Starting phenix.real_space_refine on Sat Mar 7 05:56:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sd1_10145/03_2026/6sd1_10145.map" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 23958 2.51 5 N 7359 2.21 5 O 7953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 223 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39369 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "C" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "E" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "F" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "G" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "J" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "K" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "L" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "O" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Q" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "R" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "T" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "U" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "W" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "X" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Y" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Z" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "c" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "d" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "e" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "f" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "g" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Time building chain proxies: 9.28, per 1000 atoms: 0.24 Number of scatterers: 39369 At special positions: 0 Unit cell: (244.134, 244.134, 97.818, 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 99 16.00 O 7953 8.00 N 7359 7.00 C 23958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9570 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 99 sheets defined 29.4% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.824A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.699A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.540A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.670A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.502A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.667A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 removed outlier: 3.538A pdb=" N SER D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.627A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.630A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.646A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 253 Processing helix chain 'G' and resid 253 through 258 Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.633A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 253 Processing helix chain 'H' and resid 253 through 258 Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.640A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.669A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 253 Processing helix chain 'J' and resid 253 through 258 Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.698A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.515A pdb=" N SER K 254 " --> pdb=" O GLU K 250 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.569A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.562A pdb=" N SER L 254 " --> pdb=" O GLU L 250 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.637A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.605A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.623A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 253 Processing helix chain 'O' and resid 253 through 258 Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.615A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 253 Processing helix chain 'P' and resid 253 through 258 Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.695A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 253 Processing helix chain 'Q' and resid 253 through 258 Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.628A pdb=" N LEU Q 415 " --> pdb=" O GLN Q 411 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.531A pdb=" N SER R 254 " --> pdb=" O GLU R 250 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.641A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 253 Processing helix chain 'S' and resid 253 through 258 Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.692A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.647A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.590A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.504A pdb=" N SER V 254 " --> pdb=" O GLU V 250 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.664A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 253 Processing helix chain 'W' and resid 253 through 258 Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.613A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 253 Processing helix chain 'X' and resid 253 through 258 Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.724A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 253 Processing helix chain 'Y' and resid 253 through 258 Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.644A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.682A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.628A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.510A pdb=" N GLU b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.586A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.638A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.634A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 253 Processing helix chain 'f' and resid 253 through 258 Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.592A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.646A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=B, first strand: chain 'A' and resid 429 through 434 removed outlier: 3.544A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 292 through 302 removed outlier: 4.208A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 298 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 361 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE A 300 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 359 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=E, first strand: chain 'B' and resid 429 through 434 removed outlier: 3.578A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 292 through 303 removed outlier: 4.193A pdb=" N THR B 292 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 298 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 361 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 300 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN B 359 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 302 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 357 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=H, first strand: chain 'C' and resid 429 through 434 removed outlier: 3.594A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR C 292 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 298 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN C 361 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE C 300 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN C 359 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 302 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 357 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 276 through 278 Processing sheet with id=K, first strand: chain 'D' and resid 429 through 434 removed outlier: 3.632A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'D' and resid 292 through 303 removed outlier: 4.208A pdb=" N THR D 292 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU D 298 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN D 361 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE D 300 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN D 359 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 302 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 357 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=N, first strand: chain 'E' and resid 429 through 434 removed outlier: 3.594A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'E' and resid 293 through 303 removed outlier: 6.634A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE E 300 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN E 359 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU E 302 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 357 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'F' and resid 276 through 278 Processing sheet with id=Q, first strand: chain 'F' and resid 429 through 434 removed outlier: 3.590A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'F' and resid 292 through 302 removed outlier: 4.202A pdb=" N THR F 292 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 298 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN F 361 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE F 300 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN F 359 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'G' and resid 276 through 278 Processing sheet with id=T, first strand: chain 'G' and resid 429 through 434 removed outlier: 3.596A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'G' and resid 292 through 302 removed outlier: 4.245A pdb=" N THR G 292 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU G 298 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN G 361 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE G 300 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 359 " --> pdb=" O ILE G 300 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'H' and resid 276 through 278 Processing sheet with id=W, first strand: chain 'H' and resid 429 through 434 removed outlier: 3.592A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'H' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR H 292 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE H 300 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN H 359 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU H 302 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER H 357 " --> pdb=" O GLU H 302 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'I' and resid 276 through 278 Processing sheet with id=Z, first strand: chain 'I' and resid 429 through 434 removed outlier: 3.559A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'I' and resid 292 through 302 removed outlier: 4.204A pdb=" N THR I 292 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU I 298 " --> pdb=" O ASN I 361 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN I 361 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE I 300 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN I 359 " --> pdb=" O ILE I 300 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'J' and resid 276 through 278 Processing sheet with id=AC, first strand: chain 'J' and resid 429 through 434 removed outlier: 3.614A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'J' and resid 293 through 303 removed outlier: 6.653A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU J 298 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN J 361 " --> pdb=" O LEU J 298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE J 300 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN J 359 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU J 302 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER J 357 " --> pdb=" O GLU J 302 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'K' and resid 276 through 278 Processing sheet with id=AF, first strand: chain 'K' and resid 429 through 434 removed outlier: 3.589A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'K' and resid 292 through 303 removed outlier: 4.223A pdb=" N THR K 292 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU K 298 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN K 361 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE K 300 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN K 359 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU K 302 " --> pdb=" O SER K 357 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER K 357 " --> pdb=" O GLU K 302 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'L' and resid 276 through 278 Processing sheet with id=AI, first strand: chain 'L' and resid 429 through 434 removed outlier: 3.588A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'L' and resid 292 through 303 removed outlier: 4.214A pdb=" N THR L 292 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU L 298 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN L 361 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE L 300 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN L 359 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU L 302 " --> pdb=" O SER L 357 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER L 357 " --> pdb=" O GLU L 302 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'M' and resid 276 through 278 Processing sheet with id=AL, first strand: chain 'M' and resid 429 through 434 removed outlier: 3.575A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'M' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR M 292 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 298 " --> pdb=" O ASN M 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN M 361 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE M 300 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN M 359 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU M 302 " --> pdb=" O SER M 357 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER M 357 " --> pdb=" O GLU M 302 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'N' and resid 276 through 278 Processing sheet with id=AO, first strand: chain 'N' and resid 429 through 434 removed outlier: 3.651A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'N' and resid 292 through 303 removed outlier: 4.226A pdb=" N THR N 292 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU N 298 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN N 361 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE N 300 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN N 359 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU N 302 " --> pdb=" O SER N 357 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER N 357 " --> pdb=" O GLU N 302 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'O' and resid 276 through 278 Processing sheet with id=AR, first strand: chain 'O' and resid 429 through 434 removed outlier: 3.553A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'O' and resid 292 through 302 removed outlier: 4.214A pdb=" N THR O 292 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU O 298 " --> pdb=" O ASN O 361 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN O 361 " --> pdb=" O LEU O 298 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE O 300 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN O 359 " --> pdb=" O ILE O 300 " (cutoff:3.500A) Processing sheet with id=AT, first strand: chain 'P' and resid 276 through 278 Processing sheet with id=AU, first strand: chain 'P' and resid 429 through 434 removed outlier: 3.524A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) Processing sheet with id=AV, first strand: chain 'P' and resid 292 through 303 removed outlier: 4.207A pdb=" N THR P 292 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU P 298 " --> pdb=" O ASN P 361 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN P 361 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE P 300 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN P 359 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU P 302 " --> pdb=" O SER P 357 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER P 357 " --> pdb=" O GLU P 302 " (cutoff:3.500A) Processing sheet with id=AW, first strand: chain 'Q' and resid 276 through 278 Processing sheet with id=AX, first strand: chain 'Q' and resid 429 through 434 removed outlier: 3.593A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) Processing sheet with id=AY, first strand: chain 'Q' and resid 292 through 302 removed outlier: 4.221A pdb=" N THR Q 292 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU Q 298 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN Q 361 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE Q 300 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN Q 359 " --> pdb=" O ILE Q 300 " (cutoff:3.500A) Processing sheet with id=AZ, first strand: chain 'R' and resid 276 through 278 Processing sheet with id=BA, first strand: chain 'R' and resid 429 through 434 removed outlier: 3.608A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'R' and resid 292 through 303 removed outlier: 4.189A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU R 298 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN R 361 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE R 300 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN R 359 " --> pdb=" O ILE R 300 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU R 302 " --> pdb=" O SER R 357 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER R 357 " --> pdb=" O GLU R 302 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'S' and resid 276 through 278 Processing sheet with id=BD, first strand: chain 'S' and resid 429 through 434 removed outlier: 3.624A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'S' and resid 292 through 303 removed outlier: 4.194A pdb=" N THR S 292 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU S 298 " --> pdb=" O ASN S 361 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN S 361 " --> pdb=" O LEU S 298 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE S 300 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN S 359 " --> pdb=" O ILE S 300 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU S 302 " --> pdb=" O SER S 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER S 357 " --> pdb=" O GLU S 302 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'T' and resid 276 through 278 Processing sheet with id=BG, first strand: chain 'T' and resid 429 through 434 removed outlier: 3.585A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) Processing sheet with id=BH, first strand: chain 'T' and resid 292 through 302 removed outlier: 4.232A pdb=" N THR T 292 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE T 300 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN T 359 " --> pdb=" O ILE T 300 " (cutoff:3.500A) Processing sheet with id=BI, first strand: chain 'U' and resid 276 through 278 Processing sheet with id=BJ, first strand: chain 'U' and resid 429 through 434 removed outlier: 3.577A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'U' and resid 292 through 303 removed outlier: 4.210A pdb=" N THR U 292 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU U 298 " --> pdb=" O ASN U 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN U 361 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE U 300 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN U 359 " --> pdb=" O ILE U 300 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU U 302 " --> pdb=" O SER U 357 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER U 357 " --> pdb=" O GLU U 302 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'V' and resid 276 through 278 Processing sheet with id=BM, first strand: chain 'V' and resid 429 through 434 removed outlier: 3.548A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'V' and resid 292 through 303 removed outlier: 4.197A pdb=" N THR V 292 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE V 300 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN V 359 " --> pdb=" O ILE V 300 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU V 302 " --> pdb=" O SER V 357 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER V 357 " --> pdb=" O GLU V 302 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'W' and resid 276 through 278 Processing sheet with id=BP, first strand: chain 'W' and resid 429 through 434 removed outlier: 3.535A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) Processing sheet with id=BQ, first strand: chain 'W' and resid 292 through 303 removed outlier: 4.191A pdb=" N THR W 292 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU W 298 " --> pdb=" O ASN W 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN W 361 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE W 300 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN W 359 " --> pdb=" O ILE W 300 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU W 302 " --> pdb=" O SER W 357 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER W 357 " --> pdb=" O GLU W 302 " (cutoff:3.500A) Processing sheet with id=BR, first strand: chain 'X' and resid 276 through 278 Processing sheet with id=BS, first strand: chain 'X' and resid 429 through 434 removed outlier: 3.608A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) Processing sheet with id=BT, first strand: chain 'X' and resid 292 through 303 removed outlier: 4.194A pdb=" N THR X 292 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU X 298 " --> pdb=" O ASN X 361 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN X 361 " --> pdb=" O LEU X 298 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE X 300 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN X 359 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU X 302 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER X 357 " --> pdb=" O GLU X 302 " (cutoff:3.500A) Processing sheet with id=BU, first strand: chain 'Y' and resid 276 through 278 Processing sheet with id=BV, first strand: chain 'Y' and resid 429 through 434 removed outlier: 3.543A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) Processing sheet with id=BW, first strand: chain 'Y' and resid 292 through 302 removed outlier: 4.205A pdb=" N THR Y 292 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE Y 300 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN Y 359 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) Processing sheet with id=BX, first strand: chain 'Z' and resid 276 through 278 Processing sheet with id=BY, first strand: chain 'Z' and resid 429 through 434 removed outlier: 3.603A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) Processing sheet with id=BZ, first strand: chain 'Z' and resid 292 through 303 removed outlier: 4.190A pdb=" N THR Z 292 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU Z 298 " --> pdb=" O ASN Z 361 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN Z 361 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE Z 300 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN Z 359 " --> pdb=" O ILE Z 300 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU Z 302 " --> pdb=" O SER Z 357 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER Z 357 " --> pdb=" O GLU Z 302 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'a' and resid 276 through 278 Processing sheet with id=CB, first strand: chain 'a' and resid 429 through 434 removed outlier: 3.618A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'a' and resid 292 through 303 removed outlier: 4.214A pdb=" N THR a 292 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU a 298 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN a 361 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE a 300 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN a 359 " --> pdb=" O ILE a 300 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU a 302 " --> pdb=" O SER a 357 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER a 357 " --> pdb=" O GLU a 302 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'b' and resid 276 through 278 Processing sheet with id=CE, first strand: chain 'b' and resid 429 through 434 removed outlier: 3.589A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'b' and resid 292 through 303 removed outlier: 4.201A pdb=" N THR b 292 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU b 298 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN b 361 " --> pdb=" O LEU b 298 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE b 300 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN b 359 " --> pdb=" O ILE b 300 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU b 302 " --> pdb=" O SER b 357 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER b 357 " --> pdb=" O GLU b 302 " (cutoff:3.500A) Processing sheet with id=CG, first strand: chain 'c' and resid 276 through 278 Processing sheet with id=CH, first strand: chain 'c' and resid 429 through 434 removed outlier: 3.584A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'c' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR c 292 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU c 298 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN c 361 " --> pdb=" O LEU c 298 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE c 300 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN c 359 " --> pdb=" O ILE c 300 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU c 302 " --> pdb=" O SER c 357 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER c 357 " --> pdb=" O GLU c 302 " (cutoff:3.500A) Processing sheet with id=CJ, first strand: chain 'd' and resid 276 through 278 Processing sheet with id=CK, first strand: chain 'd' and resid 429 through 434 removed outlier: 3.596A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) Processing sheet with id=CL, first strand: chain 'd' and resid 292 through 302 removed outlier: 4.202A pdb=" N THR d 292 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU d 298 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN d 361 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE d 300 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN d 359 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id=CM, first strand: chain 'e' and resid 276 through 278 Processing sheet with id=CN, first strand: chain 'e' and resid 429 through 434 removed outlier: 3.559A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) Processing sheet with id=CO, first strand: chain 'e' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR e 292 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU e 298 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN e 361 " --> pdb=" O LEU e 298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE e 300 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN e 359 " --> pdb=" O ILE e 300 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU e 302 " --> pdb=" O SER e 357 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER e 357 " --> pdb=" O GLU e 302 " (cutoff:3.500A) Processing sheet with id=CP, first strand: chain 'f' and resid 276 through 278 Processing sheet with id=CQ, first strand: chain 'f' and resid 429 through 434 removed outlier: 3.551A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) Processing sheet with id=CR, first strand: chain 'f' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR f 292 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU f 298 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN f 361 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE f 300 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN f 359 " --> pdb=" O ILE f 300 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU f 302 " --> pdb=" O SER f 357 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER f 357 " --> pdb=" O GLU f 302 " (cutoff:3.500A) Processing sheet with id=CS, first strand: chain 'g' and resid 276 through 278 Processing sheet with id=CT, first strand: chain 'g' and resid 429 through 434 removed outlier: 3.557A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) Processing sheet with id=CU, first strand: chain 'g' and resid 292 through 303 removed outlier: 4.224A pdb=" N THR g 292 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU g 298 " --> pdb=" O ASN g 361 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN g 361 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE g 300 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN g 359 " --> pdb=" O ILE g 300 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU g 302 " --> pdb=" O SER g 357 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER g 357 " --> pdb=" O GLU g 302 " (cutoff:3.500A) 1441 hydrogen bonds defined for protein. 4224 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: 8.70 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14157 1.34 - 1.46: 5214 1.46 - 1.57: 20196 1.57 - 1.69: 0 1.69 - 1.80: 198 Bond restraints: 39765 Sorted by residual: bond pdb=" CA GLU O 280 " pdb=" C GLU O 280 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.11e+00 bond pdb=" CA GLU P 280 " pdb=" C GLU P 280 " ideal model delta sigma weight residual 1.533 1.524 0.010 9.60e-03 1.09e+04 9.85e-01 bond pdb=" CA GLU d 280 " pdb=" C GLU d 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.45e-01 bond pdb=" CA GLU H 280 " pdb=" C GLU H 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.41e-01 bond pdb=" CA GLU g 280 " pdb=" C GLU g 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.34e-01 ... (remaining 39760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 50935 1.06 - 2.11: 2263 2.11 - 3.17: 260 3.17 - 4.23: 83 4.23 - 5.29: 51 Bond angle restraints: 53592 Sorted by residual: angle pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " pdb=" C GLY Y 421 " ideal model delta sigma weight residual 113.18 107.89 5.29 2.37e+00 1.78e-01 4.97e+00 angle pdb=" N GLY F 421 " pdb=" CA GLY F 421 " pdb=" C GLY F 421 " ideal model delta sigma weight residual 113.18 107.95 5.23 2.37e+00 1.78e-01 4.87e+00 angle pdb=" N GLY g 421 " pdb=" CA GLY g 421 " pdb=" C GLY g 421 " ideal model delta sigma weight residual 113.18 107.99 5.19 2.37e+00 1.78e-01 4.79e+00 angle pdb=" N GLY W 421 " pdb=" CA GLY W 421 " pdb=" C GLY W 421 " ideal model delta sigma weight residual 113.18 108.01 5.17 2.37e+00 1.78e-01 4.76e+00 angle pdb=" C TYR R 282 " pdb=" N SER R 283 " pdb=" CA SER R 283 " ideal model delta sigma weight residual 120.67 117.75 2.92 1.34e+00 5.57e-01 4.74e+00 ... (remaining 53587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 23053 18.00 - 36.00: 1526 36.00 - 54.00: 225 54.00 - 72.00: 20 72.00 - 90.00: 25 Dihedral angle restraints: 24849 sinusoidal: 10296 harmonic: 14553 Sorted by residual: dihedral pdb=" CA MET F 420 " pdb=" C MET F 420 " pdb=" N GLY F 421 " pdb=" CA GLY F 421 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA MET Y 420 " pdb=" C MET Y 420 " pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET B 420 " pdb=" C MET B 420 " pdb=" N GLY B 421 " pdb=" CA GLY B 421 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 24846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3436 0.024 - 0.048: 1714 0.048 - 0.073: 504 0.073 - 0.097: 328 0.097 - 0.121: 156 Chirality restraints: 6138 Sorted by residual: chirality pdb=" CA ILE f 382 " pdb=" N ILE f 382 " pdb=" C ILE f 382 " pdb=" CB ILE f 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE e 382 " pdb=" N ILE e 382 " pdb=" C ILE e 382 " pdb=" CB ILE e 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA ILE F 382 " pdb=" N ILE F 382 " pdb=" C ILE F 382 " pdb=" CB ILE F 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 6135 not shown) Planarity restraints: 7194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 254 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 255 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Y 254 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO Y 255 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO Y 255 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO Y 255 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 254 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO H 255 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 255 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 255 " 0.020 5.00e-02 4.00e+02 ... (remaining 7191 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 716 2.70 - 3.25: 36682 3.25 - 3.80: 60514 3.80 - 4.35: 89093 4.35 - 4.90: 142063 Nonbonded interactions: 329068 Sorted by model distance: nonbonded pdb=" O GLU B 250 " pdb=" OG SER B 254 " model vdw 2.149 3.040 nonbonded pdb=" O GLU T 250 " pdb=" OG SER T 254 " model vdw 2.156 3.040 nonbonded pdb=" O GLU L 250 " pdb=" OG SER L 254 " model vdw 2.179 3.040 nonbonded pdb=" O GLU I 250 " pdb=" OG SER I 254 " model vdw 2.182 3.040 nonbonded pdb=" O GLU U 250 " pdb=" OG SER U 254 " model vdw 2.183 3.040 ... (remaining 329063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 37.390 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.003 0.021 39765 Z= 0.163 Angle : 0.528 5.286 53592 Z= 0.322 Chirality : 0.037 0.121 6138 Planarity : 0.003 0.037 7194 Dihedral : 12.417 89.998 15279 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.11), residues: 4785 helix: -3.82 (0.07), residues: 1320 sheet: -0.64 (0.11), residues: 2442 loop : -1.66 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 248 TYR 0.020 0.002 TYR Z 393 PHE 0.011 0.001 PHE g 422 HIS 0.002 0.000 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00326 (39765) covalent geometry : angle 0.52775 (53592) hydrogen bonds : bond 0.23121 ( 1441) hydrogen bonds : angle 9.03174 ( 4224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1388 time to evaluate : 1.378 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 246 GLN cc_start: 0.8626 (tt0) cc_final: 0.8359 (tt0) REVERT: A 275 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7923 (tttt) REVERT: A 376 LYS cc_start: 0.7888 (tttt) cc_final: 0.7515 (mttp) REVERT: B 287 ASP cc_start: 0.7575 (t0) cc_final: 0.7365 (t70) REVERT: C 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7522 (mttp) REVERT: C 425 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8627 (mtmm) REVERT: D 246 GLN cc_start: 0.8538 (tt0) cc_final: 0.8312 (tt0) REVERT: D 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7355 (tp-100) REVERT: D 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7692 (mttp) REVERT: E 302 GLU cc_start: 0.6889 (tt0) cc_final: 0.6661 (tt0) REVERT: E 376 LYS cc_start: 0.7828 (tttt) cc_final: 0.7432 (mttp) REVERT: F 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7556 (mttp) REVERT: G 297 GLN cc_start: 0.7491 (tt0) cc_final: 0.7290 (tp-100) REVERT: G 376 LYS cc_start: 0.7946 (tttt) cc_final: 0.7557 (mttp) REVERT: H 297 GLN cc_start: 0.7572 (tt0) cc_final: 0.7316 (tp40) REVERT: H 376 LYS cc_start: 0.8027 (tttt) cc_final: 0.7622 (mttp) REVERT: H 410 LYS cc_start: 0.8391 (tmmt) cc_final: 0.8144 (tmmt) REVERT: I 376 LYS cc_start: 0.8056 (tttt) cc_final: 0.7637 (mttp) REVERT: J 235 LEU cc_start: 0.9192 (mt) cc_final: 0.8928 (mp) REVERT: J 246 GLN cc_start: 0.8534 (tt0) cc_final: 0.8228 (tt0) REVERT: J 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7476 (mttp) REVERT: J 383 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7579 (mt-10) REVERT: K 236 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7435 (mttm) REVERT: K 246 GLN cc_start: 0.8571 (tt0) cc_final: 0.8305 (tt0) REVERT: K 275 LYS cc_start: 0.8230 (ttmt) cc_final: 0.8020 (tttp) REVERT: K 376 LYS cc_start: 0.8027 (tttt) cc_final: 0.7668 (mttp) REVERT: L 246 GLN cc_start: 0.8606 (tt0) cc_final: 0.8405 (tt0) REVERT: L 297 GLN cc_start: 0.7539 (tt0) cc_final: 0.7327 (tp-100) REVERT: L 360 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7515 (ttt-90) REVERT: M 297 GLN cc_start: 0.7526 (tt0) cc_final: 0.7286 (tp-100) REVERT: M 376 LYS cc_start: 0.7938 (tttt) cc_final: 0.7526 (mttp) REVERT: N 297 GLN cc_start: 0.7625 (tt0) cc_final: 0.7420 (tp40) REVERT: N 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7677 (mttp) REVERT: N 383 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7559 (mt-10) REVERT: O 246 GLN cc_start: 0.8609 (tt0) cc_final: 0.8402 (tt0) REVERT: O 376 LYS cc_start: 0.7991 (tttt) cc_final: 0.7650 (mttp) REVERT: P 376 LYS cc_start: 0.8036 (tttt) cc_final: 0.7714 (mttp) REVERT: Q 297 GLN cc_start: 0.7583 (tt0) cc_final: 0.7368 (tp40) REVERT: Q 376 LYS cc_start: 0.7877 (tttt) cc_final: 0.7404 (mttp) REVERT: R 246 GLN cc_start: 0.8583 (tt0) cc_final: 0.8244 (tt0) REVERT: R 376 LYS cc_start: 0.7785 (tttt) cc_final: 0.7463 (mttp) REVERT: S 297 GLN cc_start: 0.7494 (tt0) cc_final: 0.7288 (tp-100) REVERT: S 376 LYS cc_start: 0.7943 (tttt) cc_final: 0.7550 (mttp) REVERT: T 246 GLN cc_start: 0.8576 (tt0) cc_final: 0.8313 (tt0) REVERT: T 297 GLN cc_start: 0.7527 (tt0) cc_final: 0.7286 (tp-100) REVERT: T 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7512 (mttp) REVERT: U 246 GLN cc_start: 0.8578 (tt0) cc_final: 0.8366 (tt0) REVERT: U 376 LYS cc_start: 0.7885 (tttt) cc_final: 0.7672 (ttmp) REVERT: V 297 GLN cc_start: 0.7646 (tt0) cc_final: 0.7446 (tp40) REVERT: W 376 LYS cc_start: 0.8011 (tttt) cc_final: 0.7584 (mttp) REVERT: X 370 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7751 (ttm170) REVERT: X 376 LYS cc_start: 0.7995 (tttt) cc_final: 0.7542 (mttp) REVERT: Y 246 GLN cc_start: 0.8547 (tt0) cc_final: 0.8313 (tt0) REVERT: Y 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7347 (tp-100) REVERT: Z 246 GLN cc_start: 0.8570 (tt0) cc_final: 0.8290 (tt0) REVERT: Z 376 LYS cc_start: 0.7967 (tttt) cc_final: 0.7621 (mttp) REVERT: a 246 GLN cc_start: 0.8632 (tt0) cc_final: 0.8412 (tt0) REVERT: a 275 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7980 (tttt) REVERT: a 376 LYS cc_start: 0.7811 (tttt) cc_final: 0.7434 (mttp) REVERT: b 246 GLN cc_start: 0.8629 (tt0) cc_final: 0.8315 (tt0) REVERT: b 275 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7949 (tttp) REVERT: b 297 GLN cc_start: 0.7481 (tt0) cc_final: 0.7243 (tp-100) REVERT: b 376 LYS cc_start: 0.7827 (tttt) cc_final: 0.7466 (mttp) REVERT: b 425 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8650 (mtmm) REVERT: c 297 GLN cc_start: 0.7575 (tt0) cc_final: 0.7368 (tp40) REVERT: c 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7609 (mttp) REVERT: d 376 LYS cc_start: 0.8008 (tttt) cc_final: 0.7689 (mttp) REVERT: e 276 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6979 (mt-10) REVERT: e 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7355 (tp-100) REVERT: e 376 LYS cc_start: 0.7911 (tttt) cc_final: 0.7657 (mttp) REVERT: f 376 LYS cc_start: 0.8021 (tttt) cc_final: 0.7698 (mttp) REVERT: g 246 GLN cc_start: 0.8562 (tt0) cc_final: 0.8240 (tt0) REVERT: g 376 LYS cc_start: 0.8030 (tttt) cc_final: 0.7639 (mttp) outliers start: 0 outliers final: 0 residues processed: 1388 average time/residue: 0.9383 time to fit residues: 1508.2368 Evaluate side-chains 1232 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1232 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 263 HIS A 297 GLN A 365 ASN A 434 ASN B 246 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 297 GLN B 374 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 297 GLN C 365 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 365 ASN D 434 ASN E 246 GLN E 263 HIS E 365 ASN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN F 261 ASN F 263 HIS F 269 GLN F 365 ASN F 434 ASN G 246 GLN G 261 ASN G 263 HIS G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN I 246 GLN I 261 ASN I 263 HIS I 434 ASN J 261 ASN J 434 ASN K 263 HIS K 365 ASN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 263 HIS L 365 ASN L 434 ASN M 246 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 HIS M 277 GLN M 365 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 HIS N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 365 ASN ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN O 263 HIS O 365 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 246 GLN P 261 ASN P 263 HIS P 365 ASN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Q 261 ASN Q 263 HIS Q 365 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS R 365 ASN R 434 ASN S 246 GLN ** S 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 263 HIS S 274 ASN S 365 ASN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 261 ASN T 263 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 261 ASN U 263 HIS U 434 ASN V 246 GLN V 261 ASN V 263 HIS V 365 ASN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 239 ASN W 246 GLN W 261 ASN W 263 HIS W 365 ASN ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 ASN X 246 GLN ** X 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 HIS X 269 GLN X 365 ASN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 263 HIS ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 HIS Z 365 ASN Z 431 ASN Z 434 ASN a 261 ASN a 263 HIS a 365 ASN ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 261 ASN b 263 HIS b 365 ASN b 434 ASN c 246 GLN c 261 ASN c 263 HIS c 365 ASN c 434 ASN d 246 GLN ** d 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 263 HIS d 269 GLN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 246 GLN ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 263 HIS e 269 GLN e 434 ASN f 246 GLN ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 263 HIS f 297 GLN ** f 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 231 ASN g 261 ASN g 263 HIS g 365 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120214 restraints weight = 46486.777| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.68 r_work: 0.3350 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39765 Z= 0.153 Angle : 0.490 5.177 53592 Z= 0.265 Chirality : 0.039 0.129 6138 Planarity : 0.004 0.034 7194 Dihedral : 4.747 17.923 5379 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.45 % Allowed : 12.12 % Favored : 86.43 % 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 are not related in a simple way. whole: -0.52 (0.12), residues: 4785 helix: 0.22 (0.13), residues: 1320 sheet: -0.20 (0.11), residues: 2475 loop : -0.97 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 356 TYR 0.012 0.001 TYR e 393 PHE 0.010 0.001 PHE S 422 HIS 0.003 0.000 HIS T 281 Details of bonding type rmsd covalent geometry : bond 0.00333 (39765) covalent geometry : angle 0.48953 (53592) hydrogen bonds : bond 0.04914 ( 1441) hydrogen bonds : angle 4.92896 ( 4224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1214 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8711 (tt0) cc_final: 0.8453 (tt0) REVERT: A 275 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8184 (tttt) REVERT: A 376 LYS cc_start: 0.8428 (tttt) cc_final: 0.7868 (mttp) REVERT: B 287 ASP cc_start: 0.7952 (t0) cc_final: 0.7747 (t70) REVERT: B 297 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: B 376 LYS cc_start: 0.8381 (tttt) cc_final: 0.7737 (mttp) REVERT: C 376 LYS cc_start: 0.8446 (tttt) cc_final: 0.7878 (mttp) REVERT: D 246 GLN cc_start: 0.8644 (tt0) cc_final: 0.8372 (tt0) REVERT: D 297 GLN cc_start: 0.8258 (tt0) cc_final: 0.7973 (tp-100) REVERT: D 376 LYS cc_start: 0.8378 (tttt) cc_final: 0.7762 (mttp) REVERT: E 356 ARG cc_start: 0.6487 (mpp-170) cc_final: 0.6187 (mpp-170) REVERT: E 376 LYS cc_start: 0.8361 (tttt) cc_final: 0.7740 (mttp) REVERT: F 276 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8006 (mt-10) REVERT: F 376 LYS cc_start: 0.8469 (tttt) cc_final: 0.7778 (mttp) REVERT: G 297 GLN cc_start: 0.8183 (tt0) cc_final: 0.7937 (tp40) REVERT: G 376 LYS cc_start: 0.8451 (tttt) cc_final: 0.7802 (mttp) REVERT: G 409 MET cc_start: 0.8203 (mmm) cc_final: 0.7835 (mmm) REVERT: H 296 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7718 (ttt180) REVERT: H 297 GLN cc_start: 0.8266 (tt0) cc_final: 0.7930 (tp-100) REVERT: H 376 LYS cc_start: 0.8554 (tttt) cc_final: 0.7855 (mttp) REVERT: I 376 LYS cc_start: 0.8528 (tttt) cc_final: 0.7897 (mttp) REVERT: J 246 GLN cc_start: 0.8745 (tt0) cc_final: 0.8410 (tt0) REVERT: J 376 LYS cc_start: 0.8385 (tttt) cc_final: 0.7771 (mttp) REVERT: J 383 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8029 (mt-10) REVERT: K 246 GLN cc_start: 0.8629 (tt0) cc_final: 0.8422 (tt0) REVERT: K 376 LYS cc_start: 0.8447 (tttt) cc_final: 0.7919 (mttp) REVERT: L 246 GLN cc_start: 0.8671 (tt0) cc_final: 0.8461 (tt0) REVERT: L 275 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8205 (tttm) REVERT: L 297 GLN cc_start: 0.8227 (tt0) cc_final: 0.7938 (tp-100) REVERT: L 376 LYS cc_start: 0.8368 (tttt) cc_final: 0.7998 (ttmp) REVERT: M 296 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: M 297 GLN cc_start: 0.8261 (tt0) cc_final: 0.7955 (tp40) REVERT: M 376 LYS cc_start: 0.8436 (tttt) cc_final: 0.7720 (mttp) REVERT: N 246 GLN cc_start: 0.8637 (tt0) cc_final: 0.8412 (tt0) REVERT: N 276 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8079 (mt-10) REVERT: N 287 ASP cc_start: 0.7872 (t0) cc_final: 0.7613 (t70) REVERT: N 297 GLN cc_start: 0.8302 (tt0) cc_final: 0.8076 (tp40) REVERT: N 376 LYS cc_start: 0.8461 (tttt) cc_final: 0.7836 (mttp) REVERT: O 235 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8758 (mp) REVERT: O 376 LYS cc_start: 0.8486 (tttt) cc_final: 0.7888 (mttp) REVERT: P 303 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: P 376 LYS cc_start: 0.8500 (tttt) cc_final: 0.7865 (mttp) REVERT: Q 235 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8625 (mp) REVERT: Q 297 GLN cc_start: 0.8234 (tt0) cc_final: 0.7981 (tp40) REVERT: Q 376 LYS cc_start: 0.8462 (tttt) cc_final: 0.7771 (mttp) REVERT: Q 409 MET cc_start: 0.8122 (mmm) cc_final: 0.7828 (mmm) REVERT: R 246 GLN cc_start: 0.8662 (tt0) cc_final: 0.8354 (tt0) REVERT: R 275 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8149 (mtpt) REVERT: R 376 LYS cc_start: 0.8399 (tttt) cc_final: 0.7787 (mttp) REVERT: S 297 GLN cc_start: 0.8179 (tt0) cc_final: 0.7876 (tp-100) REVERT: S 376 LYS cc_start: 0.8384 (tttt) cc_final: 0.7789 (mttp) REVERT: T 246 GLN cc_start: 0.8644 (tt0) cc_final: 0.8410 (tt0) REVERT: T 297 GLN cc_start: 0.8194 (tt0) cc_final: 0.7891 (tp-100) REVERT: T 376 LYS cc_start: 0.8347 (tttt) cc_final: 0.7735 (mttp) REVERT: U 246 GLN cc_start: 0.8666 (tt0) cc_final: 0.8445 (tt0) REVERT: U 376 LYS cc_start: 0.8354 (tttt) cc_final: 0.7702 (mttp) REVERT: V 279 GLU cc_start: 0.8032 (mp0) cc_final: 0.7780 (mp0) REVERT: V 296 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: V 297 GLN cc_start: 0.8307 (tt0) cc_final: 0.8062 (tp40) REVERT: V 362 GLU cc_start: 0.7872 (tt0) cc_final: 0.7663 (tt0) REVERT: V 410 LYS cc_start: 0.8274 (tmmt) cc_final: 0.8066 (tttm) REVERT: W 276 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7868 (mt-10) REVERT: W 376 LYS cc_start: 0.8458 (tttt) cc_final: 0.7811 (mttp) REVERT: X 287 ASP cc_start: 0.7832 (t0) cc_final: 0.7586 (t70) REVERT: X 376 LYS cc_start: 0.8519 (tttt) cc_final: 0.7767 (mttp) REVERT: X 425 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8777 (mtmm) REVERT: Y 246 GLN cc_start: 0.8599 (tt0) cc_final: 0.8360 (tt0) REVERT: Y 275 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8157 (tttt) REVERT: Y 297 GLN cc_start: 0.8207 (tt0) cc_final: 0.7923 (tp-100) REVERT: Z 246 GLN cc_start: 0.8708 (tt0) cc_final: 0.8450 (tt0) REVERT: Z 275 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8284 (tttt) REVERT: Z 376 LYS cc_start: 0.8429 (tttt) cc_final: 0.7839 (mttp) REVERT: a 235 LEU cc_start: 0.9002 (mt) cc_final: 0.8708 (mp) REVERT: a 246 GLN cc_start: 0.8683 (tt0) cc_final: 0.8415 (tt0) REVERT: a 275 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8177 (tttt) REVERT: a 376 LYS cc_start: 0.8270 (tttt) cc_final: 0.7694 (mttp) REVERT: b 246 GLN cc_start: 0.8713 (tt0) cc_final: 0.8396 (tt0) REVERT: b 287 ASP cc_start: 0.7943 (t0) cc_final: 0.7642 (t70) REVERT: b 296 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7417 (tpp-160) REVERT: b 297 GLN cc_start: 0.8161 (tt0) cc_final: 0.7921 (tp40) REVERT: b 376 LYS cc_start: 0.8371 (tttt) cc_final: 0.7737 (mttp) REVERT: b 377 MET cc_start: 0.8660 (mpt) cc_final: 0.8400 (mpt) REVERT: c 297 GLN cc_start: 0.8244 (tt0) cc_final: 0.8023 (tp40) REVERT: c 376 LYS cc_start: 0.8406 (tttt) cc_final: 0.7802 (mttp) REVERT: d 376 LYS cc_start: 0.8465 (tttt) cc_final: 0.7827 (mttp) REVERT: e 297 GLN cc_start: 0.8267 (tt0) cc_final: 0.7954 (tp-100) REVERT: e 376 LYS cc_start: 0.8429 (tttt) cc_final: 0.7832 (mttp) REVERT: f 297 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: f 376 LYS cc_start: 0.8499 (tttt) cc_final: 0.7923 (mttp) REVERT: g 246 GLN cc_start: 0.8714 (tt0) cc_final: 0.8383 (tt0) REVERT: g 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7859 (mttp) outliers start: 64 outliers final: 13 residues processed: 1251 average time/residue: 0.9001 time to fit residues: 1315.2516 Evaluate side-chains 1204 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1182 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 296 ARG Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain b residue 412 ILE Chi-restraints excluded: chain f residue 297 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 288 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 433 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 382 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 434 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 434 ASN F 246 GLN F 269 GLN G 246 GLN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 ASN H 246 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN K 434 ASN ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN O 246 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 246 GLN P 269 GLN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Q 434 ASN ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 434 ASN T 269 GLN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 246 GLN V 269 GLN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 297 GLN ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 ASN X 246 GLN ** X 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 269 GLN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 434 ASN c 246 GLN d 246 GLN ** d 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 246 GLN ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN f 246 GLN ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 297 GLN ** f 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 231 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120926 restraints weight = 46554.943| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.68 r_work: 0.3356 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39765 Z= 0.128 Angle : 0.454 4.814 53592 Z= 0.245 Chirality : 0.039 0.128 6138 Planarity : 0.003 0.050 7194 Dihedral : 4.543 16.640 5379 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.79 % Allowed : 13.77 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4785 helix: 1.96 (0.14), residues: 1320 sheet: 0.03 (0.11), residues: 2475 loop : -0.78 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 370 TYR 0.009 0.001 TYR e 393 PHE 0.010 0.001 PHE S 422 HIS 0.003 0.000 HIS H 281 Details of bonding type rmsd covalent geometry : bond 0.00273 (39765) covalent geometry : angle 0.45350 (53592) hydrogen bonds : bond 0.04176 ( 1441) hydrogen bonds : angle 4.42343 ( 4224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1191 time to evaluate : 1.592 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: A 246 GLN cc_start: 0.8683 (tt0) cc_final: 0.8392 (tt0) REVERT: A 275 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8232 (tttt) REVERT: A 297 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7173 (tp-100) REVERT: A 376 LYS cc_start: 0.8430 (tttt) cc_final: 0.7896 (mttp) REVERT: B 376 LYS cc_start: 0.8348 (tttt) cc_final: 0.7706 (mttp) REVERT: C 269 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: C 276 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7838 (mp0) REVERT: C 287 ASP cc_start: 0.7847 (t0) cc_final: 0.7635 (t70) REVERT: C 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7901 (mttp) REVERT: D 246 GLN cc_start: 0.8672 (tt0) cc_final: 0.8387 (tt0) REVERT: D 297 GLN cc_start: 0.8235 (tt0) cc_final: 0.7948 (tp-100) REVERT: D 362 GLU cc_start: 0.7857 (tt0) cc_final: 0.7648 (tt0) REVERT: D 376 LYS cc_start: 0.8423 (tttt) cc_final: 0.7835 (mttp) REVERT: E 356 ARG cc_start: 0.6462 (mpp-170) cc_final: 0.6035 (mpp-170) REVERT: E 376 LYS cc_start: 0.8388 (tttt) cc_final: 0.7787 (mttp) REVERT: F 275 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8181 (tttt) REVERT: F 376 LYS cc_start: 0.8461 (tttt) cc_final: 0.7788 (mttp) REVERT: G 235 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8827 (mp) REVERT: G 297 GLN cc_start: 0.8164 (tt0) cc_final: 0.7920 (tp40) REVERT: G 376 LYS cc_start: 0.8424 (tttt) cc_final: 0.7809 (mttp) REVERT: G 409 MET cc_start: 0.8135 (mmm) cc_final: 0.7808 (mmm) REVERT: H 296 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7481 (ttp-170) REVERT: H 297 GLN cc_start: 0.8229 (tt0) cc_final: 0.7888 (tp-100) REVERT: H 362 GLU cc_start: 0.7991 (tt0) cc_final: 0.7764 (tt0) REVERT: H 376 LYS cc_start: 0.8568 (tttt) cc_final: 0.7872 (mttp) REVERT: I 376 LYS cc_start: 0.8504 (tttt) cc_final: 0.7897 (mttp) REVERT: I 409 MET cc_start: 0.8131 (mmm) cc_final: 0.7929 (mmm) REVERT: J 246 GLN cc_start: 0.8715 (tt0) cc_final: 0.8356 (tt0) REVERT: J 376 LYS cc_start: 0.8399 (tttt) cc_final: 0.7781 (mttp) REVERT: J 383 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8006 (mt-10) REVERT: K 246 GLN cc_start: 0.8606 (tt0) cc_final: 0.8325 (tt0) REVERT: K 275 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8302 (tttt) REVERT: K 376 LYS cc_start: 0.8406 (tttt) cc_final: 0.7895 (mttp) REVERT: L 246 GLN cc_start: 0.8630 (tt0) cc_final: 0.8371 (tt0) REVERT: L 297 GLN cc_start: 0.8235 (tt0) cc_final: 0.7960 (tp-100) REVERT: L 376 LYS cc_start: 0.8377 (tttt) cc_final: 0.7716 (mttp) REVERT: M 296 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7436 (ttp-170) REVERT: M 297 GLN cc_start: 0.8222 (tt0) cc_final: 0.7988 (tp40) REVERT: M 376 LYS cc_start: 0.8469 (tttt) cc_final: 0.7737 (mttp) REVERT: N 246 GLN cc_start: 0.8569 (tt0) cc_final: 0.8301 (tt0) REVERT: N 287 ASP cc_start: 0.7919 (t0) cc_final: 0.7655 (t70) REVERT: N 297 GLN cc_start: 0.8294 (tt0) cc_final: 0.8070 (tp40) REVERT: N 376 LYS cc_start: 0.8423 (tttt) cc_final: 0.7838 (mttp) REVERT: O 246 GLN cc_start: 0.8727 (tt0) cc_final: 0.8456 (tt0) REVERT: O 376 LYS cc_start: 0.8462 (tttt) cc_final: 0.7906 (mttp) REVERT: P 296 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7709 (ttp-170) REVERT: P 376 LYS cc_start: 0.8521 (tttt) cc_final: 0.7885 (mttp) REVERT: P 435 SER cc_start: 0.8365 (t) cc_final: 0.8146 (t) REVERT: Q 235 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8604 (mp) REVERT: Q 297 GLN cc_start: 0.8169 (tt0) cc_final: 0.7909 (tp40) REVERT: Q 376 LYS cc_start: 0.8456 (tttt) cc_final: 0.7752 (mttp) REVERT: R 246 GLN cc_start: 0.8606 (tt0) cc_final: 0.8253 (tt0) REVERT: R 376 LYS cc_start: 0.8373 (tttt) cc_final: 0.7793 (mttp) REVERT: S 276 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: S 297 GLN cc_start: 0.8121 (tt0) cc_final: 0.7831 (tp-100) REVERT: S 376 LYS cc_start: 0.8331 (tttt) cc_final: 0.7768 (mttp) REVERT: T 246 GLN cc_start: 0.8633 (tt0) cc_final: 0.8416 (tt0) REVERT: T 287 ASP cc_start: 0.8025 (t0) cc_final: 0.7800 (t70) REVERT: T 297 GLN cc_start: 0.8217 (tt0) cc_final: 0.7926 (tp-100) REVERT: T 376 LYS cc_start: 0.8321 (tttt) cc_final: 0.7710 (mttp) REVERT: U 246 GLN cc_start: 0.8663 (tt0) cc_final: 0.8448 (tt0) REVERT: U 376 LYS cc_start: 0.8366 (tttt) cc_final: 0.7733 (mttp) REVERT: V 296 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7539 (ttp-170) REVERT: V 297 GLN cc_start: 0.8282 (tt0) cc_final: 0.8027 (tp40) REVERT: W 276 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7854 (mt-10) REVERT: W 376 LYS cc_start: 0.8467 (tttt) cc_final: 0.7816 (mttp) REVERT: X 275 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8220 (tttt) REVERT: X 287 ASP cc_start: 0.7867 (t0) cc_final: 0.7616 (t70) REVERT: X 376 LYS cc_start: 0.8499 (tttt) cc_final: 0.7748 (mttp) REVERT: X 425 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8757 (mtmm) REVERT: Y 246 GLN cc_start: 0.8614 (tt0) cc_final: 0.8258 (tt0) REVERT: Y 275 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8149 (tttt) REVERT: Y 297 GLN cc_start: 0.8182 (tt0) cc_final: 0.7903 (tp-100) REVERT: Y 376 LYS cc_start: 0.8485 (tttt) cc_final: 0.7884 (mttp) REVERT: Z 246 GLN cc_start: 0.8676 (tt0) cc_final: 0.8413 (tt0) REVERT: Z 276 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7850 (mt-10) REVERT: Z 376 LYS cc_start: 0.8436 (tttt) cc_final: 0.7855 (mttp) REVERT: a 246 GLN cc_start: 0.8641 (tt0) cc_final: 0.8387 (tt0) REVERT: a 275 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8182 (tttt) REVERT: a 376 LYS cc_start: 0.8258 (tttt) cc_final: 0.7700 (mttp) REVERT: b 246 GLN cc_start: 0.8666 (tt0) cc_final: 0.8294 (tt0) REVERT: b 287 ASP cc_start: 0.7998 (t0) cc_final: 0.7696 (t70) REVERT: b 296 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7178 (tpp-160) REVERT: b 297 GLN cc_start: 0.8165 (tt0) cc_final: 0.7916 (tp40) REVERT: b 376 LYS cc_start: 0.8373 (tttt) cc_final: 0.7739 (mttp) REVERT: c 297 GLN cc_start: 0.8244 (tt0) cc_final: 0.8004 (tp40) REVERT: c 376 LYS cc_start: 0.8418 (tttt) cc_final: 0.7818 (mttp) REVERT: d 279 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: d 376 LYS cc_start: 0.8443 (tttt) cc_final: 0.7842 (mttp) REVERT: e 297 GLN cc_start: 0.8240 (tt0) cc_final: 0.7925 (tp-100) REVERT: e 376 LYS cc_start: 0.8415 (tttt) cc_final: 0.7855 (mttp) REVERT: f 376 LYS cc_start: 0.8507 (tttt) cc_final: 0.7932 (mttp) REVERT: f 409 MET cc_start: 0.8249 (mmm) cc_final: 0.7962 (mmm) REVERT: g 246 GLN cc_start: 0.8655 (tt0) cc_final: 0.8279 (tt0) REVERT: g 376 LYS cc_start: 0.8473 (tttt) cc_final: 0.7874 (mttp) outliers start: 79 outliers final: 20 residues processed: 1233 average time/residue: 0.9181 time to fit residues: 1320.8937 Evaluate side-chains 1191 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 1160 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain P residue 296 ARG Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain V residue 296 ARG Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 296 ARG Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 364 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 459 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 461 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 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 261 ASN B 246 GLN B 297 GLN B 434 ASN C 246 GLN C 297 GLN E 246 GLN F 269 GLN G 246 GLN G 261 ASN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN H 263 HIS H 365 ASN H 434 ASN I 246 GLN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 365 ASN J 261 ASN J 263 HIS M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 434 ASN P 261 ASN P 269 GLN P 434 ASN Q 246 GLN Q 261 ASN S 246 GLN ** T 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 269 GLN T 434 ASN U 365 ASN V 246 GLN V 261 ASN V 434 ASN W 297 GLN W 434 ASN X 246 GLN X 269 GLN X 434 ASN Y 434 ASN a 261 ASN c 246 GLN c 261 ASN d 246 GLN d 434 ASN e 269 GLN f 246 GLN f 297 GLN f 434 ASN g 231 ASN g 261 ASN g 434 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117935 restraints weight = 46530.937| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.68 r_work: 0.3320 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 39765 Z= 0.238 Angle : 0.518 5.083 53592 Z= 0.279 Chirality : 0.040 0.132 6138 Planarity : 0.003 0.029 7194 Dihedral : 4.899 17.272 5379 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.46 % Allowed : 14.38 % Favored : 83.15 % 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 are not related in a simple way. whole: 0.74 (0.13), residues: 4785 helix: 2.30 (0.14), residues: 1320 sheet: 0.15 (0.11), residues: 2442 loop : -0.84 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 296 TYR 0.013 0.002 TYR B 393 PHE 0.012 0.001 PHE S 422 HIS 0.004 0.001 HIS H 281 Details of bonding type rmsd covalent geometry : bond 0.00520 (39765) covalent geometry : angle 0.51784 (53592) hydrogen bonds : bond 0.04935 ( 1441) hydrogen bonds : angle 4.59043 ( 4224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1187 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8745 (tt0) cc_final: 0.8434 (tt0) REVERT: A 297 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7183 (tp-100) REVERT: A 376 LYS cc_start: 0.8467 (tttt) cc_final: 0.7925 (mttp) REVERT: B 297 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: B 376 LYS cc_start: 0.8381 (tttt) cc_final: 0.7731 (mttp) REVERT: C 269 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: C 287 ASP cc_start: 0.7931 (t0) cc_final: 0.7691 (OUTLIER) REVERT: C 297 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: C 376 LYS cc_start: 0.8504 (tttt) cc_final: 0.7967 (mttp) REVERT: C 383 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7976 (mt-10) REVERT: D 246 GLN cc_start: 0.8722 (tt0) cc_final: 0.8438 (tt0) REVERT: D 297 GLN cc_start: 0.8251 (tt0) cc_final: 0.7981 (tp-100) REVERT: D 376 LYS cc_start: 0.8479 (tttt) cc_final: 0.7877 (mttp) REVERT: E 356 ARG cc_start: 0.6489 (mpp-170) cc_final: 0.6272 (mpp-170) REVERT: E 376 LYS cc_start: 0.8388 (tttt) cc_final: 0.7751 (mttp) REVERT: F 376 LYS cc_start: 0.8474 (tttt) cc_final: 0.7819 (mttp) REVERT: G 235 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8924 (mp) REVERT: G 297 GLN cc_start: 0.8194 (tt0) cc_final: 0.7962 (tp40) REVERT: G 303 GLN cc_start: 0.7451 (mt0) cc_final: 0.7066 (mp10) REVERT: G 376 LYS cc_start: 0.8445 (tttt) cc_final: 0.7850 (mttp) REVERT: G 409 MET cc_start: 0.8149 (mmm) cc_final: 0.7836 (mmm) REVERT: H 296 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7576 (ttp-170) REVERT: H 297 GLN cc_start: 0.8264 (tt0) cc_final: 0.7983 (tp-100) REVERT: H 376 LYS cc_start: 0.8581 (tttt) cc_final: 0.7863 (mttp) REVERT: I 376 LYS cc_start: 0.8528 (tttt) cc_final: 0.7916 (mttp) REVERT: I 409 MET cc_start: 0.8190 (mmm) cc_final: 0.7916 (mmm) REVERT: J 246 GLN cc_start: 0.8730 (tt0) cc_final: 0.8376 (tt0) REVERT: J 269 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: J 376 LYS cc_start: 0.8431 (tttt) cc_final: 0.7835 (mttp) REVERT: J 383 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7983 (mt-10) REVERT: J 410 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: K 246 GLN cc_start: 0.8714 (tt0) cc_final: 0.8441 (tt0) REVERT: K 275 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8335 (tttt) REVERT: K 376 LYS cc_start: 0.8463 (tttt) cc_final: 0.7932 (mttp) REVERT: L 246 GLN cc_start: 0.8722 (tt0) cc_final: 0.8454 (tt0) REVERT: L 297 GLN cc_start: 0.8278 (tt0) cc_final: 0.7983 (tp-100) REVERT: L 376 LYS cc_start: 0.8418 (tttt) cc_final: 0.7754 (mttp) REVERT: L 425 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8761 (mtmm) REVERT: M 276 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7760 (mt-10) REVERT: M 296 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7543 (ttp-170) REVERT: M 297 GLN cc_start: 0.8237 (tt0) cc_final: 0.7907 (tp40) REVERT: M 376 LYS cc_start: 0.8493 (tttt) cc_final: 0.7773 (mttp) REVERT: N 246 GLN cc_start: 0.8721 (tt0) cc_final: 0.8496 (tt0) REVERT: N 279 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: N 297 GLN cc_start: 0.8312 (tt0) cc_final: 0.8086 (tp40) REVERT: N 376 LYS cc_start: 0.8465 (tttt) cc_final: 0.7885 (mttp) REVERT: O 246 GLN cc_start: 0.8723 (tt0) cc_final: 0.8491 (tt0) REVERT: O 303 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: O 376 LYS cc_start: 0.8491 (tttt) cc_final: 0.7952 (mttp) REVERT: P 296 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7735 (ttp-170) REVERT: P 303 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: P 376 LYS cc_start: 0.8552 (tttt) cc_final: 0.7909 (mttp) REVERT: Q 235 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8659 (mp) REVERT: Q 297 GLN cc_start: 0.8192 (tt0) cc_final: 0.7926 (tp40) REVERT: Q 376 LYS cc_start: 0.8466 (tttt) cc_final: 0.7800 (mttp) REVERT: R 246 GLN cc_start: 0.8746 (tt0) cc_final: 0.8404 (tt0) REVERT: R 370 ARG cc_start: 0.8279 (ttt180) cc_final: 0.7919 (ttt-90) REVERT: R 376 LYS cc_start: 0.8408 (tttt) cc_final: 0.7789 (mttp) REVERT: S 297 GLN cc_start: 0.8137 (tt0) cc_final: 0.7872 (tp40) REVERT: S 376 LYS cc_start: 0.8387 (tttt) cc_final: 0.7838 (mttp) REVERT: T 246 GLN cc_start: 0.8749 (tt0) cc_final: 0.8462 (tt0) REVERT: T 287 ASP cc_start: 0.8001 (t0) cc_final: 0.7746 (t70) REVERT: T 297 GLN cc_start: 0.8254 (tt0) cc_final: 0.7984 (tp-100) REVERT: T 376 LYS cc_start: 0.8384 (tttt) cc_final: 0.7782 (mttp) REVERT: U 246 GLN cc_start: 0.8762 (tt0) cc_final: 0.8501 (tt0) REVERT: U 376 LYS cc_start: 0.8394 (tttt) cc_final: 0.7784 (mttp) REVERT: V 235 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8825 (mp) REVERT: V 246 GLN cc_start: 0.8701 (tt0) cc_final: 0.8351 (tt0) REVERT: V 297 GLN cc_start: 0.8339 (tt0) cc_final: 0.8095 (tp40) REVERT: V 303 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: W 376 LYS cc_start: 0.8468 (tttt) cc_final: 0.7806 (mttp) REVERT: X 275 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8279 (tttt) REVERT: X 376 LYS cc_start: 0.8542 (tttt) cc_final: 0.7790 (mttp) REVERT: X 425 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8770 (mtmm) REVERT: Y 246 GLN cc_start: 0.8727 (tt0) cc_final: 0.8413 (tt0) REVERT: Y 275 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8171 (tttt) REVERT: Y 297 GLN cc_start: 0.8210 (tt0) cc_final: 0.7955 (tp40) REVERT: Y 376 LYS cc_start: 0.8531 (tttt) cc_final: 0.7928 (mttp) REVERT: Z 246 GLN cc_start: 0.8809 (tt0) cc_final: 0.8493 (tt0) REVERT: Z 276 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7832 (mt-10) REVERT: Z 376 LYS cc_start: 0.8447 (tttt) cc_final: 0.7892 (mttp) REVERT: a 246 GLN cc_start: 0.8716 (tt0) cc_final: 0.8440 (tt0) REVERT: a 275 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8213 (tttt) REVERT: a 376 LYS cc_start: 0.8345 (tttt) cc_final: 0.7741 (mttp) REVERT: b 246 GLN cc_start: 0.8816 (tt0) cc_final: 0.8483 (tt0) REVERT: b 275 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8285 (tttt) REVERT: b 287 ASP cc_start: 0.7993 (t0) cc_final: 0.7712 (t70) REVERT: b 296 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7510 (tpp-160) REVERT: b 376 LYS cc_start: 0.8387 (tttt) cc_final: 0.7745 (mttp) REVERT: c 297 GLN cc_start: 0.8255 (tt0) cc_final: 0.8031 (tp40) REVERT: c 376 LYS cc_start: 0.8427 (tttt) cc_final: 0.7841 (mttp) REVERT: d 279 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: d 376 LYS cc_start: 0.8442 (tttt) cc_final: 0.7834 (mttp) REVERT: d 425 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8874 (mtmm) REVERT: e 246 GLN cc_start: 0.8717 (tt0) cc_final: 0.8473 (tt0) REVERT: e 297 GLN cc_start: 0.8260 (tt0) cc_final: 0.7955 (tp-100) REVERT: e 376 LYS cc_start: 0.8430 (tttt) cc_final: 0.7853 (mttp) REVERT: f 297 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: f 376 LYS cc_start: 0.8505 (tttt) cc_final: 0.7916 (mttp) REVERT: f 409 MET cc_start: 0.8285 (mmm) cc_final: 0.7955 (mmm) REVERT: g 246 GLN cc_start: 0.8786 (tt0) cc_final: 0.8444 (tt0) REVERT: g 376 LYS cc_start: 0.8535 (tttt) cc_final: 0.7928 (mttp) outliers start: 109 outliers final: 47 residues processed: 1232 average time/residue: 0.9112 time to fit residues: 1308.5327 Evaluate side-chains 1220 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1155 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 303 GLN Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 296 ARG Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 303 GLN Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 296 ARG Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 383 GLU Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 254 optimal weight: 0.0870 chunk 181 optimal weight: 5.9990 chunk 390 optimal weight: 1.9990 chunk 421 optimal weight: 0.9980 chunk 446 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 291 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 246 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 GLN G 246 GLN G 261 ASN G 269 GLN G 277 GLN H 246 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN J 261 ASN ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 261 ASN Q 246 GLN Q 261 ASN ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 261 ASN W 297 GLN X 246 GLN ** X 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 269 GLN ** Y 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 246 GLN c 261 ASN ** d 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN f 246 GLN ** f 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 231 ASN g 261 ASN g 374 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121412 restraints weight = 46409.650| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.67 r_work: 0.3371 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 39765 Z= 0.102 Angle : 0.434 4.901 53592 Z= 0.235 Chirality : 0.038 0.126 6138 Planarity : 0.002 0.023 7194 Dihedral : 4.398 16.878 5379 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Rotamer: Outliers : 1.94 % Allowed : 15.33 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4785 helix: 2.95 (0.15), residues: 1320 sheet: 0.34 (0.11), residues: 2442 loop : -0.68 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 296 TYR 0.006 0.001 TYR T 393 PHE 0.010 0.001 PHE R 422 HIS 0.003 0.000 HIS W 281 Details of bonding type rmsd covalent geometry : bond 0.00214 (39765) covalent geometry : angle 0.43431 (53592) hydrogen bonds : bond 0.03696 ( 1441) hydrogen bonds : angle 4.14808 ( 4224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1180 time to evaluate : 1.695 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: A 246 GLN cc_start: 0.8702 (tt0) cc_final: 0.8372 (tt0) REVERT: A 275 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8239 (tttt) REVERT: A 376 LYS cc_start: 0.8441 (tttt) cc_final: 0.7932 (mttp) REVERT: B 376 LYS cc_start: 0.8378 (tttt) cc_final: 0.7795 (mttp) REVERT: B 409 MET cc_start: 0.8265 (mmm) cc_final: 0.7858 (mmm) REVERT: C 269 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: C 376 LYS cc_start: 0.8441 (tttt) cc_final: 0.7921 (mttp) REVERT: C 383 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7905 (mt-10) REVERT: D 246 GLN cc_start: 0.8670 (tt0) cc_final: 0.8359 (tt0) REVERT: D 297 GLN cc_start: 0.8192 (tt0) cc_final: 0.7922 (tp-100) REVERT: D 376 LYS cc_start: 0.8437 (tttt) cc_final: 0.7873 (mttp) REVERT: E 376 LYS cc_start: 0.8389 (tttt) cc_final: 0.7832 (mttp) REVERT: F 246 GLN cc_start: 0.8615 (tt0) cc_final: 0.8243 (tt0) REVERT: F 376 LYS cc_start: 0.8460 (tttt) cc_final: 0.7828 (mttp) REVERT: F 435 SER cc_start: 0.8299 (t) cc_final: 0.8093 (t) REVERT: G 235 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8824 (mp) REVERT: G 297 GLN cc_start: 0.8191 (tt0) cc_final: 0.7943 (tp40) REVERT: G 376 LYS cc_start: 0.8447 (tttt) cc_final: 0.7855 (mttp) REVERT: G 409 MET cc_start: 0.8126 (mmm) cc_final: 0.7812 (mmm) REVERT: H 296 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7487 (ttp-170) REVERT: H 297 GLN cc_start: 0.8207 (tt0) cc_final: 0.7871 (tp-100) REVERT: H 376 LYS cc_start: 0.8573 (tttt) cc_final: 0.7875 (mttp) REVERT: I 376 LYS cc_start: 0.8493 (tttt) cc_final: 0.7896 (mttp) REVERT: J 246 GLN cc_start: 0.8741 (tt0) cc_final: 0.8348 (tt0) REVERT: J 376 LYS cc_start: 0.8380 (tttt) cc_final: 0.7824 (mttp) REVERT: J 383 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7917 (mt-10) REVERT: J 410 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7874 (ttpt) REVERT: K 235 LEU cc_start: 0.9021 (mt) cc_final: 0.8556 (mp) REVERT: K 246 GLN cc_start: 0.8544 (tt0) cc_final: 0.8277 (tt0) REVERT: K 376 LYS cc_start: 0.8420 (tttt) cc_final: 0.7910 (mttp) REVERT: K 425 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8646 (mtmm) REVERT: L 246 GLN cc_start: 0.8623 (tt0) cc_final: 0.8407 (tt0) REVERT: L 275 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8179 (tttt) REVERT: L 297 GLN cc_start: 0.8242 (tt0) cc_final: 0.7965 (tp-100) REVERT: L 376 LYS cc_start: 0.8370 (tttt) cc_final: 0.7732 (mttp) REVERT: M 276 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7709 (mt-10) REVERT: M 296 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7402 (ttp-170) REVERT: M 297 GLN cc_start: 0.8203 (tt0) cc_final: 0.7973 (tp40) REVERT: M 376 LYS cc_start: 0.8462 (tttt) cc_final: 0.7755 (mttp) REVERT: N 246 GLN cc_start: 0.8554 (tt0) cc_final: 0.8222 (tt0) REVERT: N 279 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: N 287 ASP cc_start: 0.8006 (t0) cc_final: 0.7786 (t70) REVERT: N 297 GLN cc_start: 0.8269 (tt0) cc_final: 0.8056 (tp40) REVERT: N 376 LYS cc_start: 0.8449 (tttt) cc_final: 0.7887 (mttp) REVERT: O 246 GLN cc_start: 0.8637 (tt0) cc_final: 0.8383 (tt0) REVERT: O 376 LYS cc_start: 0.8472 (tttt) cc_final: 0.7923 (mttp) REVERT: P 376 LYS cc_start: 0.8496 (tttt) cc_final: 0.7861 (mttp) REVERT: P 435 SER cc_start: 0.8351 (t) cc_final: 0.8147 (t) REVERT: Q 235 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8550 (mp) REVERT: Q 297 GLN cc_start: 0.8137 (tt0) cc_final: 0.7877 (tp40) REVERT: Q 376 LYS cc_start: 0.8443 (tttt) cc_final: 0.7810 (mttp) REVERT: Q 420 MET cc_start: 0.8734 (ptm) cc_final: 0.8532 (ptm) REVERT: R 246 GLN cc_start: 0.8643 (tt0) cc_final: 0.8247 (tt0) REVERT: R 376 LYS cc_start: 0.8383 (tttt) cc_final: 0.7784 (mttp) REVERT: R 425 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8789 (mtmm) REVERT: S 297 GLN cc_start: 0.8060 (tt0) cc_final: 0.7789 (tp40) REVERT: S 376 LYS cc_start: 0.8337 (tttt) cc_final: 0.7822 (mttp) REVERT: T 246 GLN cc_start: 0.8644 (tt0) cc_final: 0.8348 (tt0) REVERT: T 287 ASP cc_start: 0.8071 (t0) cc_final: 0.7820 (t70) REVERT: T 297 GLN cc_start: 0.8192 (tt0) cc_final: 0.7922 (tp-100) REVERT: T 376 LYS cc_start: 0.8321 (tttt) cc_final: 0.7721 (mttp) REVERT: U 246 GLN cc_start: 0.8654 (tt0) cc_final: 0.8284 (tt0) REVERT: U 376 LYS cc_start: 0.8349 (tttt) cc_final: 0.7729 (mttp) REVERT: V 235 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8636 (mp) REVERT: V 297 GLN cc_start: 0.8299 (tt0) cc_final: 0.8055 (tp40) REVERT: V 376 LYS cc_start: 0.8400 (tttt) cc_final: 0.7776 (mttp) REVERT: W 231 ASN cc_start: 0.4770 (OUTLIER) cc_final: 0.4440 (p0) REVERT: W 275 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8176 (tttt) REVERT: W 376 LYS cc_start: 0.8463 (tttt) cc_final: 0.7798 (mttp) REVERT: X 279 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: X 376 LYS cc_start: 0.8482 (tttt) cc_final: 0.7747 (mttp) REVERT: X 425 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8736 (mtmm) REVERT: Y 246 GLN cc_start: 0.8625 (tt0) cc_final: 0.8270 (tt0) REVERT: Y 275 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8126 (tttt) REVERT: Y 297 GLN cc_start: 0.8141 (tt0) cc_final: 0.7886 (tp40) REVERT: Y 376 LYS cc_start: 0.8498 (tttt) cc_final: 0.7901 (mttp) REVERT: Z 246 GLN cc_start: 0.8724 (tt0) cc_final: 0.8367 (tt0) REVERT: Z 276 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7794 (mt-10) REVERT: Z 376 LYS cc_start: 0.8391 (tttt) cc_final: 0.7862 (mttp) REVERT: a 246 GLN cc_start: 0.8632 (tt0) cc_final: 0.8288 (tt0) REVERT: a 275 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8127 (tttt) REVERT: a 376 LYS cc_start: 0.8300 (tttt) cc_final: 0.7736 (mttp) REVERT: b 246 GLN cc_start: 0.8682 (tt0) cc_final: 0.8285 (tt0) REVERT: b 376 LYS cc_start: 0.8378 (tttt) cc_final: 0.7738 (mttp) REVERT: c 287 ASP cc_start: 0.7958 (t0) cc_final: 0.7748 (t70) REVERT: c 297 GLN cc_start: 0.8232 (tt0) cc_final: 0.8002 (tp40) REVERT: c 376 LYS cc_start: 0.8410 (tttt) cc_final: 0.7823 (mttp) REVERT: d 376 LYS cc_start: 0.8427 (tttt) cc_final: 0.7850 (mttp) REVERT: d 425 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8850 (mtmm) REVERT: e 297 GLN cc_start: 0.8210 (tt0) cc_final: 0.7905 (tp-100) REVERT: e 376 LYS cc_start: 0.8434 (tttt) cc_final: 0.7843 (mttp) REVERT: f 376 LYS cc_start: 0.8508 (tttt) cc_final: 0.7936 (mttp) REVERT: f 409 MET cc_start: 0.8191 (mmm) cc_final: 0.7938 (mmm) REVERT: g 246 GLN cc_start: 0.8692 (tt0) cc_final: 0.8267 (tt0) REVERT: g 296 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7456 (ttp-170) REVERT: g 297 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7339 (tp-100) REVERT: g 376 LYS cc_start: 0.8480 (tttt) cc_final: 0.7882 (mttp) outliers start: 86 outliers final: 31 residues processed: 1220 average time/residue: 0.9145 time to fit residues: 1303.8696 Evaluate side-chains 1202 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1159 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 433 VAL Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 363 THR Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 214 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 246 GLN C 246 GLN E 246 GLN F 269 GLN G 246 GLN G 261 ASN G 269 GLN H 246 GLN I 246 GLN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Q 261 ASN Q 431 ASN S 246 GLN ** T 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 269 GLN V 261 ASN X 239 ASN X 246 GLN X 269 GLN c 246 GLN ** c 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN f 246 GLN g 231 ASN g 261 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118470 restraints weight = 46697.822| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.69 r_work: 0.3323 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39765 Z= 0.194 Angle : 0.489 4.986 53592 Z= 0.264 Chirality : 0.039 0.136 6138 Planarity : 0.003 0.023 7194 Dihedral : 4.689 17.016 5379 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.42 % Allowed : 15.58 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.13), residues: 4785 helix: 2.82 (0.15), residues: 1320 sheet: 0.36 (0.11), residues: 2442 loop : -0.70 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 296 TYR 0.009 0.001 TYR f 393 PHE 0.012 0.001 PHE Y 422 HIS 0.003 0.000 HIS H 281 Details of bonding type rmsd covalent geometry : bond 0.00422 (39765) covalent geometry : angle 0.48891 (53592) hydrogen bonds : bond 0.04518 ( 1441) hydrogen bonds : angle 4.33565 ( 4224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1189 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8740 (tt0) cc_final: 0.8402 (tt0) REVERT: A 376 LYS cc_start: 0.8449 (tttt) cc_final: 0.7916 (mttp) REVERT: B 376 LYS cc_start: 0.8406 (tttt) cc_final: 0.7754 (mttp) REVERT: B 409 MET cc_start: 0.8224 (mmm) cc_final: 0.7840 (mmm) REVERT: C 269 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: C 376 LYS cc_start: 0.8496 (tttt) cc_final: 0.7969 (mttp) REVERT: C 383 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 246 GLN cc_start: 0.8716 (tt0) cc_final: 0.8410 (tt0) REVERT: D 297 GLN cc_start: 0.8240 (tt0) cc_final: 0.7977 (tp-100) REVERT: D 376 LYS cc_start: 0.8463 (tttt) cc_final: 0.7853 (mttp) REVERT: E 356 ARG cc_start: 0.6532 (mpp-170) cc_final: 0.6236 (mpp-170) REVERT: E 376 LYS cc_start: 0.8402 (tttt) cc_final: 0.7789 (mttp) REVERT: F 376 LYS cc_start: 0.8449 (tttt) cc_final: 0.7806 (mttp) REVERT: F 435 SER cc_start: 0.8378 (t) cc_final: 0.8168 (t) REVERT: G 235 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8905 (mp) REVERT: G 297 GLN cc_start: 0.8185 (tt0) cc_final: 0.7954 (tp40) REVERT: G 376 LYS cc_start: 0.8464 (tttt) cc_final: 0.7886 (mttp) REVERT: G 409 MET cc_start: 0.8128 (mmm) cc_final: 0.7847 (mmm) REVERT: H 296 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7540 (ttp-170) REVERT: H 297 GLN cc_start: 0.8242 (tt0) cc_final: 0.7956 (tp-100) REVERT: H 362 GLU cc_start: 0.7883 (tt0) cc_final: 0.7675 (tt0) REVERT: H 376 LYS cc_start: 0.8634 (tttt) cc_final: 0.7942 (mttp) REVERT: I 376 LYS cc_start: 0.8520 (tttt) cc_final: 0.7921 (mttp) REVERT: J 246 GLN cc_start: 0.8684 (tt0) cc_final: 0.8312 (tt0) REVERT: J 269 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: J 376 LYS cc_start: 0.8424 (tttt) cc_final: 0.7826 (mttp) REVERT: J 383 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7977 (mt-10) REVERT: K 235 LEU cc_start: 0.9083 (mt) cc_final: 0.8599 (mp) REVERT: K 246 GLN cc_start: 0.8661 (tt0) cc_final: 0.8337 (tt0) REVERT: K 269 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: K 275 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8323 (tttt) REVERT: K 362 GLU cc_start: 0.7944 (tt0) cc_final: 0.7614 (tt0) REVERT: K 376 LYS cc_start: 0.8478 (tttt) cc_final: 0.7924 (mttp) REVERT: L 246 GLN cc_start: 0.8718 (tt0) cc_final: 0.8429 (tt0) REVERT: L 297 GLN cc_start: 0.8270 (tt0) cc_final: 0.7980 (tp-100) REVERT: L 376 LYS cc_start: 0.8392 (tttt) cc_final: 0.7753 (mttp) REVERT: L 425 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8759 (mtmm) REVERT: M 276 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7751 (mt-10) REVERT: M 296 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7477 (ttp-170) REVERT: M 297 GLN cc_start: 0.8216 (tt0) cc_final: 0.7896 (tp40) REVERT: M 376 LYS cc_start: 0.8498 (tttt) cc_final: 0.7733 (mttp) REVERT: N 246 GLN cc_start: 0.8685 (tt0) cc_final: 0.8434 (tt0) REVERT: N 279 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: N 297 GLN cc_start: 0.8298 (tt0) cc_final: 0.8084 (tp40) REVERT: N 303 GLN cc_start: 0.7380 (mt0) cc_final: 0.7006 (mp10) REVERT: N 376 LYS cc_start: 0.8466 (tttt) cc_final: 0.7879 (mttp) REVERT: O 376 LYS cc_start: 0.8486 (tttt) cc_final: 0.7928 (mttp) REVERT: P 246 GLN cc_start: 0.8697 (tt0) cc_final: 0.8318 (tt0) REVERT: P 303 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: P 376 LYS cc_start: 0.8517 (tttt) cc_final: 0.7896 (mttp) REVERT: Q 235 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8657 (mp) REVERT: Q 297 GLN cc_start: 0.8177 (tt0) cc_final: 0.7912 (tp40) REVERT: Q 376 LYS cc_start: 0.8467 (tttt) cc_final: 0.7792 (mttp) REVERT: R 246 GLN cc_start: 0.8748 (tt0) cc_final: 0.8377 (tt0) REVERT: R 370 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7979 (ttt-90) REVERT: R 376 LYS cc_start: 0.8391 (tttt) cc_final: 0.7764 (mttp) REVERT: S 297 GLN cc_start: 0.8100 (tt0) cc_final: 0.7824 (tp40) REVERT: S 376 LYS cc_start: 0.8392 (tttt) cc_final: 0.7825 (mttp) REVERT: T 246 GLN cc_start: 0.8727 (tt0) cc_final: 0.8402 (tt0) REVERT: T 287 ASP cc_start: 0.8044 (t0) cc_final: 0.7808 (t70) REVERT: T 297 GLN cc_start: 0.8245 (tt0) cc_final: 0.7975 (tp-100) REVERT: T 376 LYS cc_start: 0.8363 (tttt) cc_final: 0.7753 (mttp) REVERT: U 246 GLN cc_start: 0.8723 (tt0) cc_final: 0.8464 (tt0) REVERT: U 279 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: U 376 LYS cc_start: 0.8375 (tttt) cc_final: 0.7736 (mttp) REVERT: V 235 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8772 (mp) REVERT: V 246 GLN cc_start: 0.8662 (tt0) cc_final: 0.8322 (tt0) REVERT: V 297 GLN cc_start: 0.8314 (tt0) cc_final: 0.8060 (tp40) REVERT: V 376 LYS cc_start: 0.8445 (tttt) cc_final: 0.7802 (mttp) REVERT: W 231 ASN cc_start: 0.4853 (OUTLIER) cc_final: 0.4528 (p0) REVERT: W 275 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8194 (tttt) REVERT: W 376 LYS cc_start: 0.8475 (tttt) cc_final: 0.7832 (mttp) REVERT: X 376 LYS cc_start: 0.8515 (tttt) cc_final: 0.7776 (mttp) REVERT: X 425 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8769 (mtmm) REVERT: Y 246 GLN cc_start: 0.8711 (tt0) cc_final: 0.8304 (tt0) REVERT: Y 275 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8166 (tttt) REVERT: Y 297 GLN cc_start: 0.8179 (tt0) cc_final: 0.7927 (tp40) REVERT: Y 376 LYS cc_start: 0.8520 (tttt) cc_final: 0.7918 (mttp) REVERT: Y 420 MET cc_start: 0.8466 (ptm) cc_final: 0.8083 (ptm) REVERT: Z 246 GLN cc_start: 0.8800 (tt0) cc_final: 0.8450 (tt0) REVERT: Z 276 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7772 (mt-10) REVERT: Z 376 LYS cc_start: 0.8427 (tttt) cc_final: 0.7882 (mttp) REVERT: a 246 GLN cc_start: 0.8696 (tt0) cc_final: 0.8389 (tt0) REVERT: a 275 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8187 (tttt) REVERT: a 376 LYS cc_start: 0.8352 (tttt) cc_final: 0.7731 (mttp) REVERT: b 246 GLN cc_start: 0.8762 (tt0) cc_final: 0.8391 (tt0) REVERT: b 275 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8299 (tttt) REVERT: b 376 LYS cc_start: 0.8379 (tttt) cc_final: 0.7724 (mttp) REVERT: c 279 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: c 297 GLN cc_start: 0.8251 (tt0) cc_final: 0.8020 (tp40) REVERT: c 376 LYS cc_start: 0.8420 (tttt) cc_final: 0.7830 (mttp) REVERT: d 279 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: d 356 ARG cc_start: 0.6689 (mpp-170) cc_final: 0.6294 (mpp-170) REVERT: d 376 LYS cc_start: 0.8446 (tttt) cc_final: 0.7819 (mttp) REVERT: d 425 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8869 (mtmm) REVERT: e 297 GLN cc_start: 0.8240 (tt0) cc_final: 0.7939 (tp-100) REVERT: e 376 LYS cc_start: 0.8419 (tttt) cc_final: 0.7835 (mttp) REVERT: f 275 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8340 (tttt) REVERT: f 376 LYS cc_start: 0.8503 (tttt) cc_final: 0.7953 (mttp) REVERT: f 409 MET cc_start: 0.8223 (mmm) cc_final: 0.7890 (mmm) REVERT: g 246 GLN cc_start: 0.8755 (tt0) cc_final: 0.8374 (tt0) REVERT: g 296 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7574 (ttp-170) REVERT: g 297 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7375 (tp-100) REVERT: g 303 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: g 376 LYS cc_start: 0.8490 (tttt) cc_final: 0.7900 (mttp) outliers start: 107 outliers final: 57 residues processed: 1236 average time/residue: 0.8805 time to fit residues: 1273.5965 Evaluate side-chains 1249 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1175 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 287 ASP Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain d residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 235 LEU Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 342 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN B 297 GLN C 246 GLN C 297 GLN F 269 GLN G 269 GLN H 246 GLN I 246 GLN M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN P 269 GLN S 246 GLN ** T 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN X 269 GLN c 246 GLN ** c 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN f 246 GLN g 231 ASN g 261 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118867 restraints weight = 46642.217| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.69 r_work: 0.3328 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39765 Z= 0.175 Angle : 0.476 4.925 53592 Z= 0.257 Chirality : 0.039 0.137 6138 Planarity : 0.002 0.022 7194 Dihedral : 4.620 16.988 5379 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.35 % Allowed : 15.99 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4785 helix: 2.90 (0.15), residues: 1320 sheet: 0.42 (0.11), residues: 2442 loop : -0.70 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.008 0.001 TYR d 393 PHE 0.011 0.001 PHE Y 422 HIS 0.004 0.000 HIS W 281 Details of bonding type rmsd covalent geometry : bond 0.00380 (39765) covalent geometry : angle 0.47601 (53592) hydrogen bonds : bond 0.04296 ( 1441) hydrogen bonds : angle 4.26145 ( 4224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1185 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8731 (tt0) cc_final: 0.8372 (tt0) REVERT: A 376 LYS cc_start: 0.8451 (tttt) cc_final: 0.7921 (mttp) REVERT: B 297 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 376 LYS cc_start: 0.8389 (tttt) cc_final: 0.7780 (mttp) REVERT: B 409 MET cc_start: 0.8250 (mmm) cc_final: 0.7856 (mmm) REVERT: C 269 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: C 376 LYS cc_start: 0.8481 (tttt) cc_final: 0.7915 (mttp) REVERT: C 383 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 246 GLN cc_start: 0.8706 (tt0) cc_final: 0.8456 (tt0) REVERT: D 297 GLN cc_start: 0.8224 (tt0) cc_final: 0.7967 (tp-100) REVERT: D 376 LYS cc_start: 0.8434 (tttt) cc_final: 0.7829 (mttp) REVERT: E 376 LYS cc_start: 0.8382 (tttt) cc_final: 0.7776 (mttp) REVERT: F 246 GLN cc_start: 0.8654 (tt0) cc_final: 0.8256 (tt0) REVERT: F 376 LYS cc_start: 0.8433 (tttt) cc_final: 0.7779 (mttp) REVERT: F 435 SER cc_start: 0.8365 (t) cc_final: 0.8157 (t) REVERT: G 235 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8905 (mp) REVERT: G 296 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7596 (tpp-160) REVERT: G 297 GLN cc_start: 0.8180 (tt0) cc_final: 0.7953 (tp40) REVERT: G 303 GLN cc_start: 0.7331 (mt0) cc_final: 0.6968 (mp10) REVERT: G 376 LYS cc_start: 0.8450 (tttt) cc_final: 0.7851 (mttp) REVERT: G 409 MET cc_start: 0.8152 (mmm) cc_final: 0.7839 (mmm) REVERT: H 296 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7529 (ttp-170) REVERT: H 297 GLN cc_start: 0.8240 (tt0) cc_final: 0.7957 (tp-100) REVERT: H 376 LYS cc_start: 0.8629 (tttt) cc_final: 0.7950 (mttp) REVERT: I 376 LYS cc_start: 0.8529 (tttt) cc_final: 0.7915 (mttp) REVERT: J 246 GLN cc_start: 0.8686 (tt0) cc_final: 0.8290 (tt0) REVERT: J 269 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: J 376 LYS cc_start: 0.8418 (tttt) cc_final: 0.7826 (mttp) REVERT: J 383 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7963 (mt-10) REVERT: K 235 LEU cc_start: 0.9073 (mt) cc_final: 0.8601 (mp) REVERT: K 246 GLN cc_start: 0.8652 (tt0) cc_final: 0.8289 (tt0) REVERT: K 269 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: K 362 GLU cc_start: 0.7959 (tt0) cc_final: 0.7620 (tt0) REVERT: K 376 LYS cc_start: 0.8479 (tttt) cc_final: 0.7909 (mttp) REVERT: L 246 GLN cc_start: 0.8715 (tt0) cc_final: 0.8418 (tt0) REVERT: L 297 GLN cc_start: 0.8259 (tt0) cc_final: 0.7973 (tp-100) REVERT: L 376 LYS cc_start: 0.8445 (tttt) cc_final: 0.7808 (mttp) REVERT: M 276 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7755 (mt-10) REVERT: M 297 GLN cc_start: 0.8210 (tt0) cc_final: 0.7895 (tp40) REVERT: M 376 LYS cc_start: 0.8493 (tttt) cc_final: 0.7740 (mttp) REVERT: N 246 GLN cc_start: 0.8683 (tt0) cc_final: 0.8428 (tt0) REVERT: N 279 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: N 297 GLN cc_start: 0.8283 (tt0) cc_final: 0.8080 (tp40) REVERT: N 376 LYS cc_start: 0.8460 (tttt) cc_final: 0.7875 (mttp) REVERT: O 376 LYS cc_start: 0.8476 (tttt) cc_final: 0.7916 (mttp) REVERT: P 376 LYS cc_start: 0.8519 (tttt) cc_final: 0.7892 (mttp) REVERT: Q 235 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8608 (mp) REVERT: Q 297 GLN cc_start: 0.8168 (tt0) cc_final: 0.7905 (tp40) REVERT: Q 376 LYS cc_start: 0.8472 (tttt) cc_final: 0.7804 (mttp) REVERT: R 246 GLN cc_start: 0.8733 (tt0) cc_final: 0.8368 (tt0) REVERT: R 370 ARG cc_start: 0.8275 (ttt180) cc_final: 0.7993 (ttt-90) REVERT: R 376 LYS cc_start: 0.8376 (tttt) cc_final: 0.7732 (mttp) REVERT: S 297 GLN cc_start: 0.8076 (tt0) cc_final: 0.7796 (tp-100) REVERT: S 376 LYS cc_start: 0.8406 (tttt) cc_final: 0.7847 (mttp) REVERT: T 246 GLN cc_start: 0.8720 (tt0) cc_final: 0.8381 (tt0) REVERT: T 287 ASP cc_start: 0.8044 (t0) cc_final: 0.7807 (t70) REVERT: T 297 GLN cc_start: 0.8231 (tt0) cc_final: 0.7966 (tp-100) REVERT: T 376 LYS cc_start: 0.8353 (tttt) cc_final: 0.7747 (mttp) REVERT: U 246 GLN cc_start: 0.8718 (tt0) cc_final: 0.8445 (tt0) REVERT: U 376 LYS cc_start: 0.8369 (tttt) cc_final: 0.7734 (mttp) REVERT: V 235 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8759 (mp) REVERT: V 297 GLN cc_start: 0.8307 (tt0) cc_final: 0.8057 (tp40) REVERT: V 376 LYS cc_start: 0.8439 (tttt) cc_final: 0.7805 (mttp) REVERT: W 231 ASN cc_start: 0.4994 (OUTLIER) cc_final: 0.4708 (p0) REVERT: W 275 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8192 (tttt) REVERT: W 376 LYS cc_start: 0.8467 (tttt) cc_final: 0.7790 (mttp) REVERT: X 376 LYS cc_start: 0.8519 (tttt) cc_final: 0.7780 (mttp) REVERT: Y 246 GLN cc_start: 0.8705 (tt0) cc_final: 0.8294 (tt0) REVERT: Y 275 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8167 (tttt) REVERT: Y 297 GLN cc_start: 0.8169 (tt0) cc_final: 0.7919 (tp40) REVERT: Y 376 LYS cc_start: 0.8520 (tttt) cc_final: 0.7877 (mttp) REVERT: Y 420 MET cc_start: 0.8492 (ptm) cc_final: 0.8094 (ptm) REVERT: Z 246 GLN cc_start: 0.8787 (tt0) cc_final: 0.8436 (tt0) REVERT: Z 376 LYS cc_start: 0.8407 (tttt) cc_final: 0.7876 (mttp) REVERT: a 246 GLN cc_start: 0.8689 (tt0) cc_final: 0.8364 (tt0) REVERT: a 275 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8159 (ttpt) REVERT: a 376 LYS cc_start: 0.8348 (tttt) cc_final: 0.7734 (mttp) REVERT: b 246 GLN cc_start: 0.8745 (tt0) cc_final: 0.8380 (tt0) REVERT: b 275 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8293 (tttt) REVERT: b 376 LYS cc_start: 0.8380 (tttt) cc_final: 0.7726 (mttp) REVERT: c 279 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: c 297 GLN cc_start: 0.8239 (tt0) cc_final: 0.8007 (tp40) REVERT: c 376 LYS cc_start: 0.8419 (tttt) cc_final: 0.7841 (mttp) REVERT: d 279 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: d 356 ARG cc_start: 0.6701 (mpp-170) cc_final: 0.6336 (mpp-170) REVERT: d 376 LYS cc_start: 0.8444 (tttt) cc_final: 0.7808 (mttp) REVERT: d 425 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8872 (mtmm) REVERT: e 246 GLN cc_start: 0.8744 (tt0) cc_final: 0.8404 (tt0) REVERT: e 297 GLN cc_start: 0.8232 (tt0) cc_final: 0.7933 (tp-100) REVERT: e 376 LYS cc_start: 0.8428 (tttt) cc_final: 0.7863 (mttp) REVERT: f 376 LYS cc_start: 0.8498 (tttt) cc_final: 0.7951 (mttp) REVERT: f 409 MET cc_start: 0.8220 (mmm) cc_final: 0.7903 (mmm) REVERT: g 246 GLN cc_start: 0.8730 (tt0) cc_final: 0.8333 (tt0) REVERT: g 296 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7550 (ttp-170) REVERT: g 297 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7372 (tp-100) REVERT: g 376 LYS cc_start: 0.8477 (tttt) cc_final: 0.7887 (mttp) outliers start: 104 outliers final: 59 residues processed: 1229 average time/residue: 0.9018 time to fit residues: 1296.4284 Evaluate side-chains 1248 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1174 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 296 ARG Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 383 GLU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 363 THR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 429 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 461 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 446 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 246 GLN B 365 ASN C 246 GLN C 297 GLN E 246 GLN F 261 ASN F 269 GLN G 231 ASN G 269 GLN H 246 GLN I 246 GLN I 261 ASN J 261 ASN M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN O 261 ASN P 261 ASN P 269 GLN Q 246 GLN S 246 GLN T 261 ASN T 365 ASN ** U 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN X 269 GLN Y 365 ASN b 261 ASN c 246 GLN c 261 ASN d 246 GLN e 269 GLN f 246 GLN f 365 ASN g 231 ASN g 261 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115739 restraints weight = 45953.412| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.70 r_work: 0.3274 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 39765 Z= 0.409 Angle : 0.634 5.479 53592 Z= 0.340 Chirality : 0.044 0.156 6138 Planarity : 0.004 0.042 7194 Dihedral : 5.293 17.559 5379 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 15.97 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 4785 helix: 2.07 (0.14), residues: 1320 sheet: 0.23 (0.11), residues: 2442 loop : -0.88 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 373 TYR 0.016 0.002 TYR B 393 PHE 0.016 0.002 PHE Y 422 HIS 0.006 0.001 HIS W 281 Details of bonding type rmsd covalent geometry : bond 0.00906 (39765) covalent geometry : angle 0.63404 (53592) hydrogen bonds : bond 0.05786 ( 1441) hydrogen bonds : angle 4.78923 ( 4224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1196 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8871 (tt0) cc_final: 0.8587 (tt0) REVERT: A 376 LYS cc_start: 0.8430 (tttt) cc_final: 0.7860 (mttp) REVERT: B 297 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: B 376 LYS cc_start: 0.8439 (tttt) cc_final: 0.7732 (mttp) REVERT: C 269 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: C 297 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: C 376 LYS cc_start: 0.8492 (tttt) cc_final: 0.7916 (mttp) REVERT: C 383 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 425 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8764 (mtmm) REVERT: D 246 GLN cc_start: 0.8821 (tt0) cc_final: 0.8592 (tt0) REVERT: D 376 LYS cc_start: 0.8445 (tttt) cc_final: 0.7840 (mttp) REVERT: E 376 LYS cc_start: 0.8443 (tttt) cc_final: 0.7744 (mttp) REVERT: F 246 GLN cc_start: 0.8805 (tt0) cc_final: 0.8329 (tt0) REVERT: F 297 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7551 (tp-100) REVERT: F 376 LYS cc_start: 0.8441 (tttt) cc_final: 0.7799 (mttp) REVERT: F 410 LYS cc_start: 0.8291 (tmmt) cc_final: 0.8073 (tttm) REVERT: G 235 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8948 (mp) REVERT: G 246 GLN cc_start: 0.8757 (tt0) cc_final: 0.8430 (tt0) REVERT: G 296 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7809 (tpp-160) REVERT: G 297 GLN cc_start: 0.8239 (tt0) cc_final: 0.7992 (tp40) REVERT: G 303 GLN cc_start: 0.7533 (mt0) cc_final: 0.7152 (mp10) REVERT: G 376 LYS cc_start: 0.8441 (tttt) cc_final: 0.7742 (mttp) REVERT: G 409 MET cc_start: 0.8145 (mmm) cc_final: 0.7822 (mmm) REVERT: H 246 GLN cc_start: 0.8724 (tt0) cc_final: 0.8381 (tt0) REVERT: H 296 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7638 (ttp-170) REVERT: H 362 GLU cc_start: 0.7941 (tt0) cc_final: 0.7736 (tt0) REVERT: H 376 LYS cc_start: 0.8598 (tttt) cc_final: 0.7912 (mttp) REVERT: I 296 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7875 (tpp-160) REVERT: I 376 LYS cc_start: 0.8565 (tttt) cc_final: 0.7862 (mttp) REVERT: J 246 GLN cc_start: 0.8773 (tt0) cc_final: 0.8379 (tt0) REVERT: J 269 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: J 376 LYS cc_start: 0.8468 (tttt) cc_final: 0.7774 (mttp) REVERT: K 246 GLN cc_start: 0.8815 (tt0) cc_final: 0.8602 (tt0) REVERT: K 269 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: K 376 LYS cc_start: 0.8498 (tttt) cc_final: 0.7874 (mttp) REVERT: M 276 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7792 (mt-10) REVERT: M 297 GLN cc_start: 0.8269 (tt0) cc_final: 0.8036 (tp40) REVERT: M 376 LYS cc_start: 0.8480 (tttt) cc_final: 0.7768 (mttp) REVERT: N 279 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: N 297 GLN cc_start: 0.8325 (tt0) cc_final: 0.8086 (tp40) REVERT: N 303 GLN cc_start: 0.7377 (mt0) cc_final: 0.7009 (mp10) REVERT: N 376 LYS cc_start: 0.8479 (tttt) cc_final: 0.7897 (mttp) REVERT: O 376 LYS cc_start: 0.8531 (tttt) cc_final: 0.7904 (mttp) REVERT: P 246 GLN cc_start: 0.8754 (tt0) cc_final: 0.8430 (tt0) REVERT: P 296 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7792 (ttp-170) REVERT: P 303 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: P 376 LYS cc_start: 0.8556 (tttt) cc_final: 0.7928 (mttp) REVERT: Q 235 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8663 (mp) REVERT: Q 279 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: Q 376 LYS cc_start: 0.8429 (tttt) cc_final: 0.7715 (mttp) REVERT: R 246 GLN cc_start: 0.8848 (tt0) cc_final: 0.8524 (tt0) REVERT: R 377 MET cc_start: 0.8567 (mpt) cc_final: 0.8149 (mpt) REVERT: S 287 ASP cc_start: 0.7875 (t70) cc_final: 0.7621 (t70) REVERT: S 376 LYS cc_start: 0.8414 (tttt) cc_final: 0.7811 (mttp) REVERT: T 246 GLN cc_start: 0.8838 (tt0) cc_final: 0.8606 (tt0) REVERT: T 376 LYS cc_start: 0.8416 (tttt) cc_final: 0.7740 (mttp) REVERT: U 246 GLN cc_start: 0.8748 (tt0) cc_final: 0.8432 (tt0) REVERT: U 276 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7772 (mt-10) REVERT: U 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7805 (mttp) REVERT: V 235 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8831 (mp) REVERT: V 246 GLN cc_start: 0.8737 (tt0) cc_final: 0.8344 (tt0) REVERT: V 297 GLN cc_start: 0.8350 (tt0) cc_final: 0.8084 (tp40) REVERT: W 231 ASN cc_start: 0.5180 (OUTLIER) cc_final: 0.4834 (p0) REVERT: W 246 GLN cc_start: 0.8791 (tt0) cc_final: 0.8497 (tt0) REVERT: W 376 LYS cc_start: 0.8496 (tttt) cc_final: 0.7778 (mttp) REVERT: Y 297 GLN cc_start: 0.8215 (tt0) cc_final: 0.7952 (tp40) REVERT: Y 376 LYS cc_start: 0.8587 (tttt) cc_final: 0.7894 (mttp) REVERT: Y 420 MET cc_start: 0.8780 (ptm) cc_final: 0.8267 (ptm) REVERT: Z 246 GLN cc_start: 0.8822 (tt0) cc_final: 0.8487 (tt0) REVERT: Z 297 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7207 (tp-100) REVERT: Z 376 LYS cc_start: 0.8485 (tttt) cc_final: 0.7831 (mttp) REVERT: a 246 GLN cc_start: 0.8796 (tt0) cc_final: 0.8560 (tt0) REVERT: a 376 LYS cc_start: 0.8380 (tttt) cc_final: 0.7723 (mttp) REVERT: b 246 GLN cc_start: 0.8774 (tt0) cc_final: 0.8437 (tt0) REVERT: b 296 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7275 (tpp-160) REVERT: b 376 LYS cc_start: 0.8404 (tttt) cc_final: 0.7745 (mttp) REVERT: c 279 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: c 297 GLN cc_start: 0.8280 (tt0) cc_final: 0.8030 (tp40) REVERT: c 376 LYS cc_start: 0.8437 (tttt) cc_final: 0.7813 (mttp) REVERT: d 279 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: d 297 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7434 (tp-100) REVERT: d 356 ARG cc_start: 0.6768 (mpp-170) cc_final: 0.6393 (mpp-170) REVERT: d 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7774 (mttp) REVERT: e 246 GLN cc_start: 0.8833 (tt0) cc_final: 0.8470 (tt0) REVERT: e 297 GLN cc_start: 0.8267 (tt0) cc_final: 0.7999 (tp40) REVERT: e 376 LYS cc_start: 0.8485 (tttt) cc_final: 0.7884 (mttp) REVERT: f 376 LYS cc_start: 0.8551 (tttt) cc_final: 0.7899 (mttp) REVERT: f 409 MET cc_start: 0.8267 (mmm) cc_final: 0.7914 (mmm) REVERT: f 410 LYS cc_start: 0.8310 (tmmt) cc_final: 0.8075 (ttpt) REVERT: g 296 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7687 (ttp-170) REVERT: g 297 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7385 (tp-100) REVERT: g 303 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: g 376 LYS cc_start: 0.8551 (tttt) cc_final: 0.7872 (mttp) outliers start: 128 outliers final: 74 residues processed: 1253 average time/residue: 0.8750 time to fit residues: 1282.6529 Evaluate side-chains 1264 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1165 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 296 ARG Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 296 ARG Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 302 GLU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 296 ARG Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 405 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 363 THR Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 297 GLN Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 296 ARG Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 363 THR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 235 LEU Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 435 optimal weight: 0.8980 chunk 450 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 487 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 246 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN F 269 GLN G 231 ASN ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN I 246 GLN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN L 246 GLN L 297 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN ** O 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 261 ASN P 269 GLN Q 261 ASN ** S 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 269 GLN V 261 ASN ** X 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 269 GLN Y 246 GLN b 261 ASN c 246 GLN ** c 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 231 ASN g 246 GLN g 261 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119852 restraints weight = 46612.104| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.69 r_work: 0.3347 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39765 Z= 0.131 Angle : 0.464 5.386 53592 Z= 0.251 Chirality : 0.039 0.141 6138 Planarity : 0.002 0.027 7194 Dihedral : 4.548 18.107 5379 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.97 % Allowed : 17.44 % Favored : 80.60 % 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 are not related in a simple way. whole: 1.31 (0.13), residues: 4785 helix: 2.96 (0.15), residues: 1320 sheet: 0.45 (0.11), residues: 2442 loop : -0.76 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 356 TYR 0.006 0.001 TYR Y 393 PHE 0.011 0.001 PHE g 422 HIS 0.004 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00281 (39765) covalent geometry : angle 0.46409 (53592) hydrogen bonds : bond 0.03946 ( 1441) hydrogen bonds : angle 4.18560 ( 4224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1164 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8707 (tt0) cc_final: 0.8381 (tt0) REVERT: A 376 LYS cc_start: 0.8442 (tttt) cc_final: 0.7897 (mttp) REVERT: B 297 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: B 376 LYS cc_start: 0.8373 (tttt) cc_final: 0.7763 (mttp) REVERT: B 409 MET cc_start: 0.8242 (mmm) cc_final: 0.7825 (mmm) REVERT: C 269 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: C 376 LYS cc_start: 0.8466 (tttt) cc_final: 0.7928 (mttp) REVERT: C 383 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 246 GLN cc_start: 0.8692 (tt0) cc_final: 0.8462 (tt0) REVERT: D 297 GLN cc_start: 0.8238 (tt0) cc_final: 0.7965 (tp-100) REVERT: D 376 LYS cc_start: 0.8426 (tttt) cc_final: 0.7857 (mttp) REVERT: E 376 LYS cc_start: 0.8426 (tttt) cc_final: 0.7827 (mttp) REVERT: F 246 GLN cc_start: 0.8642 (tt0) cc_final: 0.8221 (tt0) REVERT: F 376 LYS cc_start: 0.8396 (tttt) cc_final: 0.7759 (mttp) REVERT: F 435 SER cc_start: 0.8374 (t) cc_final: 0.8166 (t) REVERT: G 235 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8842 (mp) REVERT: G 246 GLN cc_start: 0.8698 (tt0) cc_final: 0.8350 (tt0) REVERT: G 297 GLN cc_start: 0.8184 (tt0) cc_final: 0.7937 (tp40) REVERT: G 303 GLN cc_start: 0.7391 (mt0) cc_final: 0.7016 (mp10) REVERT: G 376 LYS cc_start: 0.8431 (tttt) cc_final: 0.7853 (mttp) REVERT: G 409 MET cc_start: 0.8112 (mmm) cc_final: 0.7798 (mmm) REVERT: H 296 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7484 (ttp-170) REVERT: H 297 GLN cc_start: 0.8183 (tt0) cc_final: 0.7866 (tp-100) REVERT: H 376 LYS cc_start: 0.8575 (tttt) cc_final: 0.7889 (mttp) REVERT: I 376 LYS cc_start: 0.8515 (tttt) cc_final: 0.7888 (mttp) REVERT: J 246 GLN cc_start: 0.8666 (tt0) cc_final: 0.8267 (tt0) REVERT: J 376 LYS cc_start: 0.8390 (tttt) cc_final: 0.7802 (mttp) REVERT: K 235 LEU cc_start: 0.9024 (mt) cc_final: 0.8530 (mp) REVERT: K 246 GLN cc_start: 0.8605 (tt0) cc_final: 0.8271 (tt0) REVERT: K 269 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: K 362 GLU cc_start: 0.7979 (tt0) cc_final: 0.7639 (tt0) REVERT: K 376 LYS cc_start: 0.8469 (tttt) cc_final: 0.7926 (mttp) REVERT: L 246 GLN cc_start: 0.8737 (tt0) cc_final: 0.8511 (tt0) REVERT: L 275 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8162 (tttt) REVERT: L 297 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7952 (tp-100) REVERT: L 376 LYS cc_start: 0.8442 (tttt) cc_final: 0.7804 (mttp) REVERT: M 276 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7721 (mt-10) REVERT: M 297 GLN cc_start: 0.8189 (tt0) cc_final: 0.7898 (tp40) REVERT: M 376 LYS cc_start: 0.8449 (tttt) cc_final: 0.7730 (mttp) REVERT: N 246 GLN cc_start: 0.8639 (tt0) cc_final: 0.8418 (tt0) REVERT: N 279 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: N 297 GLN cc_start: 0.8272 (tt0) cc_final: 0.8061 (tp40) REVERT: N 376 LYS cc_start: 0.8457 (tttt) cc_final: 0.7894 (mttp) REVERT: O 376 LYS cc_start: 0.8444 (tttt) cc_final: 0.7889 (mttp) REVERT: P 246 GLN cc_start: 0.8601 (tt0) cc_final: 0.8241 (tt0) REVERT: P 303 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: P 376 LYS cc_start: 0.8483 (tttt) cc_final: 0.7855 (mttp) REVERT: Q 235 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8571 (mp) REVERT: Q 297 GLN cc_start: 0.8162 (tt0) cc_final: 0.7933 (tp-100) REVERT: Q 376 LYS cc_start: 0.8461 (tttt) cc_final: 0.7806 (mttp) REVERT: R 246 GLN cc_start: 0.8721 (tt0) cc_final: 0.8316 (tt0) REVERT: R 376 LYS cc_start: 0.8386 (tttt) cc_final: 0.7814 (mttp) REVERT: S 297 GLN cc_start: 0.8117 (tt0) cc_final: 0.7847 (tp-100) REVERT: S 376 LYS cc_start: 0.8381 (tttt) cc_final: 0.7809 (mttp) REVERT: T 246 GLN cc_start: 0.8687 (tt0) cc_final: 0.8325 (tt0) REVERT: T 287 ASP cc_start: 0.7980 (t0) cc_final: 0.7780 (t70) REVERT: T 297 GLN cc_start: 0.8276 (tt0) cc_final: 0.7989 (tp-100) REVERT: T 376 LYS cc_start: 0.8334 (tttt) cc_final: 0.7677 (mttp) REVERT: U 246 GLN cc_start: 0.8687 (tt0) cc_final: 0.8308 (tt0) REVERT: U 376 LYS cc_start: 0.8353 (tttt) cc_final: 0.7724 (mttp) REVERT: V 235 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8654 (mp) REVERT: V 246 GLN cc_start: 0.8632 (tt0) cc_final: 0.8250 (tt0) REVERT: V 297 GLN cc_start: 0.8301 (tt0) cc_final: 0.8047 (tp40) REVERT: V 376 LYS cc_start: 0.8408 (tttt) cc_final: 0.7770 (mttp) REVERT: W 231 ASN cc_start: 0.4869 (OUTLIER) cc_final: 0.4599 (p0) REVERT: W 275 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8199 (tttt) REVERT: W 376 LYS cc_start: 0.8445 (tttt) cc_final: 0.7777 (mttp) REVERT: X 376 LYS cc_start: 0.8498 (tttt) cc_final: 0.7766 (mttp) REVERT: Y 246 GLN cc_start: 0.8646 (tt0) cc_final: 0.8313 (tt0) REVERT: Y 275 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8080 (tttt) REVERT: Y 297 GLN cc_start: 0.8167 (tt0) cc_final: 0.7916 (tp40) REVERT: Y 376 LYS cc_start: 0.8501 (tttt) cc_final: 0.7872 (mttp) REVERT: Y 420 MET cc_start: 0.8565 (ptm) cc_final: 0.8177 (ptm) REVERT: Z 246 GLN cc_start: 0.8765 (tt0) cc_final: 0.8388 (tt0) REVERT: Z 276 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7808 (mt-10) REVERT: Z 376 LYS cc_start: 0.8399 (tttt) cc_final: 0.7851 (mttp) REVERT: a 235 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8579 (mp) REVERT: a 246 GLN cc_start: 0.8652 (tt0) cc_final: 0.8347 (tt0) REVERT: a 275 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8162 (tttt) REVERT: a 376 LYS cc_start: 0.8315 (tttt) cc_final: 0.7731 (mttp) REVERT: b 246 GLN cc_start: 0.8696 (tt0) cc_final: 0.8309 (tt0) REVERT: b 376 LYS cc_start: 0.8359 (tttt) cc_final: 0.7707 (mttp) REVERT: b 409 MET cc_start: 0.8309 (mmm) cc_final: 0.8105 (mmm) REVERT: c 279 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7754 (mp0) REVERT: c 297 GLN cc_start: 0.8251 (tt0) cc_final: 0.8013 (tp40) REVERT: c 376 LYS cc_start: 0.8398 (tttt) cc_final: 0.7859 (mttp) REVERT: d 275 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8225 (tttt) REVERT: d 279 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: d 376 LYS cc_start: 0.8403 (tttt) cc_final: 0.7789 (mttp) REVERT: e 246 GLN cc_start: 0.8738 (tt0) cc_final: 0.8427 (tt0) REVERT: e 297 GLN cc_start: 0.8218 (tt0) cc_final: 0.7919 (tp-100) REVERT: e 376 LYS cc_start: 0.8420 (tttt) cc_final: 0.7837 (mttp) REVERT: f 376 LYS cc_start: 0.8486 (tttt) cc_final: 0.7888 (mttp) REVERT: f 409 MET cc_start: 0.8196 (mmm) cc_final: 0.7846 (mmm) REVERT: g 246 GLN cc_start: 0.8683 (tt0) cc_final: 0.8339 (tt0) REVERT: g 296 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7510 (ttp-170) REVERT: g 297 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7401 (tp-100) REVERT: g 303 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: g 376 LYS cc_start: 0.8460 (tttt) cc_final: 0.7875 (mttp) outliers start: 87 outliers final: 48 residues processed: 1200 average time/residue: 0.9124 time to fit residues: 1282.4603 Evaluate side-chains 1217 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1153 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 287 ASP Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 363 THR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 102 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 269 GLN B 246 GLN B 297 GLN C 246 GLN E 246 GLN F 261 ASN F 269 GLN G 269 GLN I 246 GLN J 261 ASN M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN P 261 ASN P 269 GLN Q 246 GLN Q 261 ASN S 246 GLN V 261 ASN V 269 GLN ** W 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 ASN X 269 GLN b 261 ASN c 246 GLN d 246 GLN e 269 GLN f 246 GLN g 231 ASN g 261 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115710 restraints weight = 46084.798| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.70 r_work: 0.3266 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 39765 Z= 0.390 Angle : 0.626 7.097 53592 Z= 0.336 Chirality : 0.044 0.172 6138 Planarity : 0.004 0.102 7194 Dihedral : 5.238 18.928 5379 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.26 % Allowed : 17.44 % Favored : 80.30 % 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 are not related in a simple way. whole: 0.79 (0.13), residues: 4785 helix: 2.18 (0.14), residues: 1320 sheet: 0.28 (0.11), residues: 2442 loop : -0.88 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG R 370 TYR 0.016 0.002 TYR B 393 PHE 0.016 0.002 PHE Y 422 HIS 0.006 0.001 HIS H 281 Details of bonding type rmsd covalent geometry : bond 0.00864 (39765) covalent geometry : angle 0.62631 (53592) hydrogen bonds : bond 0.05653 ( 1441) hydrogen bonds : angle 4.71177 ( 4224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1190 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8878 (tt0) cc_final: 0.8597 (tt0) REVERT: A 297 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7221 (tp-100) REVERT: A 376 LYS cc_start: 0.8435 (tttt) cc_final: 0.7843 (mttp) REVERT: B 297 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: B 376 LYS cc_start: 0.8440 (tttt) cc_final: 0.7731 (mttp) REVERT: C 269 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: C 376 LYS cc_start: 0.8511 (tttt) cc_final: 0.7947 (mttp) REVERT: C 383 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8012 (mt-10) REVERT: C 425 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8780 (mtmm) REVERT: D 246 GLN cc_start: 0.8830 (tt0) cc_final: 0.8600 (tt0) REVERT: D 376 LYS cc_start: 0.8446 (tttt) cc_final: 0.7835 (mttp) REVERT: E 376 LYS cc_start: 0.8438 (tttt) cc_final: 0.7752 (mttp) REVERT: F 376 LYS cc_start: 0.8465 (tttt) cc_final: 0.7790 (mttp) REVERT: F 410 LYS cc_start: 0.8248 (tmmt) cc_final: 0.8029 (tttm) REVERT: G 235 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8937 (mp) REVERT: G 296 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7762 (tpp-160) REVERT: G 297 GLN cc_start: 0.8238 (tt0) cc_final: 0.7986 (tp40) REVERT: G 303 GLN cc_start: 0.7495 (mt0) cc_final: 0.7099 (mp10) REVERT: G 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7747 (mttp) REVERT: G 409 MET cc_start: 0.8133 (mmm) cc_final: 0.7819 (mmm) REVERT: H 246 GLN cc_start: 0.8718 (tt0) cc_final: 0.8337 (tt0) REVERT: H 296 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7649 (ttp-170) REVERT: H 362 GLU cc_start: 0.7942 (tt0) cc_final: 0.7742 (tt0) REVERT: H 376 LYS cc_start: 0.8542 (tttt) cc_final: 0.7841 (mttp) REVERT: I 376 LYS cc_start: 0.8563 (tttt) cc_final: 0.7851 (mttp) REVERT: J 246 GLN cc_start: 0.8774 (tt0) cc_final: 0.8368 (tt0) REVERT: J 269 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: J 376 LYS cc_start: 0.8450 (tttt) cc_final: 0.7744 (mttp) REVERT: K 246 GLN cc_start: 0.8802 (tt0) cc_final: 0.8585 (tt0) REVERT: K 269 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: K 376 LYS cc_start: 0.8501 (tttt) cc_final: 0.7858 (mttp) REVERT: L 246 GLN cc_start: 0.8800 (tt0) cc_final: 0.8538 (tt0) REVERT: L 376 LYS cc_start: 0.8514 (tttt) cc_final: 0.7790 (mttp) REVERT: M 276 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7781 (mt-10) REVERT: M 296 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7548 (ttp-170) REVERT: M 297 GLN cc_start: 0.8277 (tt0) cc_final: 0.8043 (tp40) REVERT: M 303 GLN cc_start: 0.7400 (mp10) cc_final: 0.7141 (mp10) REVERT: M 376 LYS cc_start: 0.8499 (tttt) cc_final: 0.7753 (mttp) REVERT: N 279 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: N 297 GLN cc_start: 0.8347 (tt0) cc_final: 0.8119 (tp40) REVERT: N 303 GLN cc_start: 0.7363 (mt0) cc_final: 0.6992 (mp10) REVERT: N 376 LYS cc_start: 0.8491 (tttt) cc_final: 0.7895 (mttp) REVERT: O 303 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: O 376 LYS cc_start: 0.8544 (tttt) cc_final: 0.7896 (mttp) REVERT: P 246 GLN cc_start: 0.8750 (tt0) cc_final: 0.8410 (tt0) REVERT: P 303 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: P 376 LYS cc_start: 0.8547 (tttt) cc_final: 0.7909 (mttp) REVERT: Q 235 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8658 (mp) REVERT: Q 376 LYS cc_start: 0.8437 (tttt) cc_final: 0.7701 (mttp) REVERT: R 246 GLN cc_start: 0.8805 (tt0) cc_final: 0.8465 (tt0) REVERT: R 303 GLN cc_start: 0.7659 (mp10) cc_final: 0.7405 (mp10) REVERT: R 376 LYS cc_start: 0.8407 (tttt) cc_final: 0.7737 (mttp) REVERT: S 376 LYS cc_start: 0.8415 (tttt) cc_final: 0.7798 (mttp) REVERT: T 287 ASP cc_start: 0.8028 (t0) cc_final: 0.7826 (t70) REVERT: T 376 LYS cc_start: 0.8406 (tttt) cc_final: 0.7719 (mttp) REVERT: U 246 GLN cc_start: 0.8717 (tt0) cc_final: 0.8432 (tt0) REVERT: U 376 LYS cc_start: 0.8440 (tttt) cc_final: 0.7792 (mttp) REVERT: V 235 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8829 (mp) REVERT: V 246 GLN cc_start: 0.8773 (tt0) cc_final: 0.8390 (tt0) REVERT: V 297 GLN cc_start: 0.8343 (tt0) cc_final: 0.8085 (tp40) REVERT: W 231 ASN cc_start: 0.5135 (OUTLIER) cc_final: 0.4814 (p0) REVERT: W 246 GLN cc_start: 0.8783 (tt0) cc_final: 0.8500 (tt0) REVERT: W 275 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8171 (tttt) REVERT: W 376 LYS cc_start: 0.8509 (tttt) cc_final: 0.7776 (mttp) REVERT: W 383 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8055 (mt-10) REVERT: Y 297 GLN cc_start: 0.8222 (tt0) cc_final: 0.7964 (tp40) REVERT: Y 376 LYS cc_start: 0.8572 (tttt) cc_final: 0.7875 (mttp) REVERT: Y 420 MET cc_start: 0.8779 (ptm) cc_final: 0.8257 (ptm) REVERT: Z 246 GLN cc_start: 0.8803 (tt0) cc_final: 0.8445 (tt0) REVERT: Z 376 LYS cc_start: 0.8476 (tttt) cc_final: 0.7817 (mttp) REVERT: a 235 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8877 (mp) REVERT: a 246 GLN cc_start: 0.8791 (tt0) cc_final: 0.8506 (tt0) REVERT: a 376 LYS cc_start: 0.8390 (tttt) cc_final: 0.7716 (mttp) REVERT: b 246 GLN cc_start: 0.8865 (tt0) cc_final: 0.8526 (tt0) REVERT: b 296 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7299 (tpp-160) REVERT: b 376 LYS cc_start: 0.8411 (tttt) cc_final: 0.7729 (mttp) REVERT: c 279 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: c 297 GLN cc_start: 0.8287 (tt0) cc_final: 0.8044 (tp40) REVERT: c 376 LYS cc_start: 0.8439 (tttt) cc_final: 0.7797 (mttp) REVERT: d 279 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: d 356 ARG cc_start: 0.6761 (mpp-170) cc_final: 0.6393 (mpp-170) REVERT: d 376 LYS cc_start: 0.8459 (tttt) cc_final: 0.7774 (mttp) REVERT: e 246 GLN cc_start: 0.8826 (tt0) cc_final: 0.8507 (tt0) REVERT: e 297 GLN cc_start: 0.8286 (tt0) cc_final: 0.8010 (tp40) REVERT: e 376 LYS cc_start: 0.8492 (tttt) cc_final: 0.7868 (mttp) REVERT: f 376 LYS cc_start: 0.8567 (tttt) cc_final: 0.7901 (mttp) REVERT: f 383 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8059 (mt-10) REVERT: f 409 MET cc_start: 0.8219 (mmm) cc_final: 0.7877 (mmm) REVERT: f 410 LYS cc_start: 0.8293 (tmmt) cc_final: 0.8062 (ttpt) REVERT: g 296 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7693 (ttp-170) REVERT: g 297 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7413 (tp-100) REVERT: g 303 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: g 376 LYS cc_start: 0.8565 (tttt) cc_final: 0.7867 (mttp) outliers start: 100 outliers final: 60 residues processed: 1238 average time/residue: 0.9069 time to fit residues: 1312.4137 Evaluate side-chains 1254 residues out of total 4422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1172 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 296 ARG Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 303 GLN Chi-restraints excluded: chain P residue 303 GLN Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 235 LEU Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 296 ARG Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 363 THR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 235 LEU Chi-restraints excluded: chain g residue 296 ARG Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 465 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 456 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN F 269 GLN G 231 ASN ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN I 246 GLN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN L 297 GLN M 246 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN ** O 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN P 261 ASN P 269 GLN Q 246 GLN Q 261 ASN Q 297 GLN ** T 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 269 GLN V 261 ASN V 269 GLN ** X 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 269 GLN Y 246 GLN b 261 ASN c 246 GLN g 231 ASN g 246 GLN g 261 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119353 restraints weight = 46929.858| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.69 r_work: 0.3333 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39765 Z= 0.147 Angle : 0.474 6.178 53592 Z= 0.257 Chirality : 0.039 0.152 6138 Planarity : 0.002 0.038 7194 Dihedral : 4.617 20.460 5379 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.83 % Allowed : 18.00 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4785 helix: 2.93 (0.15), residues: 1320 sheet: 0.46 (0.11), residues: 2442 loop : -0.77 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 356 TYR 0.007 0.001 TYR K 393 PHE 0.011 0.001 PHE g 422 HIS 0.004 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00314 (39765) covalent geometry : angle 0.47406 (53592) hydrogen bonds : bond 0.04089 ( 1441) hydrogen bonds : angle 4.21819 ( 4224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24249.16 seconds wall clock time: 410 minutes 10.69 seconds (24610.69 seconds total)