204 Evaluate side-chains 460 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 452 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 356 ASN A 422 GLN B 103 GLN B 136 ASN B 195 ASN B 293 GLN B 315 GLN B 330 HIS B 422 GLN B 428 GLN B 432 GLN C 103 GLN C 422 GLN C 432 GLN D 543 ASN D 591 GLN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 543 ASN F 590 GLN F 652 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 33 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN K 6 GLN K 17 GLN M 30 ASN M 82AASN M 99 GLN ** N 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN P 34 GLN P 52 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 66CASN R 89 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066815 restraints weight = 83998.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068334 restraints weight = 48866.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068666 restraints weight = 35697.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068991 restraints weight = 33132.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069043 restraints weight = 30548.566| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 26850 Z= 0.373 Angle : 1.075 18.435 36669 Z= 0.476 Chirality : 0.058 0.563 4333 Planarity : 0.006 0.087 4476 Dihedral : 16.527 104.066 5740 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.47 % Favored : 92.50 % Rotamer: Outliers : 3.80 % Allowed : 17.11 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -3.11 (0.14), residues: 3105 helix: -1.98 (0.23), residues: 417 sheet: -1.61 (0.16), residues: 974 loop : -2.39 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 100 TYR 0.033 0.003 TYR L 49 PHE 0.028 0.003 PHE A 383 TRP 0.026 0.003 TRP N 103 HIS 0.008 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00831 (26692) covalent geometry : angle 0.97066 (36240) SS BOND : bond 0.00657 ( 45) SS BOND : angle 1.68287 ( 90) hydrogen bonds : bond 0.04705 ( 786) hydrogen bonds : angle 7.01412 ( 2103) link_ALPHA1-2 : bond 0.01512 ( 3) link_ALPHA1-2 : angle 3.67483 ( 9) link_ALPHA1-3 : bond 0.01499 ( 4) link_ALPHA1-3 : angle 3.67744 ( 12) link_ALPHA1-4 : bond 0.02700 ( 1) link_ALPHA1-4 : angle 4.80982 ( 3) link_ALPHA1-6 : bond 0.00371 ( 1) link_ALPHA1-6 : angle 2.54661 ( 3) link_BETA1-3 : bond 0.01500 ( 4) link_BETA1-3 : angle 2.63799 ( 12) link_BETA1-4 : bond 0.01110 ( 44) link_BETA1-4 : angle 4.04661 ( 132) link_BETA1-6 : bond 0.00337 ( 2) link_BETA1-6 : angle 3.20910 ( 6) link_NAG-ASN : bond 0.01084 ( 54) link_NAG-ASN : angle 5.69725 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 470 time to evaluate : 1.153 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: C 195 ASN cc_start: 0.7487 (p0) cc_final: 0.7118 (p0) REVERT: C 494 LEU cc_start: 0.9238 (mt) cc_final: 0.9024 (tp) REVERT: D 530 MET cc_start: 0.8504 (mtm) cc_final: 0.8089 (mmm) REVERT: D 607 ASN cc_start: 0.8413 (m-40) cc_final: 0.7891 (p0) REVERT: D 625 ASN cc_start: 0.7004 (m110) cc_final: 0.6262 (t0) REVERT: E 530 MET cc_start: 0.8218 (ttm) cc_final: 0.7980 (ttm) REVERT: E 543 ASN cc_start: 0.8128 (t0) cc_final: 0.7573 (t0) REVERT: F 650 GLN cc_start: 0.7583 (mm110) cc_final: 0.7360 (mm110) REVERT: G 96 MET cc_start: 0.7833 (tpp) cc_final: 0.7492 (tpp) REVERT: H 13 LYS cc_start: 0.8516 (mttt) cc_final: 0.8248 (mmmt) REVERT: H 48 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: H 100 ASP cc_start: 0.7506 (p0) cc_final: 0.7291 (p0) REVERT: I 97 PHE cc_start: 0.7956 (m-80) cc_final: 0.7563 (m-80) REVERT: J 78 LEU cc_start: 0.6046 (mt) cc_final: 0.5590 (tp) REVERT: K 78 LEU cc_start: 0.7124 (mm) cc_final: 0.6868 (mp) REVERT: L 61 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7244 (ttm-80) REVERT: L 79 GLN cc_start: 0.7215 (mt0) cc_final: 0.6972 (mt0) REVERT: L 85 ASP cc_start: 0.8095 (m-30) cc_final: 0.7162 (t0) REVERT: M 3 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8038 (mm-40) REVERT: M 5 GLN cc_start: 0.7563 (tp40) cc_final: 0.7097 (tp-100) REVERT: M 91 TYR cc_start: 0.6963 (m-80) cc_final: 0.6645 (m-80) REVERT: N 5 GLN cc_start: 0.8239 (tp40) cc_final: 0.7942 (tp40) REVERT: N 36 TRP cc_start: 0.7260 (m100) cc_final: 0.6975 (m-10) REVERT: O 30 ASN cc_start: 0.5974 (m110) cc_final: 0.5663 (p0) REVERT: O 77 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6676 (tp-100) REVERT: O 78 LEU cc_start: 0.6815 (tt) cc_final: 0.6024 (mp) REVERT: O 103 TRP cc_start: 0.6704 (m100) cc_final: 0.6090 (m-10) REVERT: P 49 TYR cc_start: 0.8475 (p90) cc_final: 0.7873 (p90) REVERT: Q 20 ARG cc_start: 0.7244 (mmt-90) cc_final: 0.6910 (mmp80) REVERT: Q 42 GLN cc_start: 0.6806 (tm-30) cc_final: 0.6553 (tm-30) REVERT: Q 65 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7535 (p) REVERT: Q 73 LEU cc_start: 0.8083 (tp) cc_final: 0.7655 (tp) REVERT: R 96 TRP cc_start: 0.7854 (m100) cc_final: 0.7127 (m100) outliers start: 103 outliers final: 64 residues processed: 531 average time/residue: 0.1767 time to fit residues: 148.0570 Evaluate side-chains 467 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 401 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 302 ASN A 330 HIS A 352 HIS B 136 ASN C 72 HIS C 99 ASN C 422 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 590 GLN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS J 17 GLN J 69 ASN M 31 ASN P 34 GLN P 50 ASN P 109 GLN Q 37 GLN Q 66CASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069482 restraints weight = 83665.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070965 restraints weight = 49433.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071554 restraints weight = 35181.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071723 restraints weight = 33695.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071703 restraints weight = 29304.411| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26850 Z= 0.146 Angle : 0.845 18.623 36669 Z= 0.372 Chirality : 0.051 0.374 4333 Planarity : 0.004 0.053 4476 Dihedral : 12.962 102.113 5736 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.88 % Allowed : 19.69 % Favored : 77.43 % 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 aren not related in a simple way. whole: -2.55 (0.14), residues: 3105 helix: -1.24 (0.25), residues: 414 sheet: -1.27 (0.16), residues: 929 loop : -2.09 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.028 0.002 TYR N 50 PHE 0.015 0.002 PHE K 30 TRP 0.026 0.001 TRP O 34 HIS 0.006 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00311 (26692) covalent geometry : angle 0.74920 (36240) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.31986 ( 90) hydrogen bonds : bond 0.03739 ( 786) hydrogen bonds : angle 6.30178 ( 2103) link_ALPHA1-2 : bond 0.01740 ( 3) link_ALPHA1-2 : angle 3.70159 ( 9) link_ALPHA1-3 : bond 0.02215 ( 4) link_ALPHA1-3 : angle 3.32043 ( 12) link_ALPHA1-4 : bond 0.02363 ( 1) link_ALPHA1-4 : angle 4.41777 ( 3) link_ALPHA1-6 : bond 0.00246 ( 1) link_ALPHA1-6 : angle 1.90021 ( 3) link_BETA1-3 : bond 0.01163 ( 4) link_BETA1-3 : angle 1.91756 ( 12) link_BETA1-4 : bond 0.00869 ( 44) link_BETA1-4 : angle 3.24276 ( 132) link_BETA1-6 : bond 0.00803 ( 2) link_BETA1-6 : angle 2.84070 ( 6) link_NAG-ASN : bond 0.00778 ( 54) link_NAG-ASN : angle 4.88702 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 464 time to evaluate : 1.079 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 TRP cc_start: 0.6243 (t60) cc_final: 0.5726 (t60) REVERT: B 33 ASN cc_start: 0.7276 (t0) cc_final: 0.7025 (t0) REVERT: B 104 MET cc_start: 0.8677 (ttt) cc_final: 0.8324 (ttt) REVERT: B 289 ASN cc_start: 0.7238 (p0) cc_final: 0.6788 (t0) REVERT: C 113 ASP cc_start: 0.7783 (t0) cc_final: 0.7491 (t0) REVERT: C 195 ASN cc_start: 0.7498 (p0) cc_final: 0.7121 (p0) REVERT: C 271 MET cc_start: 0.7256 (mmm) cc_final: 0.7022 (mmt) REVERT: D 607 ASN cc_start: 0.8496 (m-40) cc_final: 0.8040 (p0) REVERT: D 625 ASN cc_start: 0.6777 (m110) cc_final: 0.6204 (t0) REVERT: D 647 GLU cc_start: 0.7411 (pp20) cc_final: 0.6937 (pp20) REVERT: E 543 ASN cc_start: 0.8081 (t0) cc_final: 0.7505 (t0) REVERT: F 638 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: G 80 MET cc_start: 0.8289 (tmm) cc_final: 0.7547 (tmm) REVERT: G 95 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6465 (tp30) REVERT: H 13 LYS cc_start: 0.8474 (mttt) cc_final: 0.8224 (mmmt) REVERT: H 32 TYR cc_start: 0.8351 (m-80) cc_final: 0.8003 (m-80) REVERT: H 100 ASP cc_start: 0.7444 (p0) cc_final: 0.7177 (p0) REVERT: I 91 TYR cc_start: 0.8420 (m-80) cc_final: 0.8194 (m-80) REVERT: I 97 PHE cc_start: 0.7648 (m-80) cc_final: 0.7311 (m-80) REVERT: J 78 LEU cc_start: 0.5977 (mt) cc_final: 0.5599 (tp) REVERT: K 46 LEU cc_start: 0.6084 (tp) cc_final: 0.5351 (tp) REVERT: L 61 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7231 (ttm-80) REVERT: L 85 ASP cc_start: 0.7779 (m-30) cc_final: 0.6932 (t0) REVERT: M 3 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8091 (mm-40) REVERT: M 5 GLN cc_start: 0.7621 (tp40) cc_final: 0.7332 (tm-30) REVERT: M 51 ILE cc_start: 0.7848 (pt) cc_final: 0.7577 (mm) REVERT: M 81 LYS cc_start: 0.7321 (mppt) cc_final: 0.7061 (mmtm) REVERT: M 91 TYR cc_start: 0.6923 (m-80) cc_final: 0.6407 (m-80) REVERT: M 96 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6996 (ttp-170) REVERT: N 5 GLN cc_start: 0.8293 (tp40) cc_final: 0.7938 (tp40) REVERT: N 29 MET cc_start: 0.6100 (tpp) cc_final: 0.5592 (tmm) REVERT: N 80 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6915 (tp) REVERT: O 78 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6593 (tp) REVERT: O 103 TRP cc_start: 0.6546 (m100) cc_final: 0.6052 (m-10) REVERT: P 34 GLN cc_start: 0.8528 (mp-120) cc_final: 0.7843 (mp10) REVERT: P 49 TYR cc_start: 0.8404 (p90) cc_final: 0.8077 (p90) REVERT: P 87 TYR cc_start: 0.7943 (m-80) cc_final: 0.7645 (m-10) REVERT: Q 20 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.7044 (mmp80) REVERT: Q 42 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6796 (tm-30) REVERT: Q 65 THR cc_start: 0.8037 (m) cc_final: 0.7648 (p) REVERT: Q 73 LEU cc_start: 0.8147 (tp) cc_final: 0.7744 (tp) REVERT: Q 87 TYR cc_start: 0.6848 (m-80) cc_final: 0.6473 (m-80) REVERT: R 96 TRP cc_start: 0.7765 (m100) cc_final: 0.7069 (m100) outliers start: 78 outliers final: 41 residues processed: 512 average time/residue: 0.1869 time to fit residues: 150.7093 Evaluate side-chains 452 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 407 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 161 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 170 GLN B 195 ASN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 591 GLN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 650 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066238 restraints weight = 83813.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067713 restraints weight = 50442.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068073 restraints weight = 36356.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068269 restraints weight = 33170.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068267 restraints weight = 30168.784| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 26850 Z= 0.277 Angle : 0.903 14.034 36669 Z= 0.410 Chirality : 0.052 0.395 4333 Planarity : 0.005 0.054 4476 Dihedral : 11.960 102.695 5732 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.42 % Allowed : 20.43 % Favored : 75.15 % 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 aren not related in a simple way. whole: -2.42 (0.14), residues: 3105 helix: -1.18 (0.25), residues: 414 sheet: -1.15 (0.16), residues: 981 loop : -2.02 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.029 0.002 TYR J 49 PHE 0.024 0.002 PHE A 383 TRP 0.039 0.002 TRP O 34 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00622 (26692) covalent geometry : angle 0.82120 (36240) SS BOND : bond 0.00647 ( 45) SS BOND : angle 1.92210 ( 90) hydrogen bonds : bond 0.03767 ( 786) hydrogen bonds : angle 6.18969 ( 2103) link_ALPHA1-2 : bond 0.01286 ( 3) link_ALPHA1-2 : angle 3.66880 ( 9) link_ALPHA1-3 : bond 0.02051 ( 4) link_ALPHA1-3 : angle 3.18103 ( 12) link_ALPHA1-4 : bond 0.02747 ( 1) link_ALPHA1-4 : angle 5.22442 ( 3) link_ALPHA1-6 : bond 0.00617 ( 1) link_ALPHA1-6 : angle 2.31960 ( 3) link_BETA1-3 : bond 0.01325 ( 4) link_BETA1-3 : angle 2.28728 ( 12) link_BETA1-4 : bond 0.00890 ( 44) link_BETA1-4 : angle 3.24663 ( 132) link_BETA1-6 : bond 0.00508 ( 2) link_BETA1-6 : angle 2.54029 ( 6) link_NAG-ASN : bond 0.00795 ( 54) link_NAG-ASN : angle 4.51607 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 411 time to evaluate : 0.983 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8452 (mmmt) REVERT: B 289 ASN cc_start: 0.7672 (p0) cc_final: 0.6952 (t0) REVERT: C 69 TRP cc_start: 0.6185 (OUTLIER) cc_final: 0.5503 (t60) REVERT: C 113 ASP cc_start: 0.7968 (t0) cc_final: 0.7669 (t0) REVERT: C 195 ASN cc_start: 0.7505 (p0) cc_final: 0.7115 (p0) REVERT: C 271 MET cc_start: 0.7294 (mmm) cc_final: 0.7072 (mmt) REVERT: D 607 ASN cc_start: 0.8424 (m-40) cc_final: 0.8155 (p0) REVERT: D 647 GLU cc_start: 0.7410 (pp20) cc_final: 0.6844 (pp20) REVERT: E 543 ASN cc_start: 0.8112 (t0) cc_final: 0.7600 (t0) REVERT: E 595 ILE cc_start: 0.9209 (tp) cc_final: 0.8981 (tp) REVERT: E 634 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: G 80 MET cc_start: 0.8362 (tmm) cc_final: 0.7535 (tmm) REVERT: H 13 LYS cc_start: 0.8473 (mttt) cc_final: 0.8219 (mmmt) REVERT: H 100 ASP cc_start: 0.7382 (p0) cc_final: 0.7128 (p0) REVERT: I 97 PHE cc_start: 0.7868 (m-80) cc_final: 0.7577 (m-80) REVERT: J 55 PRO cc_start: 0.7410 (Cg_exo) cc_final: 0.7209 (Cg_endo) REVERT: J 78 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5794 (tp) REVERT: K 85 ASP cc_start: 0.7664 (t0) cc_final: 0.7442 (t0) REVERT: L 61 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7537 (ttm-80) REVERT: L 85 ASP cc_start: 0.7920 (m-30) cc_final: 0.6854 (t0) REVERT: M 3 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8097 (mm-40) REVERT: M 91 TYR cc_start: 0.7026 (m-80) cc_final: 0.6494 (m-80) REVERT: M 96 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.6842 (ttp-170) REVERT: N 5 GLN cc_start: 0.8287 (tp40) cc_final: 0.7841 (tp40) REVERT: N 33 TYR cc_start: 0.7553 (m-10) cc_final: 0.7335 (m-10) REVERT: O 38 ARG cc_start: 0.6308 (ptm-80) cc_final: 0.5977 (ptt90) REVERT: O 77 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6887 (tp-100) REVERT: O 78 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6245 (mt) REVERT: O 103 TRP cc_start: 0.6737 (m100) cc_final: 0.6185 (m-10) REVERT: P 49 TYR cc_start: 0.8561 (p90) cc_final: 0.8334 (p90) REVERT: P 70 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6642 (mtp85) REVERT: P 73 LEU cc_start: 0.8067 (tp) cc_final: 0.7856 (tp) REVERT: Q 20 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.7153 (mmp80) REVERT: Q 42 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6472 (tm-30) REVERT: Q 65 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7731 (p) REVERT: R 96 TRP cc_start: 0.7908 (m100) cc_final: 0.7122 (m100) outliers start: 120 outliers final: 72 residues processed: 490 average time/residue: 0.1841 time to fit residues: 142.8584 Evaluate side-chains 455 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 59 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 210 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 590 GLN D 650 GLN D 651 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068858 restraints weight = 83825.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069453 restraints weight = 52770.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069874 restraints weight = 41085.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070154 restraints weight = 40211.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070195 restraints weight = 35486.007| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26850 Z= 0.140 Angle : 0.771 12.900 36669 Z= 0.348 Chirality : 0.048 0.298 4333 Planarity : 0.004 0.048 4476 Dihedral : 10.698 101.310 5732 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.76 % Allowed : 21.39 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.14), residues: 3105 helix: -0.82 (0.26), residues: 414 sheet: -0.93 (0.17), residues: 935 loop : -1.87 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.033 0.002 TYR J 36 PHE 0.019 0.001 PHE I 63 TRP 0.038 0.001 TRP N 36 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd covalent geometry : bond 0.00310 (26692) covalent geometry : angle 0.70111 (36240) SS BOND : bond 0.00478 ( 45) SS BOND : angle 1.49551 ( 90) hydrogen bonds : bond 0.03268 ( 786) hydrogen bonds : angle 5.80462 ( 2103) link_ALPHA1-2 : bond 0.01702 ( 3) link_ALPHA1-2 : angle 3.81547 ( 9) link_ALPHA1-3 : bond 0.02161 ( 4) link_ALPHA1-3 : angle 3.25090 ( 12) link_ALPHA1-4 : bond 0.02422 ( 1) link_ALPHA1-4 : angle 4.60227 ( 3) link_ALPHA1-6 : bond 0.00134 ( 1) link_ALPHA1-6 : angle 2.06337 ( 3) link_BETA1-3 : bond 0.01067 ( 4) link_BETA1-3 : angle 1.97334 ( 12) link_BETA1-4 : bond 0.00790 ( 44) link_BETA1-4 : angle 2.76411 ( 132) link_BETA1-6 : bond 0.00634 ( 2) link_BETA1-6 : angle 2.29935 ( 6) link_NAG-ASN : bond 0.00589 ( 54) link_NAG-ASN : angle 3.81391 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 441 time to evaluate : 0.865 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: symmetry clash REVERT: A 69 TRP cc_start: 0.6300 (t60) cc_final: 0.5740 (t60) REVERT: B 104 MET cc_start: 0.8738 (ttt) cc_final: 0.8230 (ttt) REVERT: B 289 ASN cc_start: 0.7529 (p0) cc_final: 0.7065 (t0) REVERT: C 69 TRP cc_start: 0.6060 (OUTLIER) cc_final: 0.5415 (t60) REVERT: C 113 ASP cc_start: 0.7784 (t0) cc_final: 0.7562 (t0) REVERT: C 195 ASN cc_start: 0.7554 (p0) cc_final: 0.7192 (p0) REVERT: C 271 MET cc_start: 0.7270 (mmm) cc_final: 0.7032 (mmt) REVERT: D 590 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8279 (tp40) REVERT: D 607 ASN cc_start: 0.8554 (m-40) cc_final: 0.8104 (p0) REVERT: E 543 ASN cc_start: 0.8027 (t0) cc_final: 0.7479 (t0) REVERT: E 595 ILE cc_start: 0.9149 (tp) cc_final: 0.8907 (tp) REVERT: F 638 TYR cc_start: 0.7030 (m-80) cc_final: 0.6698 (m-80) REVERT: F 650 GLN cc_start: 0.7628 (mm110) cc_final: 0.7307 (mm110) REVERT: G 80 MET cc_start: 0.8208 (tmm) cc_final: 0.7455 (tmm) REVERT: G 96 MET cc_start: 0.8135 (mmm) cc_final: 0.7623 (tmm) REVERT: H 13 LYS cc_start: 0.8404 (mttt) cc_final: 0.8143 (mmmt) REVERT: H 32 TYR cc_start: 0.8313 (m-80) cc_final: 0.7971 (m-80) REVERT: H 48 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: H 100 ASP cc_start: 0.7146 (p0) cc_final: 0.6880 (p0) REVERT: I 91 TYR cc_start: 0.8561 (m-80) cc_final: 0.8287 (m-80) REVERT: I 97 PHE cc_start: 0.7707 (m-80) cc_final: 0.7428 (m-80) REVERT: J 78 LEU cc_start: 0.6016 (mt) cc_final: 0.5602 (tp) REVERT: K 60 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8134 (t0) REVERT: L 85 ASP cc_start: 0.7747 (m-30) cc_final: 0.6789 (t0) REVERT: L 107 LEU cc_start: 0.5969 (tp) cc_final: 0.5710 (tp) REVERT: M 2 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7148 (p) REVERT: M 3 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8028 (mm-40) REVERT: M 5 GLN cc_start: 0.7216 (tp-100) cc_final: 0.6953 (tp-100) REVERT: M 29 MET cc_start: 0.4355 (tmm) cc_final: 0.4129 (tmm) REVERT: M 96 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6833 (ttp-170) REVERT: N 5 GLN cc_start: 0.8223 (tp40) cc_final: 0.7723 (tp40) REVERT: N 29 MET cc_start: 0.6310 (tpp) cc_final: 0.5506 (tmm) REVERT: O 77 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7035 (tp-100) REVERT: O 78 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6160 (mt) REVERT: O 100 MET cc_start: 0.7797 (mmt) cc_final: 0.7261 (mmp) REVERT: O 103 TRP cc_start: 0.6555 (m100) cc_final: 0.6156 (m-10) REVERT: P 39 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.6544 (tpp80) REVERT: P 49 TYR cc_start: 0.8405 (p90) cc_final: 0.7957 (p90) REVERT: Q 20 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.7108 (mmp80) REVERT: Q 42 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6578 (tm-30) REVERT: Q 65 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7769 (p) REVERT: R 96 TRP cc_start: 0.7792 (m100) cc_final: 0.7032 (m100) outliers start: 102 outliers final: 59 residues processed: 509 average time/residue: 0.1760 time to fit residues: 143.4925 Evaluate side-chains 463 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 397 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 119 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 175 optimal weight: 0.0570 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN G 35 HIS J 38 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067678 restraints weight = 83632.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069557 restraints weight = 49979.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069888 restraints weight = 34028.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070031 restraints weight = 32320.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070027 restraints weight = 28849.755| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 26850 Z= 0.167 Angle : 0.774 16.082 36669 Z= 0.352 Chirality : 0.048 0.334 4333 Planarity : 0.004 0.048 4476 Dihedral : 10.221 99.662 5732 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.28 % Allowed : 22.42 % Favored : 74.30 % 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 aren not related in a simple way. whole: -1.98 (0.15), residues: 3105 helix: -0.69 (0.26), residues: 396 sheet: -0.85 (0.16), residues: 950 loop : -1.75 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.020 0.002 TYR J 36 PHE 0.015 0.001 PHE A 383 TRP 0.041 0.002 TRP B 96 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00378 (26692) covalent geometry : angle 0.70762 (36240) SS BOND : bond 0.00511 ( 45) SS BOND : angle 1.64543 ( 90) hydrogen bonds : bond 0.03332 ( 786) hydrogen bonds : angle 5.68287 ( 2103) link_ALPHA1-2 : bond 0.01725 ( 3) link_ALPHA1-2 : angle 3.84938 ( 9) link_ALPHA1-3 : bond 0.02135 ( 4) link_ALPHA1-3 : angle 3.29617 ( 12) link_ALPHA1-4 : bond 0.02660 ( 1) link_ALPHA1-4 : angle 4.70040 ( 3) link_ALPHA1-6 : bond 0.00267 ( 1) link_ALPHA1-6 : angle 2.05283 ( 3) link_BETA1-3 : bond 0.01074 ( 4) link_BETA1-3 : angle 1.86366 ( 12) link_BETA1-4 : bond 0.00792 ( 44) link_BETA1-4 : angle 2.71798 ( 132) link_BETA1-6 : bond 0.00494 ( 2) link_BETA1-6 : angle 2.08211 ( 6) link_NAG-ASN : bond 0.00590 ( 54) link_NAG-ASN : angle 3.67888 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 406 time to evaluate : 1.407 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 TRP cc_start: 0.6288 (t60) cc_final: 0.5767 (t60) REVERT: B 289 ASN cc_start: 0.7728 (p0) cc_final: 0.7119 (t0) REVERT: C 69 TRP cc_start: 0.6068 (OUTLIER) cc_final: 0.5327 (t60) REVERT: C 195 ASN cc_start: 0.7493 (p0) cc_final: 0.7146 (p0) REVERT: C 207 LYS cc_start: 0.7172 (mtmm) cc_final: 0.6769 (ttmm) REVERT: C 271 MET cc_start: 0.7319 (mmm) cc_final: 0.7100 (mmt) REVERT: D 607 ASN cc_start: 0.8530 (m-40) cc_final: 0.8086 (p0) REVERT: E 543 ASN cc_start: 0.8061 (t0) cc_final: 0.7521 (t0) REVERT: E 595 ILE cc_start: 0.9138 (tp) cc_final: 0.8900 (tp) REVERT: F 638 TYR cc_start: 0.7073 (m-80) cc_final: 0.6703 (m-80) REVERT: F 650 GLN cc_start: 0.7766 (mm110) cc_final: 0.7407 (mm-40) REVERT: G 80 MET cc_start: 0.8176 (tmm) cc_final: 0.7388 (tmm) REVERT: G 96 MET cc_start: 0.8138 (mmm) cc_final: 0.7685 (tmm) REVERT: H 13 LYS cc_start: 0.8405 (mttt) cc_final: 0.8188 (mmmt) REVERT: H 32 TYR cc_start: 0.8347 (m-80) cc_final: 0.7769 (m-80) REVERT: H 48 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7699 (mmm) REVERT: H 98 ASP cc_start: 0.8467 (t0) cc_final: 0.8263 (t0) REVERT: H 100 ASP cc_start: 0.7156 (p0) cc_final: 0.6866 (p0) REVERT: I 97 PHE cc_start: 0.7707 (m-80) cc_final: 0.7449 (m-80) REVERT: J 78 LEU cc_start: 0.5990 (mt) cc_final: 0.5553 (tp) REVERT: L 17 GLN cc_start: 0.6127 (pp30) cc_final: 0.5649 (pp30) REVERT: L 85 ASP cc_start: 0.7753 (m-30) cc_final: 0.6764 (t0) REVERT: M 2 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7158 (p) REVERT: M 3 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8013 (mm-40) REVERT: M 5 GLN cc_start: 0.7353 (tp-100) cc_final: 0.7090 (tp-100) REVERT: M 96 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.7012 (ttp-170) REVERT: N 5 GLN cc_start: 0.8244 (tp40) cc_final: 0.7711 (tp40) REVERT: O 38 ARG cc_start: 0.6322 (ptm-80) cc_final: 0.6094 (ptt90) REVERT: O 77 GLN cc_start: 0.7327 (tp-100) cc_final: 0.7004 (tp-100) REVERT: O 78 LEU cc_start: 0.7002 (tt) cc_final: 0.6127 (mt) REVERT: O 100 MET cc_start: 0.7786 (mmt) cc_final: 0.7242 (mmp) REVERT: O 103 TRP cc_start: 0.6638 (m100) cc_final: 0.6171 (m-10) REVERT: P 49 TYR cc_start: 0.8397 (p90) cc_final: 0.8176 (p90) REVERT: Q 20 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7208 (mmp80) REVERT: Q 65 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7774 (p) REVERT: Q 73 LEU cc_start: 0.8192 (tp) cc_final: 0.7775 (tp) REVERT: R 96 TRP cc_start: 0.7811 (m100) cc_final: 0.7007 (m100) outliers start: 89 outliers final: 64 residues processed: 465 average time/residue: 0.1790 time to fit residues: 133.7482 Evaluate side-chains 460 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 392 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 208 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 242 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 650 GLN D 651 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN J 38 GLN N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067912 restraints weight = 83650.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069593 restraints weight = 50206.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069857 restraints weight = 36396.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070075 restraints weight = 34393.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070127 restraints weight = 30683.293| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26850 Z= 0.149 Angle : 0.763 15.393 36669 Z= 0.347 Chirality : 0.047 0.321 4333 Planarity : 0.004 0.073 4476 Dihedral : 9.737 97.549 5732 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.69 % Allowed : 23.08 % Favored : 73.23 % 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 aren not related in a simple way. whole: -1.88 (0.15), residues: 3105 helix: -0.56 (0.27), residues: 396 sheet: -0.79 (0.17), residues: 923 loop : -1.69 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 71 TYR 0.031 0.002 TYR N 59 PHE 0.022 0.001 PHE B 353 TRP 0.047 0.002 TRP N 34 HIS 0.004 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00336 (26692) covalent geometry : angle 0.70026 (36240) SS BOND : bond 0.00467 ( 45) SS BOND : angle 1.83401 ( 90) hydrogen bonds : bond 0.03266 ( 786) hydrogen bonds : angle 5.55641 ( 2103) link_ALPHA1-2 : bond 0.01776 ( 3) link_ALPHA1-2 : angle 3.33251 ( 9) link_ALPHA1-3 : bond 0.02034 ( 4) link_ALPHA1-3 : angle 3.37044 ( 12) link_ALPHA1-4 : bond 0.02648 ( 1) link_ALPHA1-4 : angle 4.71531 ( 3) link_ALPHA1-6 : bond 0.00207 ( 1) link_ALPHA1-6 : angle 1.99598 ( 3) link_BETA1-3 : bond 0.01151 ( 4) link_BETA1-3 : angle 1.60447 ( 12) link_BETA1-4 : bond 0.00784 ( 44) link_BETA1-4 : angle 2.60942 ( 132) link_BETA1-6 : bond 0.00486 ( 2) link_BETA1-6 : angle 1.93440 ( 6) link_NAG-ASN : bond 0.00574 ( 54) link_NAG-ASN : angle 3.53798 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 410 time to evaluate : 1.038 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 TRP cc_start: 0.6258 (t60) cc_final: 0.5718 (t60) REVERT: A 503 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7808 (mtm180) REVERT: B 104 MET cc_start: 0.8745 (ttt) cc_final: 0.8408 (ttt) REVERT: B 217 TYR cc_start: 0.8106 (m-80) cc_final: 0.7888 (m-80) REVERT: B 289 ASN cc_start: 0.7768 (p0) cc_final: 0.7171 (t0) REVERT: C 69 TRP cc_start: 0.5981 (OUTLIER) cc_final: 0.5128 (t60) REVERT: C 195 ASN cc_start: 0.7501 (p0) cc_final: 0.7151 (p0) REVERT: C 271 MET cc_start: 0.7315 (mmm) cc_final: 0.7098 (mmt) REVERT: D 540 GLN cc_start: 0.8668 (mt0) cc_final: 0.8283 (mt0) REVERT: D 590 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: D 607 ASN cc_start: 0.8513 (m-40) cc_final: 0.8051 (p0) REVERT: E 543 ASN cc_start: 0.7998 (t0) cc_final: 0.7530 (t0) REVERT: F 638 TYR cc_start: 0.7016 (m-80) cc_final: 0.6671 (m-80) REVERT: F 650 GLN cc_start: 0.7761 (mm110) cc_final: 0.7290 (mm-40) REVERT: F 657 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7466 (mp0) REVERT: G 80 MET cc_start: 0.8139 (tmm) cc_final: 0.7366 (tmm) REVERT: G 96 MET cc_start: 0.8136 (mmm) cc_final: 0.7680 (tmm) REVERT: H 13 LYS cc_start: 0.8443 (mttt) cc_final: 0.8120 (mmmt) REVERT: H 32 TYR cc_start: 0.8293 (m-80) cc_final: 0.7768 (m-80) REVERT: H 98 ASP cc_start: 0.8459 (t0) cc_final: 0.8189 (t0) REVERT: H 100 ASP cc_start: 0.7045 (p0) cc_final: 0.6744 (p0) REVERT: I 91 TYR cc_start: 0.8572 (m-80) cc_final: 0.8241 (m-80) REVERT: I 97 PHE cc_start: 0.7660 (m-80) cc_final: 0.7408 (m-80) REVERT: J 78 LEU cc_start: 0.6011 (mt) cc_final: 0.5558 (tp) REVERT: K 85 ASP cc_start: 0.7504 (t0) cc_final: 0.7283 (t0) REVERT: L 17 GLN cc_start: 0.6162 (pp30) cc_final: 0.5797 (pp30) REVERT: L 85 ASP cc_start: 0.7744 (m-30) cc_final: 0.6706 (t0) REVERT: M 2 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7083 (p) REVERT: M 3 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7962 (mm-40) REVERT: M 96 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.7093 (ttp-170) REVERT: N 5 GLN cc_start: 0.8226 (tp40) cc_final: 0.7665 (tp40) REVERT: N 29 MET cc_start: 0.6241 (tmm) cc_final: 0.5858 (tpp) REVERT: N 34 TRP cc_start: 0.5696 (m100) cc_final: 0.5047 (m100) REVERT: O 43 LYS cc_start: 0.6789 (ttmt) cc_final: 0.6565 (tttt) REVERT: O 77 GLN cc_start: 0.7336 (tp-100) cc_final: 0.7013 (tp-100) REVERT: O 78 LEU cc_start: 0.6992 (tt) cc_final: 0.6148 (mt) REVERT: O 100 MET cc_start: 0.7758 (mmt) cc_final: 0.7201 (mmp) REVERT: O 103 TRP cc_start: 0.6652 (m100) cc_final: 0.6225 (m-10) REVERT: P 34 GLN cc_start: 0.8778 (mp-120) cc_final: 0.7974 (mp10) REVERT: P 49 TYR cc_start: 0.8313 (p90) cc_final: 0.7940 (p90) REVERT: P 70 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6825 (mtp85) REVERT: Q 42 GLN cc_start: 0.6196 (tm-30) cc_final: 0.5994 (tm-30) REVERT: Q 65 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7848 (p) REVERT: Q 73 LEU cc_start: 0.8169 (tp) cc_final: 0.7964 (tp) REVERT: Q 83 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6916 (tm-30) REVERT: R 96 TRP cc_start: 0.7796 (m100) cc_final: 0.6987 (m100) outliers start: 100 outliers final: 76 residues processed: 478 average time/residue: 0.1638 time to fit residues: 126.1302 Evaluate side-chains 472 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 391 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 27 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 151 optimal weight: 0.3980 chunk 153 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.086956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066710 restraints weight = 84681.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068328 restraints weight = 53603.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068632 restraints weight = 37789.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068798 restraints weight = 36281.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068825 restraints weight = 33564.535| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26850 Z= 0.208 Angle : 0.797 14.737 36669 Z= 0.366 Chirality : 0.048 0.316 4333 Planarity : 0.004 0.046 4476 Dihedral : 9.714 96.600 5732 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.91 % Allowed : 23.19 % Favored : 72.90 % 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 aren not related in a simple way. whole: -1.83 (0.15), residues: 3105 helix: -0.61 (0.27), residues: 396 sheet: -0.73 (0.17), residues: 971 loop : -1.65 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 25 TYR 0.022 0.002 TYR F 586 PHE 0.024 0.002 PHE P 67 TRP 0.028 0.002 TRP N 34 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00470 (26692) covalent geometry : angle 0.73613 (36240) SS BOND : bond 0.00505 ( 45) SS BOND : angle 1.73685 ( 90) hydrogen bonds : bond 0.03424 ( 786) hydrogen bonds : angle 5.60991 ( 2103) link_ALPHA1-2 : bond 0.01503 ( 3) link_ALPHA1-2 : angle 3.15231 ( 9) link_ALPHA1-3 : bond 0.01969 ( 4) link_ALPHA1-3 : angle 3.34257 ( 12) link_ALPHA1-4 : bond 0.02795 ( 1) link_ALPHA1-4 : angle 5.00770 ( 3) link_ALPHA1-6 : bond 0.00384 ( 1) link_ALPHA1-6 : angle 1.95411 ( 3) link_BETA1-3 : bond 0.01192 ( 4) link_BETA1-3 : angle 1.68545 ( 12) link_BETA1-4 : bond 0.00783 ( 44) link_BETA1-4 : angle 2.67128 ( 132) link_BETA1-6 : bond 0.00413 ( 2) link_BETA1-6 : angle 1.93929 ( 6) link_NAG-ASN : bond 0.00574 ( 54) link_NAG-ASN : angle 3.59436 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 387 time to evaluate : 0.856 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: A 503 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: B 104 MET cc_start: 0.8803 (ttt) cc_final: 0.8468 (ttt) REVERT: B 289 ASN cc_start: 0.7864 (p0) cc_final: 0.7234 (t0) REVERT: C 69 TRP cc_start: 0.6126 (OUTLIER) cc_final: 0.5036 (t60) REVERT: C 195 ASN cc_start: 0.7442 (p0) cc_final: 0.7062 (p0) REVERT: C 271 MET cc_start: 0.7246 (mmm) cc_final: 0.7033 (mmt) REVERT: C 500 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7114 (tpt170) REVERT: D 590 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: D 607 ASN cc_start: 0.8417 (m-40) cc_final: 0.8091 (p0) REVERT: D 651 ASN cc_start: 0.7414 (m-40) cc_final: 0.6936 (m-40) REVERT: E 543 ASN cc_start: 0.8062 (t0) cc_final: 0.7457 (t0) REVERT: E 655 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7288 (ttmt) REVERT: F 638 TYR cc_start: 0.7107 (m-80) cc_final: 0.6753 (m-80) REVERT: F 650 GLN cc_start: 0.7749 (mm110) cc_final: 0.7298 (mm-40) REVERT: F 655 LYS cc_start: 0.8498 (mttt) cc_final: 0.8276 (mttt) REVERT: F 657 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7524 (mp0) REVERT: G 80 MET cc_start: 0.8138 (tmm) cc_final: 0.7400 (tmm) REVERT: G 96 MET cc_start: 0.8139 (mmm) cc_final: 0.7627 (tmm) REVERT: H 13 LYS cc_start: 0.8450 (mttt) cc_final: 0.8153 (mmmt) REVERT: H 32 TYR cc_start: 0.8380 (m-80) cc_final: 0.7813 (m-80) REVERT: H 48 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7642 (mmm) REVERT: H 98 ASP cc_start: 0.8526 (t0) cc_final: 0.8250 (t0) REVERT: H 100 ASP cc_start: 0.7047 (p0) cc_final: 0.6787 (p0) REVERT: I 97 PHE cc_start: 0.7751 (m-80) cc_final: 0.7511 (m-80) REVERT: J 78 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5561 (tp) REVERT: L 17 GLN cc_start: 0.6385 (pp30) cc_final: 0.5914 (pp30) REVERT: L 85 ASP cc_start: 0.7793 (m-30) cc_final: 0.6713 (t0) REVERT: M 2 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7135 (p) REVERT: M 3 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7902 (mm-40) REVERT: M 29 MET cc_start: 0.4814 (tmm) cc_final: 0.4579 (tmm) REVERT: M 96 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.7086 (ttp-170) REVERT: N 5 GLN cc_start: 0.8152 (tp40) cc_final: 0.7600 (tp40) REVERT: N 34 TRP cc_start: 0.5837 (m100) cc_final: 0.5467 (m100) REVERT: O 43 LYS cc_start: 0.6759 (ttmt) cc_final: 0.6549 (tttt) REVERT: O 77 GLN cc_start: 0.7359 (tp-100) cc_final: 0.7066 (tp-100) REVERT: O 78 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6136 (mt) REVERT: O 100 MET cc_start: 0.7795 (mmt) cc_final: 0.7257 (mmp) REVERT: O 103 TRP cc_start: 0.6703 (m100) cc_final: 0.6244 (m-10) REVERT: P 70 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6797 (mtp85) REVERT: P 87 TYR cc_start: 0.7605 (m-80) cc_final: 0.7353 (m-80) REVERT: Q 26 GLN cc_start: 0.8028 (tp40) cc_final: 0.7806 (tp40) REVERT: Q 65 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7819 (p) REVERT: Q 73 LEU cc_start: 0.8111 (tp) cc_final: 0.7742 (tp) REVERT: R 96 TRP cc_start: 0.7841 (m100) cc_final: 0.7006 (m100) outliers start: 106 outliers final: 81 residues processed: 457 average time/residue: 0.1812 time to fit residues: 131.0481 Evaluate side-chains 464 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 375 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 59 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 171 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066310 restraints weight = 84140.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067994 restraints weight = 51040.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068337 restraints weight = 36296.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068497 restraints weight = 32855.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068603 restraints weight = 30222.105| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26850 Z= 0.213 Angle : 0.806 14.265 36669 Z= 0.372 Chirality : 0.048 0.311 4333 Planarity : 0.004 0.048 4476 Dihedral : 9.691 95.903 5732 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.76 % Allowed : 23.60 % Favored : 72.64 % 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 aren not related in a simple way. whole: -1.85 (0.15), residues: 3105 helix: -0.72 (0.26), residues: 399 sheet: -0.70 (0.17), residues: 923 loop : -1.66 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 38 TYR 0.023 0.002 TYR J 89 PHE 0.022 0.002 PHE P 67 TRP 0.024 0.002 TRP B 96 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00480 (26692) covalent geometry : angle 0.74757 (36240) SS BOND : bond 0.00772 ( 45) SS BOND : angle 1.71962 ( 90) hydrogen bonds : bond 0.03437 ( 786) hydrogen bonds : angle 5.66415 ( 2103) link_ALPHA1-2 : bond 0.01338 ( 3) link_ALPHA1-2 : angle 3.25856 ( 9) link_ALPHA1-3 : bond 0.01963 ( 4) link_ALPHA1-3 : angle 3.33594 ( 12) link_ALPHA1-4 : bond 0.02676 ( 1) link_ALPHA1-4 : angle 5.09389 ( 3) link_ALPHA1-6 : bond 0.00362 ( 1) link_ALPHA1-6 : angle 1.89460 ( 3) link_BETA1-3 : bond 0.01148 ( 4) link_BETA1-3 : angle 1.71572 ( 12) link_BETA1-4 : bond 0.00775 ( 44) link_BETA1-4 : angle 2.64389 ( 132) link_BETA1-6 : bond 0.00417 ( 2) link_BETA1-6 : angle 1.98394 ( 6) link_NAG-ASN : bond 0.00601 ( 54) link_NAG-ASN : angle 3.53826 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 381 time to evaluate : 1.043 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: A 503 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7790 (ttm170) REVERT: B 289 ASN cc_start: 0.7902 (p0) cc_final: 0.7195 (t0) REVERT: C 69 TRP cc_start: 0.6167 (OUTLIER) cc_final: 0.4725 (t60) REVERT: C 195 ASN cc_start: 0.7605 (p0) cc_final: 0.7221 (p0) REVERT: C 207 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6707 (ttmm) REVERT: C 500 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7093 (tpt170) REVERT: D 542 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7127 (ttp-170) REVERT: D 607 ASN cc_start: 0.8498 (m-40) cc_final: 0.8059 (p0) REVERT: D 651 ASN cc_start: 0.7120 (m-40) cc_final: 0.6891 (m-40) REVERT: E 543 ASN cc_start: 0.8053 (t0) cc_final: 0.7422 (t0) REVERT: F 638 TYR cc_start: 0.7174 (m-80) cc_final: 0.6799 (m-80) REVERT: F 647 GLU cc_start: 0.8033 (pt0) cc_final: 0.7604 (pt0) REVERT: F 650 GLN cc_start: 0.7771 (mm110) cc_final: 0.7306 (mm-40) REVERT: F 657 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7585 (mp0) REVERT: G 80 MET cc_start: 0.8205 (tmm) cc_final: 0.7400 (tmm) REVERT: G 96 MET cc_start: 0.8189 (mmm) cc_final: 0.7699 (tmm) REVERT: H 13 LYS cc_start: 0.8468 (mttt) cc_final: 0.8179 (mmmt) REVERT: H 32 TYR cc_start: 0.8396 (m-80) cc_final: 0.7832 (m-80) REVERT: H 48 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7652 (mmm) REVERT: H 98 ASP cc_start: 0.8558 (t0) cc_final: 0.8312 (t0) REVERT: I 97 PHE cc_start: 0.7852 (m-80) cc_final: 0.7622 (m-80) REVERT: J 78 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5508 (tp) REVERT: K 66 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7754 (mtpp) REVERT: L 17 GLN cc_start: 0.6338 (pp30) cc_final: 0.5822 (pp30) REVERT: L 85 ASP cc_start: 0.7819 (m-30) cc_final: 0.6691 (t0) REVERT: M 2 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7298 (p) REVERT: M 3 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7972 (mm-40) REVERT: N 5 GLN cc_start: 0.8131 (tp40) cc_final: 0.7561 (tp40) REVERT: N 34 TRP cc_start: 0.5795 (m100) cc_final: 0.5527 (m100) REVERT: O 43 LYS cc_start: 0.6710 (ttmt) cc_final: 0.6448 (tttt) REVERT: O 51 ILE cc_start: 0.7746 (tp) cc_final: 0.7277 (mt) REVERT: O 77 GLN cc_start: 0.7323 (tp-100) cc_final: 0.7069 (tp-100) REVERT: O 78 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6168 (mt) REVERT: O 100 MET cc_start: 0.7843 (mmt) cc_final: 0.7225 (mmp) REVERT: O 103 TRP cc_start: 0.6722 (m100) cc_final: 0.6317 (m-10) REVERT: P 70 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6867 (mtp85) REVERT: P 87 TYR cc_start: 0.7574 (m-80) cc_final: 0.7353 (m-80) REVERT: Q 65 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7809 (p) REVERT: Q 73 LEU cc_start: 0.8040 (tp) cc_final: 0.7744 (tp) REVERT: R 96 TRP cc_start: 0.7801 (m100) cc_final: 0.6972 (m100) outliers start: 102 outliers final: 81 residues processed: 448 average time/residue: 0.1668 time to fit residues: 119.1180 Evaluate side-chains 458 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 368 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 219 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 252 optimal weight: 0.0970 chunk 292 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066961 restraints weight = 84060.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068053 restraints weight = 52444.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068317 restraints weight = 40716.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068625 restraints weight = 39153.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068730 restraints weight = 33746.530| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26850 Z= 0.183 Angle : 0.786 14.214 36669 Z= 0.364 Chirality : 0.048 0.308 4333 Planarity : 0.004 0.050 4476 Dihedral : 9.509 94.522 5732 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.50 % Allowed : 23.82 % Favored : 72.68 % 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 aren not related in a simple way. whole: -1.78 (0.15), residues: 3105 helix: -0.59 (0.27), residues: 396 sheet: -0.67 (0.17), residues: 923 loop : -1.63 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 25 TYR 0.025 0.002 TYR J 89 PHE 0.027 0.001 PHE P 67 TRP 0.031 0.002 TRP O 36 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00413 (26692) covalent geometry : angle 0.73037 (36240) SS BOND : bond 0.00532 ( 45) SS BOND : angle 1.65061 ( 90) hydrogen bonds : bond 0.03349 ( 786) hydrogen bonds : angle 5.60795 ( 2103) link_ALPHA1-2 : bond 0.01256 ( 3) link_ALPHA1-2 : angle 3.29151 ( 9) link_ALPHA1-3 : bond 0.01953 ( 4) link_ALPHA1-3 : angle 3.37422 ( 12) link_ALPHA1-4 : bond 0.02866 ( 1) link_ALPHA1-4 : angle 5.19378 ( 3) link_ALPHA1-6 : bond 0.00243 ( 1) link_ALPHA1-6 : angle 1.82111 ( 3) link_BETA1-3 : bond 0.01010 ( 4) link_BETA1-3 : angle 1.60238 ( 12) link_BETA1-4 : bond 0.00763 ( 44) link_BETA1-4 : angle 2.54305 ( 132) link_BETA1-6 : bond 0.00425 ( 2) link_BETA1-6 : angle 1.96138 ( 6) link_NAG-ASN : bond 0.00556 ( 54) link_NAG-ASN : angle 3.38577 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 372 time to evaluate : 1.021 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: A 503 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7849 (mtm180) REVERT: B 289 ASN cc_start: 0.7905 (p0) cc_final: 0.7224 (t0) REVERT: C 69 TRP cc_start: 0.6174 (OUTLIER) cc_final: 0.4601 (t60) REVERT: C 195 ASN cc_start: 0.7524 (p0) cc_final: 0.7157 (p0) REVERT: C 207 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6715 (ttmm) REVERT: D 607 ASN cc_start: 0.8499 (m-40) cc_final: 0.7989 (p0) REVERT: E 543 ASN cc_start: 0.7993 (t0) cc_final: 0.7346 (t0) REVERT: F 638 TYR cc_start: 0.7184 (m-80) cc_final: 0.6827 (m-80) REVERT: F 650 GLN cc_start: 0.7754 (mm110) cc_final: 0.7275 (mm-40) REVERT: F 657 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7705 (mp0) REVERT: G 80 MET cc_start: 0.8141 (tmm) cc_final: 0.7368 (tmm) REVERT: G 96 MET cc_start: 0.8190 (mmm) cc_final: 0.7670 (tmm) REVERT: H 13 LYS cc_start: 0.8444 (mttt) cc_final: 0.8149 (mmmt) REVERT: H 32 TYR cc_start: 0.8279 (m-80) cc_final: 0.7770 (m-80) REVERT: H 48 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: H 98 ASP cc_start: 0.8532 (t0) cc_final: 0.8305 (t0) REVERT: I 97 PHE cc_start: 0.7805 (m-80) cc_final: 0.7569 (m-80) REVERT: J 78 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5403 (tp) REVERT: L 85 ASP cc_start: 0.7757 (m-30) cc_final: 0.6673 (t0) REVERT: M 2 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7168 (p) REVERT: M 3 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7861 (mm-40) REVERT: N 5 GLN cc_start: 0.8050 (tp40) cc_final: 0.7484 (tp40) REVERT: N 34 TRP cc_start: 0.5618 (m100) cc_final: 0.5349 (m100) REVERT: N 59 TYR cc_start: 0.7452 (m-10) cc_final: 0.7203 (m-10) REVERT: O 43 LYS cc_start: 0.6735 (ttmt) cc_final: 0.6467 (tttt) REVERT: O 51 ILE cc_start: 0.7751 (tp) cc_final: 0.7265 (mt) REVERT: O 77 GLN cc_start: 0.7357 (tp-100) cc_final: 0.7112 (tp-100) REVERT: O 78 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6162 (mt) REVERT: O 100 MET cc_start: 0.7770 (mmt) cc_final: 0.7183 (mmp) REVERT: O 103 TRP cc_start: 0.6643 (m100) cc_final: 0.6263 (m-10) REVERT: Q 65 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7842 (p) REVERT: Q 73 LEU cc_start: 0.8057 (tp) cc_final: 0.7697 (tp) REVERT: Q 87 TYR cc_start: 0.7071 (m-80) cc_final: 0.6763 (m-80) REVERT: R 96 TRP cc_start: 0.7774 (m100) cc_final: 0.6904 (m100) outliers start: 95 outliers final: 83 residues processed: 434 average time/residue: 0.1531 time to fit residues: 107.6482 Evaluate side-chains 453 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 363 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 218 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.086660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066681 restraints weight = 83983.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067866 restraints weight = 53219.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068083 restraints weight = 40023.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068335 restraints weight = 37941.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068432 restraints weight = 34441.660| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26850 Z= 0.194 Angle : 0.801 13.981 36669 Z= 0.371 Chirality : 0.048 0.310 4333 Planarity : 0.004 0.051 4476 Dihedral : 9.451 93.404 5732 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.61 % Allowed : 23.78 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 3105 helix: -0.62 (0.27), residues: 399 sheet: -0.67 (0.17), residues: 923 loop : -1.62 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 25 TYR 0.030 0.002 TYR D 643 PHE 0.032 0.002 PHE P 67 TRP 0.027 0.002 TRP O 36 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00439 (26692) covalent geometry : angle 0.74705 (36240) SS BOND : bond 0.00526 ( 45) SS BOND : angle 1.67178 ( 90) hydrogen bonds : bond 0.03355 ( 786) hydrogen bonds : angle 5.60093 ( 2103) link_ALPHA1-2 : bond 0.01130 ( 3) link_ALPHA1-2 : angle 3.32336 ( 9) link_ALPHA1-3 : bond 0.02029 ( 4) link_ALPHA1-3 : angle 3.38263 ( 12) link_ALPHA1-4 : bond 0.02617 ( 1) link_ALPHA1-4 : angle 5.22771 ( 3) link_ALPHA1-6 : bond 0.00293 ( 1) link_ALPHA1-6 : angle 1.79707 ( 3) link_BETA1-3 : bond 0.01060 ( 4) link_BETA1-3 : angle 1.56976 ( 12) link_BETA1-4 : bond 0.00769 ( 44) link_BETA1-4 : angle 2.53100 ( 132) link_BETA1-6 : bond 0.00436 ( 2) link_BETA1-6 : angle 1.96526 ( 6) link_NAG-ASN : bond 0.00561 ( 54) link_NAG-ASN : angle 3.35611 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.69 seconds wall clock time: 83 minutes 59.29 seconds (5039.29 seconds total)