Starting phenix.real_space_refine on Sat Mar 7 11:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d84_30612/03_2026/7d84_30612.map" } resolution = 3.7 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= -0.004 sd= 0.093 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 102 5.16 5 C 26044 2.51 5 N 7990 2.21 5 O 8568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.04s 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: 42704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h Time building chain proxies: 3.47, per 1000 atoms: 0.08 Number of scatterers: 42704 At special positions: 0 Unit cell: (262.15, 260.01, 96.3, 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 102 16.00 O 8568 8.00 N 7990 7.00 C 26044 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: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10404 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 36 sheets defined 32.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 228 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA P 291 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Q 291 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA R 291 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA S 291 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA T 291 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA V 291 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 229 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA X 291 " --> pdb=" O ALA X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Y 291 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Z 291 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 229 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 229 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA b 291 " --> pdb=" O ALA b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA c 291 " --> pdb=" O ALA c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA d 291 " --> pdb=" O ALA d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA e 291 " --> pdb=" O ALA e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 229 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA f 291 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA g 291 " --> pdb=" O ALA g 288 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 229 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 279 removed outlier: 3.518A pdb=" N GLU B 276 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 274 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 276 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 274 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 276 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 276 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN E 274 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 276 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN F 274 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 276 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 274 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 276 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU I 276 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 274 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 276 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 274 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 276 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN K 274 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU L 276 " --> pdb=" O HIS K 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN L 274 " --> pdb=" O LYS K 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU M 276 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 274 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 276 " --> pdb=" O HIS M 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN N 274 " --> pdb=" O LYS M 376 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 276 " --> pdb=" O HIS O 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN P 274 " --> pdb=" O LYS O 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 276 " --> pdb=" O HIS P 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN Q 274 " --> pdb=" O LYS P 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 276 " --> pdb=" O HIS Q 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 274 " --> pdb=" O LYS Q 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU S 276 " --> pdb=" O HIS R 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN S 274 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU T 276 " --> pdb=" O HIS S 374 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN T 274 " --> pdb=" O LYS S 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN U 274 " --> pdb=" O LYS T 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU V 276 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN V 274 " --> pdb=" O LYS U 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU W 276 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU X 276 " --> pdb=" O HIS W 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN X 274 " --> pdb=" O LYS W 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU Y 276 " --> pdb=" O HIS X 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Y 274 " --> pdb=" O LYS X 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Z 276 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN Z 274 " --> pdb=" O LYS Y 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU a 276 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN a 274 " --> pdb=" O LYS Z 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU b 276 " --> pdb=" O HIS a 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN b 274 " --> pdb=" O LYS a 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 276 " --> pdb=" O HIS b 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN c 274 " --> pdb=" O LYS b 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU d 276 " --> pdb=" O HIS c 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN d 274 " --> pdb=" O LYS c 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU e 276 " --> pdb=" O HIS d 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN e 274 " --> pdb=" O LYS d 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU f 276 " --> pdb=" O HIS e 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN f 274 " --> pdb=" O LYS e 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 276 " --> pdb=" O HIS f 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN g 274 " --> pdb=" O LYS f 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU h 276 " --> pdb=" O HIS g 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN h 274 " --> pdb=" O LYS g 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 276 " --> pdb=" O HIS h 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 274 " --> pdb=" O LYS h 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 302 removed outlier: 3.787A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 365 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 301 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 359 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG h 296 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN h 365 " --> pdb=" O SER h 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER h 301 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN h 359 " --> pdb=" O SER h 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG g 296 " --> pdb=" O SER h 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN g 365 " --> pdb=" O SER g 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER g 301 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN g 359 " --> pdb=" O SER g 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG f 296 " --> pdb=" O SER g 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN f 365 " --> pdb=" O SER f 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 301 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN f 359 " --> pdb=" O SER f 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG e 296 " --> pdb=" O SER f 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN e 365 " --> pdb=" O SER e 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER e 301 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN e 359 " --> pdb=" O SER e 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG d 296 " --> pdb=" O SER e 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN d 365 " --> pdb=" O SER d 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER d 301 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN d 359 " --> pdb=" O SER d 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG c 296 " --> pdb=" O SER d 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN c 365 " --> pdb=" O SER c 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 301 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 359 " --> pdb=" O SER c 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG b 296 " --> pdb=" O SER c 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN b 365 " --> pdb=" O SER b 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER b 301 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN b 359 " --> pdb=" O SER b 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG a 296 " --> pdb=" O SER b 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN a 365 " --> pdb=" O SER a 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER a 301 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN a 359 " --> pdb=" O SER a 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Z 296 " --> pdb=" O SER a 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Z 365 " --> pdb=" O SER Z 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Z 301 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Z 359 " --> pdb=" O SER Z 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Y 296 " --> pdb=" O SER Z 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN Y 365 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER Y 301 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN Y 359 " --> pdb=" O SER Y 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG X 296 " --> pdb=" O SER Y 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN X 365 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER X 301 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN X 359 " --> pdb=" O SER X 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 296 " --> pdb=" O SER X 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN W 365 " --> pdb=" O SER W 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER W 301 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN W 359 " --> pdb=" O SER W 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG V 296 " --> pdb=" O SER W 364 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN V 365 " --> pdb=" O SER V 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER V 301 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN V 359 " --> pdb=" O SER V 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 296 " --> pdb=" O SER V 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN U 365 " --> pdb=" O SER U 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER U 301 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN U 359 " --> pdb=" O SER U 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG T 296 " --> pdb=" O SER U 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN T 365 " --> pdb=" O SER T 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER T 301 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN T 359 " --> pdb=" O SER T 301 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG S 296 " --> pdb=" O SER T 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN S 365 " --> pdb=" O SER S 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S 301 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN S 359 " --> pdb=" O SER S 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG R 296 " --> pdb=" O SER S 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN R 365 " --> pdb=" O SER R 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 301 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN R 359 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Q 296 " --> pdb=" O SER R 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Q 365 " --> pdb=" O SER Q 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Q 301 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Q 359 " --> pdb=" O SER Q 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG P 296 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN P 365 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER P 301 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN P 359 " --> pdb=" O SER P 301 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 302 " --> pdb=" O THR P 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG O 296 " --> pdb=" O SER P 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN O 365 " --> pdb=" O SER O 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER O 301 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN O 359 " --> pdb=" O SER O 301 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG N 296 " --> pdb=" O SER O 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN N 365 " --> pdb=" O SER N 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER N 301 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN N 359 " --> pdb=" O SER N 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG M 296 " --> pdb=" O SER N 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN M 365 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER M 301 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN M 359 " --> pdb=" O SER M 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG L 296 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN L 365 " --> pdb=" O SER L 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 301 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 359 " --> pdb=" O SER L 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 296 " --> pdb=" O SER L 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN K 365 " --> pdb=" O SER K 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER K 301 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN K 359 " --> pdb=" O SER K 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG J 296 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN J 365 " --> pdb=" O SER J 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER J 301 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN J 359 " --> pdb=" O SER J 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG I 296 " --> pdb=" O SER J 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN I 365 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER I 301 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN I 359 " --> pdb=" O SER I 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG H 296 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 365 " --> pdb=" O SER H 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 301 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 359 " --> pdb=" O SER H 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 296 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN G 365 " --> pdb=" O SER G 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER G 301 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 359 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 296 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN F 365 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 301 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 359 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 296 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN E 365 " --> pdb=" O SER E 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 301 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 359 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 296 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 365 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 301 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 359 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 296 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 365 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 301 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 359 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 296 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 365 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 301 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 359 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 296 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) 2043 hydrogen bonds defined for protein. 5718 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: 10.63 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15229 1.34 - 1.45: 5119 1.45 - 1.57: 22594 1.57 - 1.68: 0 1.68 - 1.80: 204 Bond restraints: 43146 Sorted by residual: bond pdb=" CG ARG F 294 " pdb=" CD ARG F 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG W 294 " pdb=" CD ARG W 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG B 294 " pdb=" CD ARG B 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG S 294 " pdb=" CD ARG S 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG L 294 " pdb=" CD ARG L 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.62e+00 ... (remaining 43141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 56222 2.00 - 3.99: 1682 3.99 - 5.99: 202 5.99 - 7.98: 0 7.98 - 9.98: 68 Bond angle restraints: 58174 Sorted by residual: angle pdb=" N GLY P 421 " pdb=" CA GLY P 421 " pdb=" C GLY P 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY g 421 " pdb=" CA GLY g 421 " pdb=" C GLY g 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY H 421 " pdb=" CA GLY H 421 " pdb=" C GLY H 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " pdb=" C GLY Y 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY U 421 " pdb=" CA GLY U 421 " pdb=" C GLY U 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 ... (remaining 58169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.27: 21963 11.27 - 22.54: 2925 22.54 - 33.81: 1428 33.81 - 45.08: 374 45.08 - 56.35: 374 Dihedral angle restraints: 27064 sinusoidal: 11254 harmonic: 15810 Sorted by residual: dihedral pdb=" CA MET E 420 " pdb=" C MET E 420 " pdb=" N GLY E 421 " pdb=" CA GLY E 421 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET K 420 " pdb=" C MET K 420 " pdb=" N GLY K 421 " pdb=" CA GLY K 421 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+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 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 27061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3464 0.030 - 0.059: 2165 0.059 - 0.089: 640 0.089 - 0.118: 221 0.118 - 0.148: 208 Chirality restraints: 6698 Sorted by residual: chirality pdb=" CA PRO A 255 " pdb=" N PRO A 255 " pdb=" C PRO A 255 " pdb=" CB PRO A 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO R 255 " pdb=" N PRO R 255 " pdb=" C PRO R 255 " pdb=" CB PRO R 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO O 255 " pdb=" N PRO O 255 " pdb=" C PRO O 255 " pdb=" CB PRO O 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 6695 not shown) Planarity restraints: 7786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER d 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO d 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO d 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO d 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO M 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO M 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Y 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO Y 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 255 " -0.040 5.00e-02 4.00e+02 ... (remaining 7783 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 11711 2.80 - 3.32: 36254 3.32 - 3.85: 68608 3.85 - 4.37: 76405 4.37 - 4.90: 137058 Nonbonded interactions: 330036 Sorted by model distance: nonbonded pdb=" N ASP D 369 " pdb=" OD1 ASP D 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP U 369 " pdb=" OD1 ASP U 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP f 369 " pdb=" OD1 ASP f 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP C 369 " pdb=" OD1 ASP C 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP F 369 " pdb=" OD1 ASP F 369 " model vdw 2.271 3.120 ... (remaining 330031 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: 0.16 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' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 34.040 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.009 0.074 43146 Z= 0.412 Angle : 0.897 9.977 58174 Z= 0.496 Chirality : 0.047 0.148 6698 Planarity : 0.007 0.070 7786 Dihedral : 15.250 56.353 16660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 7.78 % Allowed : 7.24 % Favored : 84.98 % 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: -2.70 (0.11), residues: 5202 helix: -0.63 (0.11), residues: 1462 sheet: -1.79 (0.10), residues: 2550 loop : -2.59 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 370 TYR 0.005 0.002 TYR I 366 PHE 0.015 0.003 PHE S 422 HIS 0.003 0.001 HIS b 263 Details of bonding type rmsd covalent geometry : bond 0.00897 (43146) covalent geometry : angle 0.89670 (58174) hydrogen bonds : bond 0.18370 ( 2043) hydrogen bonds : angle 7.66612 ( 5718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 1332 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 242 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7233 (mp0) REVERT: A 267 THR cc_start: 0.9041 (m) cc_final: 0.8839 (p) REVERT: A 418 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8294 (mt-10) REVERT: A 429 THR cc_start: 0.7766 (p) cc_final: 0.6997 (p) REVERT: B 246 GLN cc_start: 0.9040 (tt0) cc_final: 0.8760 (pt0) REVERT: B 267 THR cc_start: 0.9090 (m) cc_final: 0.8805 (p) REVERT: B 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8329 (mt-10) REVERT: C 267 THR cc_start: 0.9084 (m) cc_final: 0.8727 (p) REVERT: C 280 GLU cc_start: 0.7726 (tt0) cc_final: 0.7521 (tt0) REVERT: C 418 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8348 (mt-10) REVERT: D 246 GLN cc_start: 0.8997 (tt0) cc_final: 0.8667 (pt0) REVERT: D 250 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8194 (mt-10) REVERT: D 267 THR cc_start: 0.9076 (m) cc_final: 0.8826 (p) REVERT: D 409 MET cc_start: 0.8486 (mmm) cc_final: 0.8249 (tpp) REVERT: D 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8297 (mt-10) REVERT: E 246 GLN cc_start: 0.9072 (tt0) cc_final: 0.8779 (pt0) REVERT: E 267 THR cc_start: 0.9225 (m) cc_final: 0.8961 (p) REVERT: E 418 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8417 (mt-10) REVERT: F 246 GLN cc_start: 0.9024 (tt0) cc_final: 0.8732 (pt0) REVERT: F 267 THR cc_start: 0.9079 (m) cc_final: 0.8868 (p) REVERT: F 269 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8645 (mm-40) REVERT: F 302 GLU cc_start: 0.7877 (tt0) cc_final: 0.7473 (tm-30) REVERT: F 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8295 (mt-10) REVERT: G 246 GLN cc_start: 0.9026 (tt0) cc_final: 0.8679 (pt0) REVERT: G 267 THR cc_start: 0.9084 (m) cc_final: 0.8774 (p) REVERT: G 418 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8397 (mt-10) REVERT: H 267 THR cc_start: 0.9103 (m) cc_final: 0.8873 (p) REVERT: H 418 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8334 (mt-10) REVERT: I 246 GLN cc_start: 0.8982 (tt0) cc_final: 0.8654 (pt0) REVERT: I 267 THR cc_start: 0.9090 (m) cc_final: 0.8873 (p) REVERT: I 299 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: I 409 MET cc_start: 0.8580 (mmm) cc_final: 0.8349 (tpp) REVERT: I 418 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8216 (mt-10) REVERT: J 267 THR cc_start: 0.9059 (m) cc_final: 0.8849 (p) REVERT: K 246 GLN cc_start: 0.9122 (tt0) cc_final: 0.8851 (pt0) REVERT: K 252 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9061 (tp) REVERT: K 267 THR cc_start: 0.9167 (m) cc_final: 0.8870 (p) REVERT: K 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7877 (tt0) REVERT: K 418 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8285 (mt-10) REVERT: L 246 GLN cc_start: 0.9035 (tt0) cc_final: 0.8813 (pt0) REVERT: L 267 THR cc_start: 0.9097 (m) cc_final: 0.8834 (p) REVERT: L 302 GLU cc_start: 0.7788 (tt0) cc_final: 0.7545 (tm-30) REVERT: L 418 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8254 (mt-10) REVERT: M 246 GLN cc_start: 0.9088 (tt0) cc_final: 0.8766 (pt0) REVERT: M 267 THR cc_start: 0.9115 (m) cc_final: 0.8857 (p) REVERT: M 418 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8259 (mt-10) REVERT: N 267 THR cc_start: 0.9104 (m) cc_final: 0.8858 (p) REVERT: N 418 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8227 (mt-10) REVERT: O 267 THR cc_start: 0.9091 (m) cc_final: 0.8842 (p) REVERT: O 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8162 (mt-10) REVERT: P 246 GLN cc_start: 0.9013 (tt0) cc_final: 0.8660 (pt0) REVERT: P 267 THR cc_start: 0.9110 (m) cc_final: 0.8838 (p) REVERT: P 382 ILE cc_start: 0.9181 (mt) cc_final: 0.8953 (mm) REVERT: P 418 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8421 (mt-10) REVERT: Q 246 GLN cc_start: 0.9087 (tt0) cc_final: 0.8802 (pt0) REVERT: Q 252 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9136 (tp) REVERT: Q 267 THR cc_start: 0.9119 (m) cc_final: 0.8874 (p) REVERT: Q 302 GLU cc_start: 0.7770 (tt0) cc_final: 0.7470 (tm-30) REVERT: Q 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8372 (mt-10) REVERT: R 242 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7228 (mp0) REVERT: R 267 THR cc_start: 0.9039 (m) cc_final: 0.8817 (p) REVERT: R 418 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8295 (mt-10) REVERT: S 246 GLN cc_start: 0.9038 (tt0) cc_final: 0.8755 (pt0) REVERT: S 267 THR cc_start: 0.9094 (m) cc_final: 0.8805 (p) REVERT: S 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7021 (mm-30) REVERT: T 246 GLN cc_start: 0.9086 (tt0) cc_final: 0.8763 (pt0) REVERT: T 267 THR cc_start: 0.9068 (m) cc_final: 0.8713 (p) REVERT: T 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8402 (mt-10) REVERT: T 429 THR cc_start: 0.7972 (p) cc_final: 0.7718 (p) REVERT: U 246 GLN cc_start: 0.8994 (tt0) cc_final: 0.8671 (pt0) REVERT: U 250 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8191 (mt-10) REVERT: U 267 THR cc_start: 0.9075 (m) cc_final: 0.8817 (p) REVERT: U 409 MET cc_start: 0.8482 (mmm) cc_final: 0.8241 (tpp) REVERT: U 418 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8298 (mt-10) REVERT: V 246 GLN cc_start: 0.9075 (tt0) cc_final: 0.8777 (pt0) REVERT: V 267 THR cc_start: 0.9222 (m) cc_final: 0.8965 (p) REVERT: V 418 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8399 (mt-10) REVERT: W 246 GLN cc_start: 0.9029 (tt0) cc_final: 0.8722 (pt0) REVERT: W 267 THR cc_start: 0.9081 (m) cc_final: 0.8880 (p) REVERT: W 269 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8633 (mm-40) REVERT: W 302 GLU cc_start: 0.7879 (tt0) cc_final: 0.7485 (tm-30) REVERT: W 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8285 (mt-10) REVERT: X 246 GLN cc_start: 0.9028 (tt0) cc_final: 0.8683 (pt0) REVERT: X 267 THR cc_start: 0.9084 (m) cc_final: 0.8771 (p) REVERT: X 418 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8398 (mt-10) REVERT: Y 267 THR cc_start: 0.9107 (m) cc_final: 0.8876 (p) REVERT: Y 418 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8334 (mt-10) REVERT: Z 246 GLN cc_start: 0.8989 (tt0) cc_final: 0.8654 (pt0) REVERT: Z 267 THR cc_start: 0.9088 (m) cc_final: 0.8873 (p) REVERT: Z 299 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: Z 409 MET cc_start: 0.8589 (mmm) cc_final: 0.8360 (tpp) REVERT: Z 418 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8208 (mt-10) REVERT: a 267 THR cc_start: 0.9063 (m) cc_final: 0.8853 (p) REVERT: b 246 GLN cc_start: 0.9125 (tt0) cc_final: 0.8854 (pt0) REVERT: b 252 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9067 (tp) REVERT: b 267 THR cc_start: 0.9170 (m) cc_final: 0.8873 (p) REVERT: b 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7873 (tt0) REVERT: b 418 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8280 (mt-10) REVERT: c 246 GLN cc_start: 0.9033 (tt0) cc_final: 0.8810 (pt0) REVERT: c 267 THR cc_start: 0.9100 (m) cc_final: 0.8840 (p) REVERT: c 302 GLU cc_start: 0.7795 (tt0) cc_final: 0.7548 (tm-30) REVERT: c 418 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8253 (mt-10) REVERT: d 246 GLN cc_start: 0.9092 (tt0) cc_final: 0.8772 (pt0) REVERT: d 267 THR cc_start: 0.9114 (m) cc_final: 0.8860 (p) REVERT: d 418 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8248 (mt-10) REVERT: e 267 THR cc_start: 0.9108 (m) cc_final: 0.8856 (p) REVERT: e 418 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8211 (mt-10) REVERT: f 267 THR cc_start: 0.9136 (m) cc_final: 0.8875 (p) REVERT: f 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8221 (mt-10) REVERT: g 246 GLN cc_start: 0.9009 (tt0) cc_final: 0.8663 (pt0) REVERT: g 267 THR cc_start: 0.9105 (m) cc_final: 0.8845 (p) REVERT: g 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8421 (mt-10) REVERT: h 246 GLN cc_start: 0.9088 (tt0) cc_final: 0.8799 (pt0) REVERT: h 252 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9133 (tp) REVERT: h 267 THR cc_start: 0.9113 (m) cc_final: 0.8871 (p) REVERT: h 302 GLU cc_start: 0.7769 (tt0) cc_final: 0.7458 (tm-30) REVERT: h 418 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7510 (mm-30) outliers start: 373 outliers final: 138 residues processed: 1570 average time/residue: 0.2646 time to fit residues: 677.5735 Evaluate side-chains 1288 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1144 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 274 ASN Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 435 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 435 SER Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 252 ILE Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 274 ASN Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 435 SER Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 299 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 435 SER Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN D 434 ASN E 434 ASN F 434 ASN G 434 ASN H 408 GLN H 434 ASN I 434 ASN J 408 GLN J 434 ASN K 434 ASN L 408 GLN L 434 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN N 434 ASN O 434 ASN P 434 ASN Q 408 GLN Q 434 ASN R 434 ASN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 434 ASN T 434 ASN U 434 ASN V 434 ASN W 434 ASN X 434 ASN Y 408 GLN Y 434 ASN Z 434 ASN a 408 GLN a 434 ASN b 434 ASN c 408 GLN c 434 ASN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 434 ASN e 434 ASN f 434 ASN g 434 ASN h 408 GLN h 434 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.199900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.152705 restraints weight = 86780.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.156129 restraints weight = 55128.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.156161 restraints weight = 37823.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.156288 restraints weight = 35866.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.156403 restraints weight = 34002.349| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 43146 Z= 0.164 Angle : 0.653 6.777 58174 Z= 0.333 Chirality : 0.040 0.126 6698 Planarity : 0.004 0.042 7786 Dihedral : 5.890 55.254 6102 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.42 % Allowed : 19.44 % Favored : 78.14 % 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: -0.70 (0.12), residues: 5202 helix: 2.55 (0.13), residues: 1462 sheet: -1.29 (0.11), residues: 2584 loop : -2.12 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 244 TYR 0.009 0.001 TYR E 366 PHE 0.015 0.001 PHE G 422 HIS 0.003 0.001 HIS N 374 Details of bonding type rmsd covalent geometry : bond 0.00370 (43146) covalent geometry : angle 0.65255 (58174) hydrogen bonds : bond 0.03603 ( 2043) hydrogen bonds : angle 4.53436 ( 5718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1188 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 242 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7546 (mp0) REVERT: A 267 THR cc_start: 0.9078 (m) cc_final: 0.8732 (p) REVERT: A 377 MET cc_start: 0.8232 (mmm) cc_final: 0.7702 (mmm) REVERT: A 394 LYS cc_start: 0.7564 (ptpp) cc_final: 0.7137 (pttm) REVERT: A 410 LYS cc_start: 0.8734 (tptt) cc_final: 0.8413 (tptt) REVERT: A 418 GLU cc_start: 0.8712 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 267 THR cc_start: 0.9060 (m) cc_final: 0.8646 (p) REVERT: B 418 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 267 THR cc_start: 0.9053 (m) cc_final: 0.8605 (p) REVERT: C 280 GLU cc_start: 0.7909 (tt0) cc_final: 0.7560 (tt0) REVERT: C 418 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 267 THR cc_start: 0.9067 (m) cc_final: 0.8725 (p) REVERT: D 377 MET cc_start: 0.8305 (mmm) cc_final: 0.7985 (mmm) REVERT: D 411 GLN cc_start: 0.9048 (pt0) cc_final: 0.8839 (pt0) REVERT: D 418 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7514 (mm-30) REVERT: E 267 THR cc_start: 0.9167 (m) cc_final: 0.8846 (p) REVERT: E 377 MET cc_start: 0.8112 (tpp) cc_final: 0.7893 (mmm) REVERT: E 409 MET cc_start: 0.8347 (tpp) cc_final: 0.8121 (tpt) REVERT: E 410 LYS cc_start: 0.8817 (tptt) cc_final: 0.8495 (tptt) REVERT: E 412 ILE cc_start: 0.9175 (mt) cc_final: 0.8524 (mm) REVERT: E 431 ASN cc_start: 0.8327 (t0) cc_final: 0.7994 (p0) REVERT: F 256 ILE cc_start: 0.8985 (mm) cc_final: 0.8756 (mm) REVERT: F 267 THR cc_start: 0.9066 (m) cc_final: 0.8765 (p) REVERT: F 302 GLU cc_start: 0.7447 (tt0) cc_final: 0.6493 (tm-30) REVERT: F 418 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7471 (mm-30) REVERT: F 431 ASN cc_start: 0.8424 (t0) cc_final: 0.8032 (p0) REVERT: G 242 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: G 267 THR cc_start: 0.9103 (m) cc_final: 0.8647 (p) REVERT: G 376 LYS cc_start: 0.8324 (tmtt) cc_final: 0.8116 (tptp) REVERT: G 394 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6620 (pttm) REVERT: G 418 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7701 (mm-30) REVERT: G 431 ASN cc_start: 0.8291 (t0) cc_final: 0.8022 (p0) REVERT: H 242 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 246 GLN cc_start: 0.9088 (pt0) cc_final: 0.8867 (pt0) REVERT: H 267 THR cc_start: 0.9043 (m) cc_final: 0.8736 (p) REVERT: H 302 GLU cc_start: 0.7637 (tt0) cc_final: 0.7005 (tm-30) REVERT: I 267 THR cc_start: 0.9072 (m) cc_final: 0.8708 (p) REVERT: I 376 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7953 (ttmm) REVERT: I 377 MET cc_start: 0.8172 (mmm) cc_final: 0.7767 (mmm) REVERT: I 410 LYS cc_start: 0.8868 (tptt) cc_final: 0.8504 (tptt) REVERT: J 242 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: J 246 GLN cc_start: 0.9082 (tt0) cc_final: 0.8854 (pt0) REVERT: J 267 THR cc_start: 0.9071 (m) cc_final: 0.8778 (p) REVERT: J 302 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6910 (tm-30) REVERT: J 377 MET cc_start: 0.8387 (mmm) cc_final: 0.8159 (tpp) REVERT: J 394 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7202 (pttm) REVERT: J 400 LYS cc_start: 0.8853 (mppt) cc_final: 0.8649 (mtmm) REVERT: K 267 THR cc_start: 0.9160 (m) cc_final: 0.8772 (p) REVERT: K 410 LYS cc_start: 0.8745 (tptt) cc_final: 0.8538 (tptt) REVERT: K 418 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7564 (mm-30) REVERT: L 267 THR cc_start: 0.9097 (m) cc_final: 0.8727 (p) REVERT: L 418 GLU cc_start: 0.8647 (mm-30) cc_final: 0.6719 (mm-30) REVERT: M 267 THR cc_start: 0.9086 (m) cc_final: 0.8734 (p) REVERT: M 394 LYS cc_start: 0.7125 (ptpt) cc_final: 0.6865 (pttm) REVERT: M 410 LYS cc_start: 0.8912 (tptt) cc_final: 0.8631 (tptt) REVERT: M 418 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7332 (mm-30) REVERT: N 267 THR cc_start: 0.9137 (m) cc_final: 0.8719 (p) REVERT: N 394 LYS cc_start: 0.7619 (ptpt) cc_final: 0.7009 (pttm) REVERT: N 410 LYS cc_start: 0.8824 (tptt) cc_final: 0.8593 (tptt) REVERT: N 431 ASN cc_start: 0.8352 (t0) cc_final: 0.7938 (p0) REVERT: O 242 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: O 265 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8310 (mm-40) REVERT: O 267 THR cc_start: 0.9094 (m) cc_final: 0.8712 (p) REVERT: O 410 LYS cc_start: 0.8908 (tptt) cc_final: 0.8648 (tptt) REVERT: O 418 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7324 (mm-30) REVERT: P 267 THR cc_start: 0.9082 (m) cc_final: 0.8780 (p) REVERT: P 394 LYS cc_start: 0.7856 (ptpp) cc_final: 0.7482 (ptpp) REVERT: P 410 LYS cc_start: 0.8955 (tptt) cc_final: 0.8747 (tptt) REVERT: P 418 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7281 (mm-30) REVERT: P 431 ASN cc_start: 0.8339 (t0) cc_final: 0.7967 (p0) REVERT: Q 267 THR cc_start: 0.9121 (m) cc_final: 0.8726 (p) REVERT: Q 302 GLU cc_start: 0.7385 (tt0) cc_final: 0.6622 (tm-30) REVERT: Q 410 LYS cc_start: 0.8664 (tptt) cc_final: 0.8419 (tptt) REVERT: Q 418 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7254 (mm-30) REVERT: Q 431 ASN cc_start: 0.8441 (t0) cc_final: 0.8107 (p0) REVERT: R 242 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7546 (mp0) REVERT: R 267 THR cc_start: 0.9084 (m) cc_final: 0.8720 (p) REVERT: R 377 MET cc_start: 0.8238 (mmm) cc_final: 0.7706 (mmm) REVERT: R 394 LYS cc_start: 0.7533 (ptpp) cc_final: 0.7161 (pttm) REVERT: R 410 LYS cc_start: 0.8729 (tptt) cc_final: 0.8397 (tptt) REVERT: R 418 GLU cc_start: 0.8715 (mm-30) cc_final: 0.7690 (mm-30) REVERT: R 431 ASN cc_start: 0.8444 (t0) cc_final: 0.8078 (p0) REVERT: S 267 THR cc_start: 0.9063 (m) cc_final: 0.8650 (p) REVERT: S 418 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7762 (mt-10) REVERT: T 267 THR cc_start: 0.9025 (m) cc_final: 0.8583 (p) REVERT: T 302 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6693 (tm-30) REVERT: T 418 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7481 (mm-30) REVERT: U 267 THR cc_start: 0.9062 (m) cc_final: 0.8725 (p) REVERT: U 377 MET cc_start: 0.8308 (mmm) cc_final: 0.7967 (mmm) REVERT: U 418 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7494 (mm-30) REVERT: V 267 THR cc_start: 0.9167 (m) cc_final: 0.8831 (p) REVERT: V 377 MET cc_start: 0.8417 (mmm) cc_final: 0.8063 (mmm) REVERT: V 409 MET cc_start: 0.8378 (tpp) cc_final: 0.8172 (tpt) REVERT: V 410 LYS cc_start: 0.8892 (tptt) cc_final: 0.8572 (tptt) REVERT: V 418 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7639 (mm-30) REVERT: V 431 ASN cc_start: 0.8308 (t0) cc_final: 0.8024 (p0) REVERT: W 256 ILE cc_start: 0.8984 (mm) cc_final: 0.8754 (mm) REVERT: W 267 THR cc_start: 0.9066 (m) cc_final: 0.8771 (p) REVERT: W 302 GLU cc_start: 0.7447 (tt0) cc_final: 0.6499 (tm-30) REVERT: W 394 LYS cc_start: 0.7506 (pttt) cc_final: 0.7265 (ptpp) REVERT: W 410 LYS cc_start: 0.8877 (tptt) cc_final: 0.8670 (tptt) REVERT: W 418 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7466 (mm-30) REVERT: W 431 ASN cc_start: 0.8428 (t0) cc_final: 0.8078 (p0) REVERT: X 242 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: X 267 THR cc_start: 0.9104 (m) cc_final: 0.8653 (p) REVERT: X 376 LYS cc_start: 0.8326 (tmtt) cc_final: 0.8119 (tptp) REVERT: X 394 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6605 (pttm) REVERT: X 418 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7673 (mm-30) REVERT: X 431 ASN cc_start: 0.8287 (t0) cc_final: 0.8020 (p0) REVERT: Y 242 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: Y 246 GLN cc_start: 0.9087 (pt0) cc_final: 0.8865 (pt0) REVERT: Y 267 THR cc_start: 0.9046 (m) cc_final: 0.8740 (p) REVERT: Y 302 GLU cc_start: 0.7634 (tt0) cc_final: 0.7001 (tm-30) REVERT: Y 394 LYS cc_start: 0.7548 (ptpt) cc_final: 0.7292 (ptpp) REVERT: Z 242 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: Z 267 THR cc_start: 0.9068 (m) cc_final: 0.8705 (p) REVERT: Z 376 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7949 (ttmm) REVERT: Z 377 MET cc_start: 0.8170 (mmm) cc_final: 0.7766 (mmm) REVERT: Z 410 LYS cc_start: 0.8871 (tptt) cc_final: 0.8506 (tptt) REVERT: Z 418 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8406 (mm-30) REVERT: a 242 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: a 246 GLN cc_start: 0.9083 (tt0) cc_final: 0.8857 (pt0) REVERT: a 267 THR cc_start: 0.9069 (m) cc_final: 0.8774 (p) REVERT: a 302 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6918 (tm-30) REVERT: a 377 MET cc_start: 0.8379 (mmm) cc_final: 0.8154 (tpp) REVERT: b 267 THR cc_start: 0.9162 (m) cc_final: 0.8779 (p) REVERT: b 410 LYS cc_start: 0.8747 (tptt) cc_final: 0.8526 (tptt) REVERT: b 418 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7505 (mm-30) REVERT: c 267 THR cc_start: 0.9064 (m) cc_final: 0.8698 (p) REVERT: c 418 GLU cc_start: 0.8646 (mm-30) cc_final: 0.6718 (mm-30) REVERT: c 431 ASN cc_start: 0.8395 (t0) cc_final: 0.8053 (p0) REVERT: d 267 THR cc_start: 0.9091 (m) cc_final: 0.8739 (p) REVERT: d 394 LYS cc_start: 0.7112 (ptpt) cc_final: 0.6856 (pttm) REVERT: d 410 LYS cc_start: 0.8913 (tptt) cc_final: 0.8632 (tptt) REVERT: d 418 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7335 (mm-30) REVERT: e 267 THR cc_start: 0.9137 (m) cc_final: 0.8718 (p) REVERT: e 394 LYS cc_start: 0.7627 (ptpt) cc_final: 0.7019 (pttm) REVERT: e 410 LYS cc_start: 0.8794 (tptt) cc_final: 0.8558 (tptt) REVERT: e 431 ASN cc_start: 0.8357 (t0) cc_final: 0.7936 (p0) REVERT: f 242 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: f 265 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8472 (mm-40) REVERT: f 267 THR cc_start: 0.9097 (m) cc_final: 0.8710 (p) REVERT: f 302 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6754 (tm-30) REVERT: f 394 LYS cc_start: 0.7337 (ptpt) cc_final: 0.6616 (pttm) REVERT: f 410 LYS cc_start: 0.8977 (tptt) cc_final: 0.8687 (tptt) REVERT: f 418 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7322 (mm-30) REVERT: g 267 THR cc_start: 0.9056 (m) cc_final: 0.8681 (p) REVERT: g 377 MET cc_start: 0.8258 (mmm) cc_final: 0.7764 (tmm) REVERT: g 394 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7492 (ptpp) REVERT: g 418 GLU cc_start: 0.8487 (mm-30) cc_final: 0.6668 (mt-10) REVERT: g 431 ASN cc_start: 0.8366 (t0) cc_final: 0.7995 (p0) REVERT: h 267 THR cc_start: 0.9121 (m) cc_final: 0.8725 (p) REVERT: h 302 GLU cc_start: 0.7370 (tt0) cc_final: 0.6616 (tm-30) REVERT: h 418 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7693 (mt-10) REVERT: h 431 ASN cc_start: 0.8401 (t0) cc_final: 0.7901 (p0) outliers start: 116 outliers final: 45 residues processed: 1243 average time/residue: 0.2771 time to fit residues: 548.2920 Evaluate side-chains 1108 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1053 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain L residue 377 MET Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 413 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain T residue 377 MET Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 435 SER Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 377 MET Chi-restraints excluded: chain c residue 377 MET Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 435 SER Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Chi-restraints excluded: chain h residue 243 SER Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 396 LEU Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 291 optimal weight: 0.3980 chunk 296 optimal weight: 2.9990 chunk 392 optimal weight: 4.9990 chunk 305 optimal weight: 0.5980 chunk 469 optimal weight: 6.9990 chunk 440 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 508 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 261 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN C 434 ASN F 411 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 GLN H 411 GLN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 GLN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 GLN ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 408 GLN T 411 GLN W 411 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 411 GLN Y 411 GLN ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 411 GLN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 411 GLN ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 411 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.202568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.156810 restraints weight = 86271.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.159968 restraints weight = 51369.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.159743 restraints weight = 43238.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.159892 restraints weight = 39018.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.160140 restraints weight = 31309.225| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43146 Z= 0.115 Angle : 0.579 7.706 58174 Z= 0.296 Chirality : 0.040 0.144 6698 Planarity : 0.003 0.031 7786 Dihedral : 4.574 39.000 5876 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.38 % Allowed : 19.17 % Favored : 78.45 % 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: -0.08 (0.13), residues: 5202 helix: 3.18 (0.13), residues: 1428 sheet: -0.93 (0.11), residues: 2550 loop : -1.82 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 370 TYR 0.005 0.001 TYR E 366 PHE 0.024 0.001 PHE e 237 HIS 0.001 0.000 HIS U 374 Details of bonding type rmsd covalent geometry : bond 0.00262 (43146) covalent geometry : angle 0.57947 (58174) hydrogen bonds : bond 0.03038 ( 2043) hydrogen bonds : angle 4.14474 ( 5718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1239 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 THR cc_start: 0.9068 (m) cc_final: 0.8688 (p) REVERT: A 370 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7635 (ttm-80) REVERT: A 394 LYS cc_start: 0.7631 (ptpp) cc_final: 0.7333 (pttm) REVERT: B 242 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: B 267 THR cc_start: 0.9021 (m) cc_final: 0.8786 (p) REVERT: B 394 LYS cc_start: 0.7454 (pttm) cc_final: 0.7169 (pttm) REVERT: B 418 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 267 THR cc_start: 0.9083 (m) cc_final: 0.8634 (p) REVERT: C 280 GLU cc_start: 0.7779 (tt0) cc_final: 0.7458 (tt0) REVERT: C 410 LYS cc_start: 0.8890 (tptt) cc_final: 0.8681 (tptt) REVERT: C 418 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7442 (mm-30) REVERT: D 242 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: D 267 THR cc_start: 0.9069 (m) cc_final: 0.8824 (p) REVERT: D 418 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7523 (mm-30) REVERT: E 267 THR cc_start: 0.9152 (m) cc_final: 0.8831 (p) REVERT: E 370 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7492 (ttm-80) REVERT: E 394 LYS cc_start: 0.7477 (pttm) cc_final: 0.7014 (pttm) REVERT: E 409 MET cc_start: 0.8437 (tpp) cc_final: 0.8058 (tpt) REVERT: E 410 LYS cc_start: 0.8948 (tptt) cc_final: 0.8725 (tptt) REVERT: E 430 LEU cc_start: 0.8889 (tp) cc_final: 0.8415 (tt) REVERT: E 431 ASN cc_start: 0.8349 (t0) cc_final: 0.8095 (p0) REVERT: F 242 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: F 267 THR cc_start: 0.9080 (m) cc_final: 0.8853 (p) REVERT: F 302 GLU cc_start: 0.7346 (tt0) cc_final: 0.6827 (mp0) REVERT: F 376 LYS cc_start: 0.8374 (tptp) cc_final: 0.8082 (tppp) REVERT: F 383 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8159 (mt-10) REVERT: F 394 LYS cc_start: 0.7467 (pttm) cc_final: 0.7022 (pttm) REVERT: F 410 LYS cc_start: 0.8752 (tptt) cc_final: 0.8422 (tptt) REVERT: F 418 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8397 (mm-30) REVERT: F 430 LEU cc_start: 0.8910 (tp) cc_final: 0.8533 (tp) REVERT: G 242 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: G 246 GLN cc_start: 0.9036 (pt0) cc_final: 0.8793 (pt0) REVERT: G 267 THR cc_start: 0.9046 (m) cc_final: 0.8714 (p) REVERT: G 302 GLU cc_start: 0.7370 (tt0) cc_final: 0.7020 (mp0) REVERT: G 418 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7723 (mm-30) REVERT: H 242 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: H 267 THR cc_start: 0.9162 (m) cc_final: 0.8946 (p) REVERT: H 302 GLU cc_start: 0.7542 (tt0) cc_final: 0.7295 (mp0) REVERT: H 410 LYS cc_start: 0.8729 (tptt) cc_final: 0.8517 (tptt) REVERT: H 418 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7102 (mm-30) REVERT: H 430 LEU cc_start: 0.8864 (tp) cc_final: 0.8211 (tt) REVERT: I 267 THR cc_start: 0.9146 (m) cc_final: 0.8819 (p) REVERT: I 394 LYS cc_start: 0.7418 (pttm) cc_final: 0.7136 (pttm) REVERT: I 418 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7454 (mm-30) REVERT: I 431 ASN cc_start: 0.8504 (t0) cc_final: 0.8212 (p0) REVERT: J 242 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: J 267 THR cc_start: 0.9106 (m) cc_final: 0.8808 (p) REVERT: J 302 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6924 (mp0) REVERT: J 412 ILE cc_start: 0.9366 (mm) cc_final: 0.9017 (mt) REVERT: J 431 ASN cc_start: 0.8443 (t0) cc_final: 0.8145 (p0) REVERT: K 267 THR cc_start: 0.9153 (m) cc_final: 0.8704 (p) REVERT: K 418 GLU cc_start: 0.8478 (mm-30) cc_final: 0.6595 (mm-30) REVERT: L 242 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: L 267 THR cc_start: 0.9072 (m) cc_final: 0.8730 (p) REVERT: L 281 HIS cc_start: 0.7620 (t70) cc_final: 0.7390 (t70) REVERT: L 283 SER cc_start: 0.9010 (m) cc_final: 0.8706 (p) REVERT: L 376 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8195 (tptp) REVERT: L 430 LEU cc_start: 0.8831 (tp) cc_final: 0.8061 (tt) REVERT: L 431 ASN cc_start: 0.8451 (t0) cc_final: 0.7979 (p0) REVERT: M 242 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: M 267 THR cc_start: 0.9101 (m) cc_final: 0.8796 (p) REVERT: M 376 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7946 (tptp) REVERT: M 394 LYS cc_start: 0.6664 (ptpt) cc_final: 0.6216 (pttm) REVERT: M 418 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8136 (mm-30) REVERT: N 242 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: N 267 THR cc_start: 0.9195 (m) cc_final: 0.8824 (p) REVERT: N 370 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7536 (ttm-80) REVERT: N 410 LYS cc_start: 0.8936 (tptt) cc_final: 0.8691 (tptt) REVERT: N 418 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8321 (mm-30) REVERT: O 242 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: O 267 THR cc_start: 0.9121 (m) cc_final: 0.8839 (p) REVERT: O 410 LYS cc_start: 0.8918 (tptt) cc_final: 0.8643 (tptt) REVERT: O 418 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7802 (mm-30) REVERT: P 267 THR cc_start: 0.9091 (m) cc_final: 0.8784 (p) REVERT: P 418 GLU cc_start: 0.8453 (mm-30) cc_final: 0.6766 (mm-30) REVERT: P 431 ASN cc_start: 0.8435 (t0) cc_final: 0.8050 (p0) REVERT: Q 267 THR cc_start: 0.9117 (m) cc_final: 0.8745 (p) REVERT: Q 302 GLU cc_start: 0.7351 (tt0) cc_final: 0.6972 (mp0) REVERT: Q 410 LYS cc_start: 0.8697 (tptt) cc_final: 0.8485 (tptt) REVERT: Q 418 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7248 (mm-30) REVERT: Q 431 ASN cc_start: 0.8395 (t0) cc_final: 0.8058 (p0) REVERT: R 267 THR cc_start: 0.9055 (m) cc_final: 0.8665 (p) REVERT: R 370 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7631 (ttm-80) REVERT: R 394 LYS cc_start: 0.7614 (ptpp) cc_final: 0.7131 (pttm) REVERT: R 400 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8335 (mmtt) REVERT: R 408 GLN cc_start: 0.8470 (tt0) cc_final: 0.8214 (tt0) REVERT: R 431 ASN cc_start: 0.8365 (t0) cc_final: 0.8023 (p0) REVERT: S 242 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: S 267 THR cc_start: 0.9025 (m) cc_final: 0.8754 (p) REVERT: S 394 LYS cc_start: 0.7447 (pttm) cc_final: 0.7162 (pttm) REVERT: S 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7774 (mt-10) REVERT: T 242 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: T 267 THR cc_start: 0.9034 (m) cc_final: 0.8683 (p) REVERT: T 280 GLU cc_start: 0.7608 (tt0) cc_final: 0.7392 (tt0) REVERT: T 410 LYS cc_start: 0.8922 (tptt) cc_final: 0.8719 (tptt) REVERT: U 242 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: U 267 THR cc_start: 0.9066 (m) cc_final: 0.8822 (p) REVERT: U 302 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6776 (mp0) REVERT: U 410 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8695 (tptp) REVERT: U 418 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7517 (mm-30) REVERT: V 267 THR cc_start: 0.9139 (m) cc_final: 0.8786 (p) REVERT: V 302 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6619 (mp0) REVERT: V 370 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: V 410 LYS cc_start: 0.8960 (tptt) cc_final: 0.8690 (tptt) REVERT: V 418 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7646 (mm-30) REVERT: V 431 ASN cc_start: 0.8357 (t0) cc_final: 0.8104 (p0) REVERT: W 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: W 267 THR cc_start: 0.9079 (m) cc_final: 0.8850 (p) REVERT: W 302 GLU cc_start: 0.7343 (tt0) cc_final: 0.6845 (mp0) REVERT: W 376 LYS cc_start: 0.8375 (tptp) cc_final: 0.8082 (tppp) REVERT: W 383 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8171 (mt-10) REVERT: W 410 LYS cc_start: 0.8871 (tptt) cc_final: 0.8637 (tptt) REVERT: W 431 ASN cc_start: 0.8408 (t0) cc_final: 0.8056 (p0) REVERT: X 242 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: X 246 GLN cc_start: 0.9039 (pt0) cc_final: 0.8797 (pt0) REVERT: X 267 THR cc_start: 0.9049 (m) cc_final: 0.8714 (p) REVERT: X 302 GLU cc_start: 0.7361 (tt0) cc_final: 0.7006 (mp0) REVERT: X 418 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7719 (mm-30) REVERT: Y 267 THR cc_start: 0.9153 (m) cc_final: 0.8853 (p) REVERT: Y 302 GLU cc_start: 0.7533 (tt0) cc_final: 0.7302 (mp0) REVERT: Y 410 LYS cc_start: 0.8730 (tptt) cc_final: 0.8529 (tptt) REVERT: Y 430 LEU cc_start: 0.8870 (tp) cc_final: 0.8217 (tt) REVERT: Z 242 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: Z 267 THR cc_start: 0.9142 (m) cc_final: 0.8873 (p) REVERT: Z 394 LYS cc_start: 0.7427 (pttm) cc_final: 0.7149 (pttm) REVERT: Z 418 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7373 (mm-30) REVERT: a 242 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: a 267 THR cc_start: 0.9107 (m) cc_final: 0.8803 (p) REVERT: a 302 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6922 (mp0) REVERT: a 412 ILE cc_start: 0.9370 (mm) cc_final: 0.9013 (mt) REVERT: a 431 ASN cc_start: 0.8407 (t0) cc_final: 0.8130 (p0) REVERT: b 267 THR cc_start: 0.9156 (m) cc_final: 0.8709 (p) REVERT: c 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: c 267 THR cc_start: 0.9137 (m) cc_final: 0.8784 (p) REVERT: c 281 HIS cc_start: 0.7630 (t70) cc_final: 0.7391 (t70) REVERT: c 283 SER cc_start: 0.9036 (m) cc_final: 0.8719 (p) REVERT: c 376 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8197 (tptp) REVERT: c 430 LEU cc_start: 0.8712 (tp) cc_final: 0.8119 (tt) REVERT: c 431 ASN cc_start: 0.8464 (t0) cc_final: 0.7988 (p0) REVERT: d 242 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: d 267 THR cc_start: 0.9101 (m) cc_final: 0.8799 (p) REVERT: d 376 LYS cc_start: 0.8269 (tmtt) cc_final: 0.7948 (tptp) REVERT: d 394 LYS cc_start: 0.6647 (ptpt) cc_final: 0.6212 (pttm) REVERT: d 418 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8139 (mm-30) REVERT: e 242 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: e 267 THR cc_start: 0.9196 (m) cc_final: 0.8824 (p) REVERT: e 376 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7932 (tptp) REVERT: e 410 LYS cc_start: 0.8951 (tptt) cc_final: 0.8673 (tptt) REVERT: e 418 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8315 (mm-30) REVERT: f 242 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: f 267 THR cc_start: 0.9131 (m) cc_final: 0.8863 (p) REVERT: f 302 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6846 (tm-30) REVERT: f 402 LEU cc_start: 0.9085 (tp) cc_final: 0.8622 (tp) REVERT: f 410 LYS cc_start: 0.9004 (tptt) cc_final: 0.8664 (tptt) REVERT: f 418 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7702 (mm-30) REVERT: g 267 THR cc_start: 0.9094 (m) cc_final: 0.8800 (p) REVERT: g 418 GLU cc_start: 0.8447 (mm-30) cc_final: 0.6751 (mm-30) REVERT: g 431 ASN cc_start: 0.8479 (t0) cc_final: 0.8150 (p0) REVERT: h 267 THR cc_start: 0.9116 (m) cc_final: 0.8746 (p) REVERT: h 302 GLU cc_start: 0.7343 (tt0) cc_final: 0.6973 (mp0) REVERT: h 431 ASN cc_start: 0.8381 (t0) cc_final: 0.8048 (p0) outliers start: 114 outliers final: 26 residues processed: 1295 average time/residue: 0.2815 time to fit residues: 575.6654 Evaluate side-chains 1201 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1151 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 243 SER Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 243 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 450 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 427 optimal weight: 0.0370 chunk 51 optimal weight: 0.0010 chunk 445 optimal weight: 0.0970 chunk 339 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 463 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 409 optimal weight: 6.9990 overall best weight: 0.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN D 239 ASN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 408 GLN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 411 GLN U 239 ASN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 239 ASN b 408 GLN ** c 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 408 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 411 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.206058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.159604 restraints weight = 86256.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.161981 restraints weight = 59375.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.162324 restraints weight = 43582.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.162685 restraints weight = 36739.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.162849 restraints weight = 33552.391| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43146 Z= 0.099 Angle : 0.569 8.184 58174 Z= 0.285 Chirality : 0.040 0.142 6698 Planarity : 0.003 0.028 7786 Dihedral : 4.268 37.687 5852 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.50 % Allowed : 20.67 % Favored : 77.83 % 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: 0.17 (0.13), residues: 5202 helix: 3.06 (0.14), residues: 1428 sheet: -0.66 (0.11), residues: 2550 loop : -1.55 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 370 TYR 0.007 0.001 TYR R 393 PHE 0.024 0.001 PHE Z 237 HIS 0.001 0.000 HIS U 281 Details of bonding type rmsd covalent geometry : bond 0.00229 (43146) covalent geometry : angle 0.56854 (58174) hydrogen bonds : bond 0.02732 ( 2043) hydrogen bonds : angle 4.01976 ( 5718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1337 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 THR cc_start: 0.9075 (m) cc_final: 0.8720 (p) REVERT: A 280 GLU cc_start: 0.7610 (tt0) cc_final: 0.6975 (tm-30) REVERT: A 370 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7400 (ttm-80) REVERT: A 394 LYS cc_start: 0.7640 (ptpp) cc_final: 0.7371 (pttm) REVERT: A 408 GLN cc_start: 0.8468 (tt0) cc_final: 0.8234 (tt0) REVERT: A 410 LYS cc_start: 0.8850 (tptp) cc_final: 0.8310 (tptt) REVERT: A 413 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 418 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 242 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: B 246 GLN cc_start: 0.9194 (pt0) cc_final: 0.8958 (pt0) REVERT: B 267 THR cc_start: 0.9068 (m) cc_final: 0.8835 (p) REVERT: B 302 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6571 (mp0) REVERT: B 418 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 246 GLN cc_start: 0.9030 (pt0) cc_final: 0.8813 (pt0) REVERT: C 267 THR cc_start: 0.9050 (m) cc_final: 0.8624 (p) REVERT: C 280 GLU cc_start: 0.7675 (tt0) cc_final: 0.7433 (tt0) REVERT: C 302 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7050 (mp0) REVERT: C 394 LYS cc_start: 0.7586 (pttm) cc_final: 0.7203 (pttm) REVERT: C 410 LYS cc_start: 0.8952 (tptt) cc_final: 0.8751 (tptt) REVERT: C 418 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 242 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: D 267 THR cc_start: 0.9116 (m) cc_final: 0.8853 (p) REVERT: D 280 GLU cc_start: 0.7687 (tt0) cc_final: 0.7003 (tm-30) REVERT: D 283 SER cc_start: 0.9035 (m) cc_final: 0.8694 (p) REVERT: D 370 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7350 (ttp80) REVERT: D 394 LYS cc_start: 0.7507 (pttm) cc_final: 0.7042 (pttm) REVERT: D 418 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 267 THR cc_start: 0.9124 (m) cc_final: 0.8805 (p) REVERT: E 280 GLU cc_start: 0.7558 (tt0) cc_final: 0.7321 (tt0) REVERT: E 376 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7975 (ttmm) REVERT: E 377 MET cc_start: 0.8460 (mmm) cc_final: 0.7957 (tpp) REVERT: E 394 LYS cc_start: 0.7217 (pttm) cc_final: 0.6949 (pttm) REVERT: E 410 LYS cc_start: 0.8994 (tptt) cc_final: 0.8536 (tptt) REVERT: E 418 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 431 ASN cc_start: 0.8302 (t0) cc_final: 0.8095 (p0) REVERT: F 242 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: F 302 GLU cc_start: 0.7273 (tt0) cc_final: 0.7026 (mp0) REVERT: F 376 LYS cc_start: 0.8344 (tptp) cc_final: 0.8048 (tppp) REVERT: F 383 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8050 (mt-10) REVERT: F 410 LYS cc_start: 0.8816 (tptt) cc_final: 0.8577 (tptt) REVERT: F 418 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7020 (mm-30) REVERT: G 242 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: G 267 THR cc_start: 0.9069 (m) cc_final: 0.8746 (p) REVERT: G 302 GLU cc_start: 0.7465 (tt0) cc_final: 0.7097 (mp0) REVERT: G 370 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7089 (ttm-80) REVERT: G 376 LYS cc_start: 0.8451 (tptp) cc_final: 0.8201 (tppp) REVERT: G 410 LYS cc_start: 0.8951 (tptt) cc_final: 0.8747 (tptt) REVERT: G 418 GLU cc_start: 0.8476 (mm-30) cc_final: 0.6626 (mm-30) REVERT: H 242 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: H 267 THR cc_start: 0.9138 (m) cc_final: 0.8901 (p) REVERT: H 410 LYS cc_start: 0.8870 (tptt) cc_final: 0.8559 (tptt) REVERT: H 418 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7028 (mm-30) REVERT: H 431 ASN cc_start: 0.8319 (t0) cc_final: 0.8048 (p0) REVERT: I 246 GLN cc_start: 0.9053 (pt0) cc_final: 0.8653 (pt0) REVERT: I 267 THR cc_start: 0.9122 (m) cc_final: 0.8811 (p) REVERT: I 376 LYS cc_start: 0.8282 (tptp) cc_final: 0.7958 (tppp) REVERT: I 377 MET cc_start: 0.8286 (mmm) cc_final: 0.7912 (mmm) REVERT: I 404 LEU cc_start: 0.9220 (mp) cc_final: 0.8854 (mp) REVERT: I 418 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7299 (mm-30) REVERT: J 242 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: J 267 THR cc_start: 0.9092 (m) cc_final: 0.8636 (p) REVERT: J 302 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6632 (mp0) REVERT: J 410 LYS cc_start: 0.8714 (tptt) cc_final: 0.8073 (tptt) REVERT: J 414 ASP cc_start: 0.8451 (m-30) cc_final: 0.7571 (m-30) REVERT: K 267 THR cc_start: 0.9198 (m) cc_final: 0.8733 (p) REVERT: K 283 SER cc_start: 0.9123 (m) cc_final: 0.8753 (p) REVERT: K 376 LYS cc_start: 0.8504 (tptp) cc_final: 0.8230 (tppp) REVERT: K 418 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7410 (mm-30) REVERT: L 242 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: L 250 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8206 (mt-10) REVERT: L 267 THR cc_start: 0.9070 (m) cc_final: 0.8718 (p) REVERT: L 270 LEU cc_start: 0.9504 (mm) cc_final: 0.9188 (mm) REVERT: L 414 ASP cc_start: 0.8375 (m-30) cc_final: 0.7311 (m-30) REVERT: L 418 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8192 (mm-30) REVERT: M 267 THR cc_start: 0.9067 (m) cc_final: 0.8669 (p) REVERT: M 394 LYS cc_start: 0.6734 (ptpt) cc_final: 0.6222 (pttm) REVERT: M 402 LEU cc_start: 0.9147 (tp) cc_final: 0.8879 (tp) REVERT: M 418 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7754 (mm-30) REVERT: N 240 ASP cc_start: 0.9197 (t0) cc_final: 0.8876 (t0) REVERT: N 242 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: N 267 THR cc_start: 0.9229 (m) cc_final: 0.8861 (p) REVERT: N 302 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6655 (mp0) REVERT: N 370 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7375 (ttm-80) REVERT: N 377 MET cc_start: 0.8216 (mmm) cc_final: 0.7911 (mmm) REVERT: N 418 GLU cc_start: 0.8530 (mm-30) cc_final: 0.6778 (mm-30) REVERT: N 431 ASN cc_start: 0.8383 (t0) cc_final: 0.8123 (p0) REVERT: O 242 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: O 267 THR cc_start: 0.9178 (m) cc_final: 0.8943 (p) REVERT: O 376 LYS cc_start: 0.8408 (tptp) cc_final: 0.8078 (tppp) REVERT: O 418 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7659 (mm-30) REVERT: O 431 ASN cc_start: 0.8405 (t0) cc_final: 0.8059 (p0) REVERT: P 246 GLN cc_start: 0.9290 (pt0) cc_final: 0.8982 (pt0) REVERT: P 267 THR cc_start: 0.9080 (m) cc_final: 0.8792 (p) REVERT: P 431 ASN cc_start: 0.8440 (t0) cc_final: 0.8121 (p0) REVERT: Q 232 ASP cc_start: 0.8460 (m-30) cc_final: 0.8229 (m-30) REVERT: Q 242 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: Q 246 GLN cc_start: 0.9182 (pt0) cc_final: 0.8843 (pt0) REVERT: Q 267 THR cc_start: 0.9168 (m) cc_final: 0.8880 (p) REVERT: Q 418 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7188 (mm-30) REVERT: R 267 THR cc_start: 0.9085 (m) cc_final: 0.8639 (p) REVERT: R 280 GLU cc_start: 0.7647 (tt0) cc_final: 0.7013 (tm-30) REVERT: R 370 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7382 (ttm-80) REVERT: R 431 ASN cc_start: 0.8301 (t0) cc_final: 0.7922 (p0) REVERT: S 242 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: S 246 GLN cc_start: 0.9196 (pt0) cc_final: 0.8963 (pt0) REVERT: S 267 THR cc_start: 0.9062 (m) cc_final: 0.8840 (p) REVERT: S 302 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6585 (mp0) REVERT: S 418 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7658 (mt-10) REVERT: T 267 THR cc_start: 0.9173 (m) cc_final: 0.8692 (p) REVERT: T 302 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7105 (mp0) REVERT: T 362 GLU cc_start: 0.7337 (tt0) cc_final: 0.7097 (tt0) REVERT: T 376 LYS cc_start: 0.8496 (tptp) cc_final: 0.8106 (tppp) REVERT: T 394 LYS cc_start: 0.7556 (pttm) cc_final: 0.7200 (pttm) REVERT: T 418 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8050 (mt-10) REVERT: U 242 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: U 267 THR cc_start: 0.9129 (m) cc_final: 0.8876 (p) REVERT: U 280 GLU cc_start: 0.7706 (tt0) cc_final: 0.7034 (tm-30) REVERT: U 283 SER cc_start: 0.9039 (m) cc_final: 0.8699 (p) REVERT: U 370 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7318 (ttp80) REVERT: U 394 LYS cc_start: 0.7415 (pttm) cc_final: 0.7061 (pttm) REVERT: U 418 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7438 (mm-30) REVERT: U 430 LEU cc_start: 0.8942 (tp) cc_final: 0.8698 (tt) REVERT: V 267 THR cc_start: 0.9142 (m) cc_final: 0.8801 (p) REVERT: V 280 GLU cc_start: 0.7647 (tt0) cc_final: 0.7195 (mp0) REVERT: V 302 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6603 (mp0) REVERT: V 370 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7237 (ttm-80) REVERT: V 410 LYS cc_start: 0.8961 (tptt) cc_final: 0.8739 (tptt) REVERT: V 418 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7376 (mm-30) REVERT: V 431 ASN cc_start: 0.8263 (t0) cc_final: 0.8053 (p0) REVERT: W 242 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: W 267 THR cc_start: 0.9100 (m) cc_final: 0.8898 (p) REVERT: W 302 GLU cc_start: 0.7227 (tt0) cc_final: 0.6953 (mp0) REVERT: W 376 LYS cc_start: 0.8353 (tptp) cc_final: 0.8063 (tppp) REVERT: W 383 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8022 (mt-10) REVERT: W 410 LYS cc_start: 0.8932 (tptt) cc_final: 0.8694 (tptt) REVERT: W 418 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7024 (mm-30) REVERT: W 431 ASN cc_start: 0.8368 (t0) cc_final: 0.8064 (p0) REVERT: X 242 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: X 267 THR cc_start: 0.9072 (m) cc_final: 0.8752 (p) REVERT: X 302 GLU cc_start: 0.7458 (tt0) cc_final: 0.7090 (mp0) REVERT: X 370 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7057 (ttm-80) REVERT: X 376 LYS cc_start: 0.8452 (tptp) cc_final: 0.8221 (tppp) REVERT: X 410 LYS cc_start: 0.8952 (tptt) cc_final: 0.8750 (tptt) REVERT: X 418 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7612 (mm-30) REVERT: X 431 ASN cc_start: 0.8395 (t0) cc_final: 0.8174 (p0) REVERT: Y 242 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: Y 267 THR cc_start: 0.9112 (m) cc_final: 0.8896 (p) REVERT: Y 410 LYS cc_start: 0.8769 (tptt) cc_final: 0.8443 (tptt) REVERT: Y 418 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7061 (mm-30) REVERT: Z 242 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: Z 246 GLN cc_start: 0.9062 (pt0) cc_final: 0.8701 (pt0) REVERT: Z 267 THR cc_start: 0.9136 (m) cc_final: 0.8899 (p) REVERT: Z 376 LYS cc_start: 0.8280 (tptp) cc_final: 0.7953 (tppp) REVERT: Z 377 MET cc_start: 0.8281 (mmm) cc_final: 0.7911 (mmm) REVERT: Z 404 LEU cc_start: 0.9179 (mp) cc_final: 0.8634 (mp) REVERT: Z 418 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7311 (mm-30) REVERT: a 242 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: a 267 THR cc_start: 0.9095 (m) cc_final: 0.8654 (p) REVERT: a 302 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6634 (mp0) REVERT: a 410 LYS cc_start: 0.8725 (tptt) cc_final: 0.8064 (tptt) REVERT: a 414 ASP cc_start: 0.8453 (m-30) cc_final: 0.7572 (m-30) REVERT: b 267 THR cc_start: 0.9194 (m) cc_final: 0.8729 (p) REVERT: b 283 SER cc_start: 0.9124 (m) cc_final: 0.8757 (p) REVERT: b 376 LYS cc_start: 0.8539 (tptp) cc_final: 0.8265 (tppp) REVERT: b 418 GLU cc_start: 0.8383 (mm-30) cc_final: 0.6121 (mm-30) REVERT: c 242 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: c 250 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8210 (mt-10) REVERT: c 267 THR cc_start: 0.9095 (m) cc_final: 0.8744 (p) REVERT: c 414 ASP cc_start: 0.8357 (m-30) cc_final: 0.7273 (m-30) REVERT: c 418 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7518 (mt-10) REVERT: c 431 ASN cc_start: 0.8410 (t0) cc_final: 0.8063 (p0) REVERT: d 267 THR cc_start: 0.9072 (m) cc_final: 0.8664 (p) REVERT: d 394 LYS cc_start: 0.6700 (ptpt) cc_final: 0.6226 (pttm) REVERT: d 402 LEU cc_start: 0.9153 (tp) cc_final: 0.8879 (tp) REVERT: d 418 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7770 (mm-30) REVERT: e 240 ASP cc_start: 0.9208 (t0) cc_final: 0.8884 (t0) REVERT: e 242 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: e 267 THR cc_start: 0.9229 (m) cc_final: 0.8868 (p) REVERT: e 302 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6674 (mp0) REVERT: e 376 LYS cc_start: 0.8279 (tmtt) cc_final: 0.7905 (tptp) REVERT: e 418 GLU cc_start: 0.8531 (mm-30) cc_final: 0.6750 (mm-30) REVERT: e 431 ASN cc_start: 0.8388 (t0) cc_final: 0.8135 (p0) REVERT: f 242 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: f 302 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6663 (mp0) REVERT: f 376 LYS cc_start: 0.8387 (tptp) cc_final: 0.8034 (tppp) REVERT: f 377 MET cc_start: 0.8567 (mmm) cc_final: 0.7889 (tpt) REVERT: f 409 MET cc_start: 0.8343 (tpp) cc_final: 0.8066 (tpt) REVERT: f 410 LYS cc_start: 0.8986 (tptt) cc_final: 0.8714 (tptt) REVERT: f 418 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7710 (mm-30) REVERT: f 431 ASN cc_start: 0.8409 (t0) cc_final: 0.8080 (p0) REVERT: g 246 GLN cc_start: 0.9312 (pt0) cc_final: 0.8998 (pt0) REVERT: g 267 THR cc_start: 0.9081 (m) cc_final: 0.8784 (p) REVERT: g 431 ASN cc_start: 0.8439 (t0) cc_final: 0.8114 (p0) REVERT: h 232 ASP cc_start: 0.8468 (m-30) cc_final: 0.8221 (m-30) REVERT: h 242 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: h 246 GLN cc_start: 0.9194 (pt0) cc_final: 0.8927 (pt0) REVERT: h 267 THR cc_start: 0.9159 (m) cc_final: 0.8887 (p) REVERT: h 302 GLU cc_start: 0.7443 (tt0) cc_final: 0.7185 (mp0) REVERT: h 414 ASP cc_start: 0.8531 (m-30) cc_final: 0.7755 (m-30) REVERT: h 418 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7731 (mt-10) outliers start: 72 outliers final: 21 residues processed: 1358 average time/residue: 0.2726 time to fit residues: 595.4299 Evaluate side-chains 1247 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 1203 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 413 GLU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 396 LEU Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 404 LEU Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 390 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 0.4980 chunk 437 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 448 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 409 optimal weight: 0.9980 chunk 405 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 411 GLN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 411 GLN ** a 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 239 ASN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 411 GLN ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.204095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.158730 restraints weight = 85653.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.162083 restraints weight = 50517.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.161737 restraints weight = 37718.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.162088 restraints weight = 32526.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.162207 restraints weight = 29408.123| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43146 Z= 0.114 Angle : 0.589 8.815 58174 Z= 0.293 Chirality : 0.040 0.157 6698 Planarity : 0.003 0.040 7786 Dihedral : 4.287 36.064 5852 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.50 % Allowed : 23.74 % Favored : 74.76 % 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: 0.28 (0.12), residues: 5202 helix: 2.90 (0.14), residues: 1428 sheet: -0.49 (0.11), residues: 2550 loop : -1.40 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 417 TYR 0.005 0.001 TYR X 366 PHE 0.029 0.002 PHE P 237 HIS 0.002 0.000 HIS c 281 Details of bonding type rmsd covalent geometry : bond 0.00263 (43146) covalent geometry : angle 0.58922 (58174) hydrogen bonds : bond 0.02737 ( 2043) hydrogen bonds : angle 3.98739 ( 5718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1275 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.9274 (pt0) cc_final: 0.8849 (pm20) REVERT: A 267 THR cc_start: 0.9063 (m) cc_final: 0.8745 (p) REVERT: A 280 GLU cc_start: 0.7662 (tt0) cc_final: 0.6902 (tm-30) REVERT: B 242 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: B 267 THR cc_start: 0.9100 (m) cc_final: 0.8880 (p) REVERT: B 302 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6739 (mp0) REVERT: B 410 LYS cc_start: 0.8733 (tptt) cc_final: 0.8526 (tptt) REVERT: C 240 ASP cc_start: 0.9217 (t0) cc_final: 0.9011 (t0) REVERT: C 246 GLN cc_start: 0.9052 (pt0) cc_final: 0.8814 (pt0) REVERT: C 267 THR cc_start: 0.9024 (m) cc_final: 0.8636 (p) REVERT: C 280 GLU cc_start: 0.7648 (tt0) cc_final: 0.7404 (tt0) REVERT: C 302 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7216 (mp0) REVERT: C 362 GLU cc_start: 0.7377 (tt0) cc_final: 0.7132 (tt0) REVERT: C 394 LYS cc_start: 0.7256 (pttm) cc_final: 0.7045 (pttm) REVERT: C 404 LEU cc_start: 0.8896 (mp) cc_final: 0.8633 (mp) REVERT: C 410 LYS cc_start: 0.8907 (tptt) cc_final: 0.8138 (tptt) REVERT: C 414 ASP cc_start: 0.8326 (m-30) cc_final: 0.7660 (m-30) REVERT: C 418 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7878 (mt-10) REVERT: D 232 ASP cc_start: 0.8460 (m-30) cc_final: 0.8130 (m-30) REVERT: D 242 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: D 267 THR cc_start: 0.9170 (m) cc_final: 0.8915 (p) REVERT: D 280 GLU cc_start: 0.7673 (tt0) cc_final: 0.7035 (tm-30) REVERT: D 283 SER cc_start: 0.9041 (m) cc_final: 0.8690 (p) REVERT: D 370 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7242 (ttp80) REVERT: D 394 LYS cc_start: 0.7449 (pttm) cc_final: 0.7056 (pttm) REVERT: D 418 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7510 (mm-30) REVERT: E 267 THR cc_start: 0.9160 (m) cc_final: 0.8826 (p) REVERT: E 370 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7269 (ttm-80) REVERT: E 376 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8051 (ttmm) REVERT: E 377 MET cc_start: 0.8443 (mmm) cc_final: 0.8052 (mmm) REVERT: E 410 LYS cc_start: 0.8809 (tptt) cc_final: 0.8510 (tptt) REVERT: E 413 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8180 (tm-30) REVERT: E 418 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7829 (mt-10) REVERT: F 240 ASP cc_start: 0.9195 (t0) cc_final: 0.8928 (t0) REVERT: F 242 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: F 302 GLU cc_start: 0.7222 (tt0) cc_final: 0.6909 (mp0) REVERT: F 376 LYS cc_start: 0.8371 (tptp) cc_final: 0.8108 (tppp) REVERT: F 383 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8057 (mt-10) REVERT: F 410 LYS cc_start: 0.8871 (tptt) cc_final: 0.8142 (tptt) REVERT: F 414 ASP cc_start: 0.8245 (m-30) cc_final: 0.7394 (m-30) REVERT: F 418 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7747 (mt-10) REVERT: G 242 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: G 267 THR cc_start: 0.9097 (m) cc_final: 0.8808 (p) REVERT: G 302 GLU cc_start: 0.7431 (tt0) cc_final: 0.7161 (mp0) REVERT: G 376 LYS cc_start: 0.8464 (tptp) cc_final: 0.8191 (tppp) REVERT: G 377 MET cc_start: 0.8367 (mmm) cc_final: 0.8143 (mmm) REVERT: G 400 LYS cc_start: 0.8247 (mmtm) cc_final: 0.8039 (mmtm) REVERT: G 410 LYS cc_start: 0.8891 (tptt) cc_final: 0.8642 (tptt) REVERT: H 242 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: H 267 THR cc_start: 0.9184 (m) cc_final: 0.8964 (p) REVERT: H 281 HIS cc_start: 0.7718 (t70) cc_final: 0.7428 (t70) REVERT: H 302 GLU cc_start: 0.7264 (mp0) cc_final: 0.6782 (mp0) REVERT: H 418 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7816 (mt-10) REVERT: I 267 THR cc_start: 0.9199 (m) cc_final: 0.8836 (p) REVERT: I 376 LYS cc_start: 0.8418 (tptp) cc_final: 0.8121 (tppp) REVERT: I 377 MET cc_start: 0.8258 (mmm) cc_final: 0.7842 (mmm) REVERT: I 418 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8091 (mt-10) REVERT: J 242 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: J 267 THR cc_start: 0.9137 (m) cc_final: 0.8773 (p) REVERT: J 302 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6669 (mp0) REVERT: K 267 THR cc_start: 0.9204 (m) cc_final: 0.8826 (p) REVERT: K 283 SER cc_start: 0.9102 (m) cc_final: 0.8834 (p) REVERT: K 376 LYS cc_start: 0.8463 (tptp) cc_final: 0.8136 (tppp) REVERT: K 409 MET cc_start: 0.8738 (tpt) cc_final: 0.8530 (tpt) REVERT: K 418 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7271 (tt0) REVERT: L 242 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: L 267 THR cc_start: 0.9167 (m) cc_final: 0.8864 (p) REVERT: L 281 HIS cc_start: 0.7510 (t70) cc_final: 0.7304 (t70) REVERT: M 267 THR cc_start: 0.9122 (m) cc_final: 0.8777 (p) REVERT: M 280 GLU cc_start: 0.7870 (tt0) cc_final: 0.7197 (mp0) REVERT: M 394 LYS cc_start: 0.6528 (ptpt) cc_final: 0.6164 (pttm) REVERT: M 402 LEU cc_start: 0.9047 (tp) cc_final: 0.8733 (tp) REVERT: M 418 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7411 (mm-30) REVERT: N 242 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: N 267 THR cc_start: 0.9231 (m) cc_final: 0.8876 (p) REVERT: N 280 GLU cc_start: 0.7759 (tt0) cc_final: 0.7221 (mp0) REVERT: N 302 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6650 (mp0) REVERT: N 418 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7284 (mm-30) REVERT: N 431 ASN cc_start: 0.8444 (t0) cc_final: 0.8058 (p0) REVERT: O 232 ASP cc_start: 0.8471 (m-30) cc_final: 0.8101 (m-30) REVERT: O 242 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: O 302 GLU cc_start: 0.7506 (mp0) cc_final: 0.7198 (mp0) REVERT: O 376 LYS cc_start: 0.8449 (tptp) cc_final: 0.8128 (tppp) REVERT: O 394 LYS cc_start: 0.7596 (pttm) cc_final: 0.7379 (pttm) REVERT: O 410 LYS cc_start: 0.8813 (tptt) cc_final: 0.7946 (tptt) REVERT: O 414 ASP cc_start: 0.8526 (m-30) cc_final: 0.6968 (m-30) REVERT: O 418 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7658 (mm-30) REVERT: P 239 ASN cc_start: 0.9308 (t0) cc_final: 0.9055 (t0) REVERT: P 246 GLN cc_start: 0.9318 (pt0) cc_final: 0.9037 (pt0) REVERT: P 267 THR cc_start: 0.9115 (m) cc_final: 0.8845 (p) REVERT: P 418 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7753 (mt-10) REVERT: P 431 ASN cc_start: 0.8387 (t0) cc_final: 0.8087 (p0) REVERT: Q 242 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: Q 246 GLN cc_start: 0.9204 (pt0) cc_final: 0.8945 (pt0) REVERT: Q 267 THR cc_start: 0.9216 (m) cc_final: 0.8951 (p) REVERT: Q 418 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7293 (mm-30) REVERT: R 242 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7243 (pt0) REVERT: R 246 GLN cc_start: 0.9256 (pt0) cc_final: 0.8789 (pm20) REVERT: R 267 THR cc_start: 0.9074 (m) cc_final: 0.8713 (p) REVERT: R 280 GLU cc_start: 0.7698 (tt0) cc_final: 0.6933 (tm-30) REVERT: R 431 ASN cc_start: 0.8341 (t0) cc_final: 0.8007 (p0) REVERT: S 242 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: S 267 THR cc_start: 0.9129 (m) cc_final: 0.8916 (p) REVERT: S 302 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6741 (mp0) REVERT: T 267 THR cc_start: 0.9052 (m) cc_final: 0.8594 (p) REVERT: T 376 LYS cc_start: 0.8551 (tptp) cc_final: 0.8145 (tppp) REVERT: T 404 LEU cc_start: 0.9225 (mp) cc_final: 0.8703 (mp) REVERT: T 418 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7899 (mm-30) REVERT: U 232 ASP cc_start: 0.8563 (m-30) cc_final: 0.8201 (m-30) REVERT: U 242 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: U 267 THR cc_start: 0.9165 (m) cc_final: 0.8917 (p) REVERT: U 280 GLU cc_start: 0.7698 (tt0) cc_final: 0.7040 (tm-30) REVERT: U 283 SER cc_start: 0.9052 (m) cc_final: 0.8688 (p) REVERT: U 370 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7194 (ttp80) REVERT: U 394 LYS cc_start: 0.7540 (pttm) cc_final: 0.7268 (pttm) REVERT: U 418 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7462 (mm-30) REVERT: V 267 THR cc_start: 0.9148 (m) cc_final: 0.8812 (p) REVERT: V 302 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6696 (mp0) REVERT: V 370 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7251 (ttm-80) REVERT: V 418 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7409 (mm-30) REVERT: V 431 ASN cc_start: 0.8270 (t0) cc_final: 0.8010 (p0) REVERT: W 240 ASP cc_start: 0.9200 (t0) cc_final: 0.8934 (t0) REVERT: W 242 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: W 302 GLU cc_start: 0.7219 (tt0) cc_final: 0.6913 (mp0) REVERT: W 376 LYS cc_start: 0.8374 (tptp) cc_final: 0.8113 (tppp) REVERT: W 383 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8073 (mt-10) REVERT: W 418 GLU cc_start: 0.8686 (mm-30) cc_final: 0.6830 (mm-30) REVERT: W 431 ASN cc_start: 0.8379 (t0) cc_final: 0.8072 (p0) REVERT: X 242 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: X 267 THR cc_start: 0.9100 (m) cc_final: 0.8795 (p) REVERT: X 302 GLU cc_start: 0.7430 (tt0) cc_final: 0.7144 (mp0) REVERT: X 376 LYS cc_start: 0.8465 (tptp) cc_final: 0.8192 (tppp) REVERT: X 377 MET cc_start: 0.8364 (mmm) cc_final: 0.8132 (mmm) REVERT: X 400 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8086 (mmtm) REVERT: X 410 LYS cc_start: 0.8894 (tptt) cc_final: 0.8639 (tptt) REVERT: X 418 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7700 (mm-30) REVERT: Y 242 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: Y 267 THR cc_start: 0.9180 (m) cc_final: 0.8969 (p) REVERT: Y 281 HIS cc_start: 0.7720 (t70) cc_final: 0.7435 (t70) REVERT: Y 302 GLU cc_start: 0.7273 (mp0) cc_final: 0.6796 (mp0) REVERT: Y 418 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7521 (mt-10) REVERT: Y 422 PHE cc_start: 0.8344 (t80) cc_final: 0.8131 (t80) REVERT: Z 242 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: Z 267 THR cc_start: 0.9204 (m) cc_final: 0.8898 (p) REVERT: Z 376 LYS cc_start: 0.8423 (tptp) cc_final: 0.8106 (tppp) REVERT: Z 377 MET cc_start: 0.8255 (mmm) cc_final: 0.7839 (mmm) REVERT: a 242 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: a 267 THR cc_start: 0.9143 (m) cc_final: 0.8789 (p) REVERT: a 302 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6665 (mp0) REVERT: a 410 LYS cc_start: 0.8760 (tptt) cc_final: 0.8538 (tptt) REVERT: b 267 THR cc_start: 0.9213 (m) cc_final: 0.8811 (p) REVERT: b 283 SER cc_start: 0.9106 (m) cc_final: 0.8657 (p) REVERT: b 376 LYS cc_start: 0.8488 (tptp) cc_final: 0.8141 (tppp) REVERT: b 410 LYS cc_start: 0.8806 (tptt) cc_final: 0.8029 (tptt) REVERT: b 414 ASP cc_start: 0.8532 (m-30) cc_final: 0.7257 (m-30) REVERT: b 418 GLU cc_start: 0.8503 (mm-30) cc_final: 0.6413 (mm-30) REVERT: c 242 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: c 267 THR cc_start: 0.9196 (m) cc_final: 0.8944 (p) REVERT: c 281 HIS cc_start: 0.7507 (t70) cc_final: 0.7203 (t70) REVERT: c 383 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8398 (pm20) REVERT: c 431 ASN cc_start: 0.8336 (t0) cc_final: 0.7885 (p0) REVERT: d 267 THR cc_start: 0.9073 (m) cc_final: 0.8719 (p) REVERT: d 280 GLU cc_start: 0.7861 (tt0) cc_final: 0.7156 (mp0) REVERT: d 394 LYS cc_start: 0.6597 (ptpt) cc_final: 0.6291 (pttm) REVERT: d 402 LEU cc_start: 0.9007 (tp) cc_final: 0.8739 (tp) REVERT: d 418 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7741 (mm-30) REVERT: e 242 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: e 267 THR cc_start: 0.9235 (m) cc_final: 0.8876 (p) REVERT: e 280 GLU cc_start: 0.7917 (tt0) cc_final: 0.6966 (tm-30) REVERT: e 302 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6699 (mp0) REVERT: e 376 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7906 (tptp) REVERT: e 418 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7750 (mm-30) REVERT: e 431 ASN cc_start: 0.8429 (t0) cc_final: 0.8060 (p0) REVERT: f 232 ASP cc_start: 0.8473 (m-30) cc_final: 0.8112 (m-30) REVERT: f 242 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: f 302 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6706 (mp0) REVERT: f 376 LYS cc_start: 0.8456 (tptp) cc_final: 0.8120 (tppp) REVERT: f 377 MET cc_start: 0.8524 (mmm) cc_final: 0.8247 (mmm) REVERT: f 409 MET cc_start: 0.8423 (tpp) cc_final: 0.8126 (tpt) REVERT: f 414 ASP cc_start: 0.8613 (m-30) cc_final: 0.8290 (t0) REVERT: f 418 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7657 (mm-30) REVERT: g 239 ASN cc_start: 0.9309 (t0) cc_final: 0.9058 (t0) REVERT: g 246 GLN cc_start: 0.9328 (pt0) cc_final: 0.9035 (pt0) REVERT: g 267 THR cc_start: 0.9081 (m) cc_final: 0.8839 (p) REVERT: g 409 MET cc_start: 0.8569 (mmt) cc_final: 0.8361 (tpt) REVERT: g 418 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7359 (mm-30) REVERT: g 431 ASN cc_start: 0.8353 (t0) cc_final: 0.8119 (p0) REVERT: h 242 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: h 246 GLN cc_start: 0.9218 (pt0) cc_final: 0.8958 (pt0) REVERT: h 267 THR cc_start: 0.9161 (m) cc_final: 0.8924 (p) REVERT: h 418 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7738 (mt-10) REVERT: h 430 LEU cc_start: 0.8705 (tp) cc_final: 0.8475 (tt) REVERT: h 431 ASN cc_start: 0.8420 (t0) cc_final: 0.8011 (p0) outliers start: 72 outliers final: 16 residues processed: 1296 average time/residue: 0.2792 time to fit residues: 580.6798 Evaluate side-chains 1132 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 1093 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 413 GLU Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain b residue 408 GLN Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 377 MET Chi-restraints excluded: chain d residue 412 ILE Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 172 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 487 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 411 GLN ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 HIS ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.201009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.154790 restraints weight = 86347.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.158387 restraints weight = 50404.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.157546 restraints weight = 38130.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.157924 restraints weight = 41594.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.158127 restraints weight = 30603.620| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43146 Z= 0.165 Angle : 0.626 8.601 58174 Z= 0.314 Chirality : 0.041 0.190 6698 Planarity : 0.003 0.034 7786 Dihedral : 4.455 35.586 5852 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 1.73 % Allowed : 25.39 % Favored : 72.88 % 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: 0.25 (0.12), residues: 5202 helix: 2.78 (0.13), residues: 1428 sheet: -0.49 (0.11), residues: 2516 loop : -1.33 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 417 TYR 0.009 0.001 TYR V 366 PHE 0.029 0.002 PHE Z 422 HIS 0.004 0.001 HIS V 281 Details of bonding type rmsd covalent geometry : bond 0.00376 (43146) covalent geometry : angle 0.62612 (58174) hydrogen bonds : bond 0.03025 ( 2043) hydrogen bonds : angle 4.11681 ( 5718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1134 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.9290 (pt0) cc_final: 0.9061 (pt0) REVERT: A 267 THR cc_start: 0.9092 (m) cc_final: 0.8795 (p) REVERT: A 410 LYS cc_start: 0.9024 (tptp) cc_final: 0.8720 (tptt) REVERT: B 242 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: B 418 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7854 (mm-30) REVERT: C 267 THR cc_start: 0.9065 (m) cc_final: 0.8756 (p) REVERT: C 280 GLU cc_start: 0.7872 (tt0) cc_final: 0.7539 (tt0) REVERT: C 410 LYS cc_start: 0.8843 (tptt) cc_final: 0.8607 (tptt) REVERT: C 418 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7900 (mt-10) REVERT: D 242 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: D 267 THR cc_start: 0.9173 (m) cc_final: 0.8962 (p) REVERT: D 280 GLU cc_start: 0.7767 (tt0) cc_final: 0.7454 (tm-30) REVERT: D 370 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7540 (ttp80) REVERT: D 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8017 (mt-10) REVERT: E 267 THR cc_start: 0.9125 (m) cc_final: 0.8856 (p) REVERT: E 413 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8549 (tm-30) REVERT: F 242 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: F 302 GLU cc_start: 0.7310 (tt0) cc_final: 0.6894 (mp0) REVERT: F 376 LYS cc_start: 0.8422 (tptp) cc_final: 0.8138 (tppp) REVERT: F 383 GLU cc_start: 0.8719 (mt-10) cc_final: 0.7934 (mt-10) REVERT: F 418 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7773 (mt-10) REVERT: F 422 PHE cc_start: 0.8408 (t80) cc_final: 0.8008 (t80) REVERT: G 242 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: G 267 THR cc_start: 0.9206 (m) cc_final: 0.8906 (p) REVERT: G 302 GLU cc_start: 0.7478 (tt0) cc_final: 0.7123 (mp0) REVERT: G 370 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7131 (ttm-80) REVERT: G 376 LYS cc_start: 0.8472 (tptp) cc_final: 0.8175 (tppp) REVERT: G 418 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7211 (mm-30) REVERT: H 242 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: H 267 THR cc_start: 0.9230 (m) cc_final: 0.9010 (p) REVERT: H 281 HIS cc_start: 0.7679 (t70) cc_final: 0.7390 (t70) REVERT: H 302 GLU cc_start: 0.7704 (mp0) cc_final: 0.7227 (mp0) REVERT: H 418 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7676 (mt-10) REVERT: H 431 ASN cc_start: 0.8271 (t0) cc_final: 0.7975 (p0) REVERT: I 246 GLN cc_start: 0.9148 (pt0) cc_final: 0.8887 (pt0) REVERT: I 267 THR cc_start: 0.9265 (m) cc_final: 0.9061 (p) REVERT: I 376 LYS cc_start: 0.8433 (tptp) cc_final: 0.8126 (tppp) REVERT: I 377 MET cc_start: 0.8303 (mmm) cc_final: 0.7857 (mmm) REVERT: I 418 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8094 (mt-10) REVERT: J 242 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: J 267 THR cc_start: 0.9126 (m) cc_final: 0.8906 (p) REVERT: J 302 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6722 (mp0) REVERT: K 267 THR cc_start: 0.9105 (m) cc_final: 0.8770 (p) REVERT: K 283 SER cc_start: 0.9147 (m) cc_final: 0.8874 (p) REVERT: K 376 LYS cc_start: 0.8518 (tptp) cc_final: 0.8181 (tppp) REVERT: K 409 MET cc_start: 0.8783 (tpt) cc_final: 0.8573 (tpt) REVERT: L 242 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: L 267 THR cc_start: 0.9109 (m) cc_final: 0.8874 (p) REVERT: L 281 HIS cc_start: 0.7627 (t70) cc_final: 0.7337 (t70) REVERT: M 267 THR cc_start: 0.9158 (m) cc_final: 0.8853 (p) REVERT: M 280 GLU cc_start: 0.7991 (tt0) cc_final: 0.7239 (tm-30) REVERT: M 394 LYS cc_start: 0.6904 (ptpt) cc_final: 0.6636 (pttm) REVERT: M 402 LEU cc_start: 0.8913 (tp) cc_final: 0.8512 (tp) REVERT: M 418 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7408 (mm-30) REVERT: M 422 PHE cc_start: 0.8450 (t80) cc_final: 0.7850 (t80) REVERT: N 242 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: N 267 THR cc_start: 0.9214 (m) cc_final: 0.8890 (p) REVERT: N 302 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6612 (mp0) REVERT: N 418 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7195 (mt-10) REVERT: N 431 ASN cc_start: 0.8464 (t0) cc_final: 0.7939 (p0) REVERT: O 242 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: O 280 GLU cc_start: 0.8097 (tt0) cc_final: 0.7046 (tm-30) REVERT: O 302 GLU cc_start: 0.7768 (mp0) cc_final: 0.7261 (mp0) REVERT: O 376 LYS cc_start: 0.8539 (tptp) cc_final: 0.8203 (tppp) REVERT: O 377 MET cc_start: 0.8276 (tpp) cc_final: 0.7824 (mmm) REVERT: O 409 MET cc_start: 0.8742 (tpt) cc_final: 0.8484 (tpp) REVERT: O 410 LYS cc_start: 0.8570 (tptt) cc_final: 0.8196 (tptt) REVERT: O 418 GLU cc_start: 0.8570 (mm-30) cc_final: 0.6498 (mt-10) REVERT: O 431 ASN cc_start: 0.7293 (p0) cc_final: 0.6279 (p0) REVERT: P 246 GLN cc_start: 0.9321 (pt0) cc_final: 0.9038 (pt0) REVERT: P 302 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6969 (mp0) REVERT: P 376 LYS cc_start: 0.8279 (tppt) cc_final: 0.7870 (tptp) REVERT: P 410 LYS cc_start: 0.9324 (tptp) cc_final: 0.8930 (tptt) REVERT: P 418 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7813 (mt-10) REVERT: P 431 ASN cc_start: 0.8404 (t0) cc_final: 0.8111 (p0) REVERT: Q 246 GLN cc_start: 0.9229 (pt0) cc_final: 0.9016 (pt0) REVERT: Q 267 THR cc_start: 0.9198 (m) cc_final: 0.8951 (p) REVERT: Q 377 MET cc_start: 0.8436 (tpt) cc_final: 0.8148 (tpt) REVERT: Q 418 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7406 (mm-30) REVERT: R 246 GLN cc_start: 0.9298 (pt0) cc_final: 0.9029 (pt0) REVERT: R 267 THR cc_start: 0.9095 (m) cc_final: 0.8785 (p) REVERT: R 431 ASN cc_start: 0.8441 (t0) cc_final: 0.8075 (p0) REVERT: S 242 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: S 246 GLN cc_start: 0.9132 (pt0) cc_final: 0.8887 (pt0) REVERT: S 253 LEU cc_start: 0.8794 (mt) cc_final: 0.8450 (mt) REVERT: T 267 THR cc_start: 0.9062 (m) cc_final: 0.8762 (p) REVERT: T 376 LYS cc_start: 0.8576 (tptp) cc_final: 0.8184 (tppp) REVERT: T 418 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8041 (mt-10) REVERT: U 242 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: U 267 THR cc_start: 0.9191 (m) cc_final: 0.8985 (p) REVERT: U 280 GLU cc_start: 0.7768 (tt0) cc_final: 0.7455 (tm-30) REVERT: U 370 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7505 (ttp80) REVERT: U 376 LYS cc_start: 0.8428 (tppt) cc_final: 0.8062 (tptp) REVERT: U 418 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7466 (mm-30) REVERT: V 246 GLN cc_start: 0.9103 (pt0) cc_final: 0.8660 (pm20) REVERT: V 267 THR cc_start: 0.9108 (m) cc_final: 0.8805 (p) REVERT: V 410 LYS cc_start: 0.8864 (tptt) cc_final: 0.8369 (tptt) REVERT: V 418 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7790 (mm-30) REVERT: V 422 PHE cc_start: 0.8303 (t80) cc_final: 0.7585 (t80) REVERT: V 431 ASN cc_start: 0.8278 (t0) cc_final: 0.7946 (p0) REVERT: W 242 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: W 302 GLU cc_start: 0.7319 (tt0) cc_final: 0.6898 (mp0) REVERT: W 376 LYS cc_start: 0.8418 (tptp) cc_final: 0.8136 (tppp) REVERT: W 418 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7723 (mt-10) REVERT: W 431 ASN cc_start: 0.8465 (t0) cc_final: 0.8073 (p0) REVERT: X 242 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: X 267 THR cc_start: 0.9195 (m) cc_final: 0.8903 (p) REVERT: X 302 GLU cc_start: 0.7484 (tt0) cc_final: 0.7141 (mp0) REVERT: X 370 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7143 (ttm-80) REVERT: X 376 LYS cc_start: 0.8473 (tptp) cc_final: 0.8171 (tppp) REVERT: X 410 LYS cc_start: 0.8905 (tptt) cc_final: 0.8699 (tptt) REVERT: X 418 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7872 (mt-10) REVERT: Y 242 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: Y 267 THR cc_start: 0.9248 (m) cc_final: 0.9028 (p) REVERT: Y 281 HIS cc_start: 0.7688 (t70) cc_final: 0.7400 (t70) REVERT: Y 302 GLU cc_start: 0.7712 (mp0) cc_final: 0.7239 (mp0) REVERT: Y 409 MET cc_start: 0.8142 (tpp) cc_final: 0.7929 (tpt) REVERT: Z 242 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: Z 246 GLN cc_start: 0.9166 (pt0) cc_final: 0.8876 (pt0) REVERT: Z 376 LYS cc_start: 0.8432 (tptp) cc_final: 0.8120 (tppp) REVERT: Z 377 MET cc_start: 0.8297 (mmm) cc_final: 0.7857 (mmm) REVERT: a 242 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: a 267 THR cc_start: 0.9148 (m) cc_final: 0.8919 (p) REVERT: a 302 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6722 (mp0) REVERT: a 422 PHE cc_start: 0.8574 (t80) cc_final: 0.7893 (t80) REVERT: b 267 THR cc_start: 0.9113 (m) cc_final: 0.8754 (p) REVERT: b 376 LYS cc_start: 0.8506 (tptp) cc_final: 0.8187 (tppp) REVERT: b 418 GLU cc_start: 0.8615 (mm-30) cc_final: 0.6586 (mt-10) REVERT: c 242 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: c 267 THR cc_start: 0.9126 (m) cc_final: 0.8887 (p) REVERT: c 270 LEU cc_start: 0.9529 (mm) cc_final: 0.9317 (mm) REVERT: c 281 HIS cc_start: 0.7582 (t70) cc_final: 0.7258 (t70) REVERT: c 431 ASN cc_start: 0.8384 (t0) cc_final: 0.7691 (p0) REVERT: d 267 THR cc_start: 0.9167 (m) cc_final: 0.8842 (p) REVERT: d 280 GLU cc_start: 0.7983 (tt0) cc_final: 0.7211 (tm-30) REVERT: d 394 LYS cc_start: 0.6897 (ptpt) cc_final: 0.6660 (pttm) REVERT: d 402 LEU cc_start: 0.8905 (tp) cc_final: 0.8557 (tp) REVERT: d 418 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7402 (mm-30) REVERT: d 422 PHE cc_start: 0.8475 (t80) cc_final: 0.7734 (t80) REVERT: e 242 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: e 267 THR cc_start: 0.9217 (m) cc_final: 0.8889 (p) REVERT: e 302 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6686 (mp0) REVERT: e 418 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7752 (mt-10) REVERT: e 431 ASN cc_start: 0.8480 (t0) cc_final: 0.7987 (p0) REVERT: f 232 ASP cc_start: 0.8473 (m-30) cc_final: 0.8101 (m-30) REVERT: f 242 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: f 376 LYS cc_start: 0.8556 (tptp) cc_final: 0.8201 (tppp) REVERT: f 377 MET cc_start: 0.8547 (mmm) cc_final: 0.8180 (mmm) REVERT: g 246 GLN cc_start: 0.9320 (pt0) cc_final: 0.9023 (pt0) REVERT: g 267 THR cc_start: 0.9130 (m) cc_final: 0.8898 (p) REVERT: g 302 GLU cc_start: 0.7526 (mp0) cc_final: 0.7098 (mp0) REVERT: g 418 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7279 (mm-30) REVERT: g 431 ASN cc_start: 0.8476 (t0) cc_final: 0.8066 (p0) REVERT: h 246 GLN cc_start: 0.9240 (pt0) cc_final: 0.9009 (pt0) REVERT: h 267 THR cc_start: 0.9178 (m) cc_final: 0.8928 (p) REVERT: h 302 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (mp0) REVERT: h 377 MET cc_start: 0.8447 (tpt) cc_final: 0.8148 (tpt) REVERT: h 418 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7735 (mt-10) outliers start: 83 outliers final: 22 residues processed: 1163 average time/residue: 0.2704 time to fit residues: 500.5686 Evaluate side-chains 1100 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 1059 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 382 ILE Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 413 GLU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 408 GLN Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 179 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 474 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 493 optimal weight: 0.6980 chunk 490 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 432 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 431 ASN ** O 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 431 ASN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 431 ASN ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.202753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.157146 restraints weight = 85824.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.160348 restraints weight = 52393.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.160142 restraints weight = 36130.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.160566 restraints weight = 34035.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.160641 restraints weight = 29575.769| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43146 Z= 0.126 Angle : 0.631 9.893 58174 Z= 0.313 Chirality : 0.041 0.188 6698 Planarity : 0.003 0.050 7786 Dihedral : 4.355 30.576 5852 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 1.54 % Allowed : 25.93 % Favored : 72.53 % 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: 0.43 (0.12), residues: 5202 helix: 2.74 (0.14), residues: 1428 sheet: -0.33 (0.11), residues: 2516 loop : -1.13 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 417 TYR 0.006 0.001 TYR c 393 PHE 0.034 0.002 PHE Z 422 HIS 0.004 0.000 HIS e 281 Details of bonding type rmsd covalent geometry : bond 0.00290 (43146) covalent geometry : angle 0.63080 (58174) hydrogen bonds : bond 0.02841 ( 2043) hydrogen bonds : angle 4.02465 ( 5718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1115 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.7539 (tt0) cc_final: 0.6995 (tm-30) REVERT: B 242 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6617 (mt-10) REVERT: B 246 GLN cc_start: 0.9129 (pt0) cc_final: 0.8819 (pm20) REVERT: B 302 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7046 (mp0) REVERT: C 242 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: C 246 GLN cc_start: 0.9109 (pt0) cc_final: 0.8873 (pt0) REVERT: C 280 GLU cc_start: 0.7689 (tt0) cc_final: 0.7385 (tt0) REVERT: C 410 LYS cc_start: 0.8853 (tptt) cc_final: 0.8555 (tptt) REVERT: C 418 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7964 (mt-10) REVERT: C 422 PHE cc_start: 0.8350 (t80) cc_final: 0.7578 (t80) REVERT: D 242 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: D 377 MET cc_start: 0.8123 (mmm) cc_final: 0.7681 (tpt) REVERT: D 422 PHE cc_start: 0.8226 (t80) cc_final: 0.7523 (t80) REVERT: E 267 THR cc_start: 0.9121 (m) cc_final: 0.8912 (p) REVERT: E 422 PHE cc_start: 0.7973 (t80) cc_final: 0.7557 (t80) REVERT: E 425 LYS cc_start: 0.9556 (mtmm) cc_final: 0.9215 (mtmm) REVERT: F 242 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: F 376 LYS cc_start: 0.8543 (tptp) cc_final: 0.8342 (tppp) REVERT: F 377 MET cc_start: 0.8246 (tpt) cc_final: 0.7800 (tpt) REVERT: F 412 ILE cc_start: 0.9425 (mm) cc_final: 0.9030 (mt) REVERT: F 418 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7802 (mt-10) REVERT: F 422 PHE cc_start: 0.8248 (t80) cc_final: 0.8021 (t80) REVERT: G 232 ASP cc_start: 0.8168 (m-30) cc_final: 0.7830 (m-30) REVERT: G 242 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: G 267 THR cc_start: 0.9217 (m) cc_final: 0.8971 (p) REVERT: G 376 LYS cc_start: 0.8564 (tptp) cc_final: 0.8361 (tppp) REVERT: G 418 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7062 (mm-30) REVERT: H 242 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: H 281 HIS cc_start: 0.7667 (t70) cc_final: 0.7428 (t70) REVERT: H 418 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7934 (mt-10) REVERT: I 246 GLN cc_start: 0.9249 (pt0) cc_final: 0.8834 (pt0) REVERT: I 376 LYS cc_start: 0.8568 (tptp) cc_final: 0.8300 (tppp) REVERT: I 377 MET cc_start: 0.8023 (mmm) cc_final: 0.7743 (mmm) REVERT: I 420 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8496 (ptm) REVERT: I 425 LYS cc_start: 0.9527 (mtmm) cc_final: 0.9130 (mtmt) REVERT: J 242 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: J 283 SER cc_start: 0.8967 (m) cc_final: 0.8580 (p) REVERT: J 302 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7034 (mp0) REVERT: K 242 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: K 283 SER cc_start: 0.9033 (m) cc_final: 0.8805 (p) REVERT: K 376 LYS cc_start: 0.8653 (tptp) cc_final: 0.8383 (tppp) REVERT: L 242 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: L 281 HIS cc_start: 0.7504 (t70) cc_final: 0.7252 (t70) REVERT: M 242 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: M 280 GLU cc_start: 0.7770 (tt0) cc_final: 0.7346 (tm-30) REVERT: M 394 LYS cc_start: 0.6748 (ptpt) cc_final: 0.6537 (pttm) REVERT: M 402 LEU cc_start: 0.8569 (tp) cc_final: 0.8294 (tp) REVERT: M 418 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7498 (mm-30) REVERT: N 242 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: N 267 THR cc_start: 0.9210 (m) cc_final: 0.8972 (p) REVERT: N 302 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6944 (mp0) REVERT: N 431 ASN cc_start: 0.8390 (t0) cc_final: 0.8166 (p0) REVERT: O 242 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: O 280 GLU cc_start: 0.7733 (tt0) cc_final: 0.7216 (tm-30) REVERT: O 376 LYS cc_start: 0.8635 (tptp) cc_final: 0.8331 (tppp) REVERT: O 410 LYS cc_start: 0.8725 (tptt) cc_final: 0.8449 (tptt) REVERT: O 418 GLU cc_start: 0.8497 (mm-30) cc_final: 0.6865 (mm-30) REVERT: P 246 GLN cc_start: 0.9336 (pt0) cc_final: 0.9062 (pt0) REVERT: P 376 LYS cc_start: 0.8371 (tppt) cc_final: 0.7976 (tptp) REVERT: P 383 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8196 (mp0) REVERT: P 410 LYS cc_start: 0.9258 (tptp) cc_final: 0.9003 (tptt) REVERT: P 418 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7735 (mt-10) REVERT: Q 246 GLN cc_start: 0.9221 (pt0) cc_final: 0.9004 (pt0) REVERT: Q 377 MET cc_start: 0.8266 (tpt) cc_final: 0.8038 (tpt) REVERT: R 246 GLN cc_start: 0.9320 (pt0) cc_final: 0.9051 (pt0) REVERT: R 280 GLU cc_start: 0.7552 (tt0) cc_final: 0.7003 (tm-30) REVERT: R 410 LYS cc_start: 0.8414 (tptt) cc_final: 0.8212 (tptt) REVERT: S 242 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6768 (mt-10) REVERT: S 302 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7048 (mp0) REVERT: T 376 LYS cc_start: 0.8628 (tptp) cc_final: 0.8329 (tppp) REVERT: T 418 GLU cc_start: 0.8394 (mm-30) cc_final: 0.6965 (mm-30) REVERT: U 242 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: U 394 LYS cc_start: 0.7386 (pttm) cc_final: 0.7077 (pttm) REVERT: U 418 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7336 (mm-30) REVERT: V 246 GLN cc_start: 0.9162 (pt0) cc_final: 0.8926 (pt0) REVERT: V 267 THR cc_start: 0.9079 (m) cc_final: 0.8846 (p) REVERT: V 280 GLU cc_start: 0.7606 (tt0) cc_final: 0.6891 (tm-30) REVERT: V 302 GLU cc_start: 0.7710 (mp0) cc_final: 0.7341 (mp0) REVERT: V 410 LYS cc_start: 0.8757 (tptt) cc_final: 0.8365 (tptt) REVERT: V 413 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8336 (tm-30) REVERT: V 425 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9165 (mtmm) REVERT: W 242 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: W 376 LYS cc_start: 0.8566 (tptp) cc_final: 0.8350 (tppp) REVERT: W 377 MET cc_start: 0.8282 (tpt) cc_final: 0.7811 (tpt) REVERT: W 418 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7931 (mt-10) REVERT: W 422 PHE cc_start: 0.8367 (t80) cc_final: 0.8057 (t80) REVERT: X 242 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: X 267 THR cc_start: 0.9214 (m) cc_final: 0.8990 (p) REVERT: X 376 LYS cc_start: 0.8568 (tptp) cc_final: 0.8360 (tppp) REVERT: X 418 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8092 (mt-10) REVERT: Y 242 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: Y 281 HIS cc_start: 0.7674 (t70) cc_final: 0.7441 (t70) REVERT: Y 418 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7715 (mt-10) REVERT: Z 242 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: Z 376 LYS cc_start: 0.8571 (tptp) cc_final: 0.8291 (tppp) REVERT: Z 377 MET cc_start: 0.8025 (mmm) cc_final: 0.7736 (mmm) REVERT: Z 425 LYS cc_start: 0.9468 (mtmm) cc_final: 0.9103 (mtmt) REVERT: a 242 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: a 283 SER cc_start: 0.8973 (m) cc_final: 0.8588 (p) REVERT: a 302 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7053 (mp0) REVERT: a 410 LYS cc_start: 0.8740 (tptt) cc_final: 0.8218 (tptt) REVERT: b 242 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: b 246 GLN cc_start: 0.9182 (pt0) cc_final: 0.8882 (pm20) REVERT: b 376 LYS cc_start: 0.8673 (tptp) cc_final: 0.8410 (tppp) REVERT: b 410 LYS cc_start: 0.8792 (tptt) cc_final: 0.8263 (tptt) REVERT: b 418 GLU cc_start: 0.8612 (mm-30) cc_final: 0.6861 (mt-10) REVERT: c 242 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: c 281 HIS cc_start: 0.7472 (t70) cc_final: 0.7188 (t70) REVERT: c 431 ASN cc_start: 0.8178 (t0) cc_final: 0.7830 (p0) REVERT: d 242 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: d 280 GLU cc_start: 0.7734 (tt0) cc_final: 0.7309 (tm-30) REVERT: d 402 LEU cc_start: 0.8664 (tp) cc_final: 0.8445 (tp) REVERT: d 418 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7486 (mm-30) REVERT: e 242 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: e 267 THR cc_start: 0.9213 (m) cc_final: 0.8979 (p) REVERT: e 302 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6963 (mp0) REVERT: f 232 ASP cc_start: 0.8316 (m-30) cc_final: 0.7946 (m-30) REVERT: f 242 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: f 302 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7105 (mp0) REVERT: f 376 LYS cc_start: 0.8647 (tptp) cc_final: 0.8324 (tppp) REVERT: f 377 MET cc_start: 0.8226 (mmm) cc_final: 0.8008 (mmm) REVERT: f 414 ASP cc_start: 0.8599 (t0) cc_final: 0.8395 (t0) REVERT: f 428 ASP cc_start: 0.7637 (m-30) cc_final: 0.6829 (m-30) REVERT: g 246 GLN cc_start: 0.9347 (pt0) cc_final: 0.9057 (pt0) REVERT: g 409 MET cc_start: 0.7983 (tpp) cc_final: 0.7729 (tpt) REVERT: g 412 ILE cc_start: 0.9423 (mm) cc_final: 0.9118 (mt) REVERT: g 418 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7503 (mt-10) REVERT: g 431 ASN cc_start: 0.8093 (t0) cc_final: 0.6538 (t0) REVERT: h 246 GLN cc_start: 0.9234 (pt0) cc_final: 0.9013 (pt0) REVERT: h 377 MET cc_start: 0.8298 (tpt) cc_final: 0.8062 (tpt) REVERT: h 431 ASN cc_start: 0.7608 (p0) cc_final: 0.6211 (p0) outliers start: 74 outliers final: 19 residues processed: 1147 average time/residue: 0.2703 time to fit residues: 495.3353 Evaluate side-chains 1032 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 988 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 408 GLN Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 253 LEU Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 44 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 447 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 405 optimal weight: 0.0570 chunk 456 optimal weight: 4.9990 chunk 428 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 455 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 425 optimal weight: 3.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 411 GLN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 408 GLN ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.202583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.156847 restraints weight = 86427.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.159909 restraints weight = 52896.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.159374 restraints weight = 41483.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.159805 restraints weight = 43105.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.160022 restraints weight = 32352.666| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 43146 Z= 0.135 Angle : 0.662 11.457 58174 Z= 0.328 Chirality : 0.041 0.254 6698 Planarity : 0.003 0.048 7786 Dihedral : 4.404 28.073 5852 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.40 % Allowed : 26.93 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.12), residues: 5202 helix: 2.58 (0.14), residues: 1428 sheet: -0.24 (0.11), residues: 2516 loop : -1.00 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 417 TYR 0.006 0.001 TYR V 366 PHE 0.029 0.002 PHE Z 422 HIS 0.003 0.000 HIS e 281 Details of bonding type rmsd covalent geometry : bond 0.00317 (43146) covalent geometry : angle 0.66234 (58174) hydrogen bonds : bond 0.02902 ( 2043) hydrogen bonds : angle 4.07941 ( 5718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 1059 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.9184 (pt0) cc_final: 0.8761 (pm20) REVERT: A 280 GLU cc_start: 0.7725 (tt0) cc_final: 0.6853 (tm-30) REVERT: A 418 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 242 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: B 302 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6848 (mp0) REVERT: C 246 GLN cc_start: 0.9077 (pt0) cc_final: 0.8822 (pt0) REVERT: C 280 GLU cc_start: 0.7826 (tt0) cc_final: 0.7450 (tt0) REVERT: C 410 LYS cc_start: 0.8777 (tptt) cc_final: 0.8426 (tptt) REVERT: C 418 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7866 (mt-10) REVERT: D 242 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: D 280 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: D 283 SER cc_start: 0.8931 (m) cc_final: 0.8528 (p) REVERT: E 267 THR cc_start: 0.9159 (m) cc_final: 0.8860 (p) REVERT: E 410 LYS cc_start: 0.8659 (tptp) cc_final: 0.8359 (tptt) REVERT: E 425 LYS cc_start: 0.9507 (mtmm) cc_final: 0.9185 (mtmt) REVERT: F 242 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: F 376 LYS cc_start: 0.8491 (tptp) cc_final: 0.8221 (tppp) REVERT: F 377 MET cc_start: 0.8523 (tpt) cc_final: 0.7945 (tpt) REVERT: F 412 ILE cc_start: 0.9383 (mm) cc_final: 0.8994 (mt) REVERT: F 418 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7563 (mt-10) REVERT: F 422 PHE cc_start: 0.8420 (t80) cc_final: 0.8192 (t80) REVERT: G 242 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: G 267 THR cc_start: 0.9197 (m) cc_final: 0.8887 (p) REVERT: G 376 LYS cc_start: 0.8481 (tptp) cc_final: 0.8231 (tppp) REVERT: G 418 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7885 (mt-10) REVERT: H 242 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: H 281 HIS cc_start: 0.7709 (t70) cc_final: 0.7452 (t70) REVERT: H 376 LYS cc_start: 0.8516 (tptp) cc_final: 0.8038 (tppp) REVERT: I 246 GLN cc_start: 0.9167 (pt0) cc_final: 0.8922 (pt0) REVERT: I 376 LYS cc_start: 0.8441 (tptp) cc_final: 0.8125 (tppp) REVERT: I 377 MET cc_start: 0.8285 (mmm) cc_final: 0.7901 (mmm) REVERT: I 420 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8510 (ptm) REVERT: I 422 PHE cc_start: 0.8191 (t80) cc_final: 0.7851 (t80) REVERT: I 425 LYS cc_start: 0.9563 (mtmm) cc_final: 0.9202 (mtmt) REVERT: J 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: J 246 GLN cc_start: 0.9160 (pt0) cc_final: 0.8881 (pt0) REVERT: J 283 SER cc_start: 0.9037 (m) cc_final: 0.8584 (p) REVERT: J 302 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6782 (mp0) REVERT: K 242 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: K 246 GLN cc_start: 0.9122 (pt0) cc_final: 0.8840 (pm20) REVERT: K 283 SER cc_start: 0.9116 (m) cc_final: 0.8818 (p) REVERT: K 376 LYS cc_start: 0.8583 (tptp) cc_final: 0.8244 (tppp) REVERT: K 377 MET cc_start: 0.8567 (mmm) cc_final: 0.8221 (mmm) REVERT: L 242 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: L 281 HIS cc_start: 0.7638 (t70) cc_final: 0.7351 (t70) REVERT: M 394 LYS cc_start: 0.7074 (ptpt) cc_final: 0.6803 (pttm) REVERT: M 402 LEU cc_start: 0.8914 (tp) cc_final: 0.8601 (tp) REVERT: M 418 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7395 (mm-30) REVERT: N 240 ASP cc_start: 0.9213 (t0) cc_final: 0.8927 (t0) REVERT: N 242 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: N 267 THR cc_start: 0.9230 (m) cc_final: 0.8923 (p) REVERT: N 302 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6641 (mp0) REVERT: N 418 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7923 (mm-30) REVERT: N 431 ASN cc_start: 0.8398 (t0) cc_final: 0.8067 (p0) REVERT: O 242 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: O 280 GLU cc_start: 0.7898 (tt0) cc_final: 0.7055 (tm-30) REVERT: O 377 MET cc_start: 0.8512 (mmm) cc_final: 0.7993 (tpp) REVERT: O 418 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7923 (mt-10) REVERT: O 425 LYS cc_start: 0.9420 (ttpp) cc_final: 0.9047 (ptpp) REVERT: P 246 GLN cc_start: 0.9325 (pt0) cc_final: 0.9020 (pt0) REVERT: P 376 LYS cc_start: 0.8304 (tppt) cc_final: 0.7806 (tptp) REVERT: P 383 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8107 (mp0) REVERT: P 418 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7623 (mt-10) REVERT: Q 246 GLN cc_start: 0.9162 (pt0) cc_final: 0.8894 (pt0) REVERT: Q 376 LYS cc_start: 0.8479 (tptp) cc_final: 0.8246 (tptp) REVERT: Q 377 MET cc_start: 0.8466 (tpt) cc_final: 0.8121 (tpt) REVERT: Q 418 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7826 (mt-10) REVERT: R 246 GLN cc_start: 0.9285 (pt0) cc_final: 0.9009 (pt0) REVERT: R 280 GLU cc_start: 0.7726 (tt0) cc_final: 0.6859 (tm-30) REVERT: R 418 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7982 (mm-30) REVERT: S 230 LEU cc_start: 0.9284 (pt) cc_final: 0.9083 (pp) REVERT: S 242 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: S 246 GLN cc_start: 0.9119 (pt0) cc_final: 0.8712 (pm20) REVERT: S 253 LEU cc_start: 0.8788 (mt) cc_final: 0.8338 (mt) REVERT: S 302 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6789 (mp0) REVERT: T 246 GLN cc_start: 0.9108 (pt0) cc_final: 0.8825 (pt0) REVERT: T 376 LYS cc_start: 0.8532 (tptp) cc_final: 0.8124 (tppp) REVERT: T 418 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7821 (mt-10) REVERT: T 422 PHE cc_start: 0.8228 (t80) cc_final: 0.7462 (t80) REVERT: U 242 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: U 280 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: U 283 SER cc_start: 0.8931 (m) cc_final: 0.8531 (p) REVERT: U 377 MET cc_start: 0.8513 (mmm) cc_final: 0.7907 (tpt) REVERT: U 394 LYS cc_start: 0.7679 (pttm) cc_final: 0.7347 (pttm) REVERT: U 418 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8001 (mt-10) REVERT: U 422 PHE cc_start: 0.8330 (t80) cc_final: 0.7751 (t80) REVERT: V 246 GLN cc_start: 0.9189 (pt0) cc_final: 0.8974 (pt0) REVERT: V 267 THR cc_start: 0.9079 (m) cc_final: 0.8779 (p) REVERT: V 280 GLU cc_start: 0.7598 (tt0) cc_final: 0.6839 (tm-30) REVERT: V 410 LYS cc_start: 0.8766 (tptt) cc_final: 0.8394 (tptt) REVERT: V 413 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8522 (tm-30) REVERT: V 425 LYS cc_start: 0.9525 (mtmm) cc_final: 0.9263 (mtmt) REVERT: W 242 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: W 376 LYS cc_start: 0.8485 (tptp) cc_final: 0.8218 (tppp) REVERT: W 377 MET cc_start: 0.8550 (tpt) cc_final: 0.7963 (tpt) REVERT: W 414 ASP cc_start: 0.8578 (t0) cc_final: 0.8134 (t0) REVERT: W 418 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7663 (mt-10) REVERT: W 428 ASP cc_start: 0.7747 (m-30) cc_final: 0.6900 (m-30) REVERT: X 242 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: X 246 GLN cc_start: 0.9146 (pt0) cc_final: 0.8806 (pt0) REVERT: X 267 THR cc_start: 0.9221 (m) cc_final: 0.8949 (p) REVERT: X 376 LYS cc_start: 0.8491 (tptp) cc_final: 0.8220 (tppp) REVERT: X 410 LYS cc_start: 0.8833 (tptt) cc_final: 0.8598 (tptt) REVERT: X 418 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7911 (mt-10) REVERT: Y 242 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: Y 281 HIS cc_start: 0.7696 (t70) cc_final: 0.7442 (t70) REVERT: Z 242 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: Z 376 LYS cc_start: 0.8439 (tptp) cc_final: 0.8118 (tppp) REVERT: Z 377 MET cc_start: 0.8283 (mmm) cc_final: 0.7898 (mmm) REVERT: Z 425 LYS cc_start: 0.9561 (mtmm) cc_final: 0.9174 (mtmt) REVERT: a 242 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: a 246 GLN cc_start: 0.9179 (pt0) cc_final: 0.8726 (pt0) REVERT: a 283 SER cc_start: 0.9045 (m) cc_final: 0.8596 (p) REVERT: a 302 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6780 (mp0) REVERT: b 242 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: b 376 LYS cc_start: 0.8617 (tptp) cc_final: 0.8267 (tppp) REVERT: b 418 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7414 (mm-30) REVERT: c 242 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: c 281 HIS cc_start: 0.7618 (t70) cc_final: 0.7295 (t70) REVERT: c 431 ASN cc_start: 0.8312 (t0) cc_final: 0.7995 (p0) REVERT: d 418 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7794 (mt-10) REVERT: e 240 ASP cc_start: 0.9219 (t0) cc_final: 0.8920 (t0) REVERT: e 242 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: e 267 THR cc_start: 0.9237 (m) cc_final: 0.8935 (p) REVERT: e 280 GLU cc_start: 0.7864 (tt0) cc_final: 0.7295 (mp0) REVERT: e 281 HIS cc_start: 0.7672 (t70) cc_final: 0.7404 (t70) REVERT: e 302 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6659 (mp0) REVERT: f 232 ASP cc_start: 0.8435 (m-30) cc_final: 0.8056 (m-30) REVERT: f 240 ASP cc_start: 0.9073 (t0) cc_final: 0.8850 (t0) REVERT: f 242 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: f 302 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6838 (mp0) REVERT: f 376 LYS cc_start: 0.8570 (tptp) cc_final: 0.8201 (tppp) REVERT: f 377 MET cc_start: 0.8507 (mmm) cc_final: 0.8133 (mmm) REVERT: f 414 ASP cc_start: 0.8679 (t0) cc_final: 0.8442 (t0) REVERT: f 425 LYS cc_start: 0.9424 (ttpp) cc_final: 0.8952 (ptpp) REVERT: g 246 GLN cc_start: 0.9330 (pt0) cc_final: 0.9020 (pt0) REVERT: g 409 MET cc_start: 0.8301 (tpp) cc_final: 0.8062 (tpt) REVERT: g 412 ILE cc_start: 0.9335 (mm) cc_final: 0.9050 (mt) REVERT: g 418 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7739 (mt-10) REVERT: g 431 ASN cc_start: 0.8248 (t0) cc_final: 0.7911 (m-40) REVERT: h 246 GLN cc_start: 0.9174 (pt0) cc_final: 0.8947 (pt0) REVERT: h 376 LYS cc_start: 0.8473 (tptp) cc_final: 0.8237 (tptp) REVERT: h 377 MET cc_start: 0.8475 (tpt) cc_final: 0.8128 (tpt) REVERT: h 418 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8202 (mm-30) outliers start: 67 outliers final: 19 residues processed: 1082 average time/residue: 0.2857 time to fit residues: 490.6592 Evaluate side-chains 1036 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 993 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 280 GLU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 413 GLU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 243 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 303 optimal weight: 7.9990 chunk 450 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 354 optimal weight: 5.9990 chunk 465 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 239 ASN ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.202101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.156376 restraints weight = 86017.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.159794 restraints weight = 51484.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.159315 restraints weight = 37667.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.159653 restraints weight = 34176.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.159706 restraints weight = 30474.610| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43146 Z= 0.142 Angle : 0.678 11.039 58174 Z= 0.336 Chirality : 0.041 0.235 6698 Planarity : 0.004 0.048 7786 Dihedral : 4.399 15.763 5848 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.44 % Allowed : 27.60 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.12), residues: 5202 helix: 2.48 (0.14), residues: 1428 sheet: -0.24 (0.11), residues: 2516 loop : -0.89 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 244 TYR 0.007 0.001 TYR d 393 PHE 0.037 0.002 PHE Z 422 HIS 0.004 0.001 HIS M 281 Details of bonding type rmsd covalent geometry : bond 0.00330 (43146) covalent geometry : angle 0.67848 (58174) hydrogen bonds : bond 0.02944 ( 2043) hydrogen bonds : angle 4.11787 ( 5718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1048 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.9271 (t0) cc_final: 0.9040 (t0) REVERT: A 246 GLN cc_start: 0.9225 (pt0) cc_final: 0.8824 (pm20) REVERT: A 280 GLU cc_start: 0.7762 (tt0) cc_final: 0.6850 (tm-30) REVERT: A 418 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 428 ASP cc_start: 0.7800 (m-30) cc_final: 0.7278 (m-30) REVERT: B 242 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: B 246 GLN cc_start: 0.9075 (pt0) cc_final: 0.8735 (pm20) REVERT: B 253 LEU cc_start: 0.8787 (mt) cc_final: 0.8454 (mt) REVERT: B 302 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6843 (mp0) REVERT: C 246 GLN cc_start: 0.9098 (pt0) cc_final: 0.8859 (pt0) REVERT: C 280 GLU cc_start: 0.7823 (tt0) cc_final: 0.7458 (tt0) REVERT: C 410 LYS cc_start: 0.8783 (tptt) cc_final: 0.8506 (tptt) REVERT: C 418 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7851 (mt-10) REVERT: D 242 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: D 280 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: D 377 MET cc_start: 0.8385 (mmm) cc_final: 0.7792 (tpt) REVERT: D 418 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7984 (tt0) REVERT: E 267 THR cc_start: 0.9122 (m) cc_final: 0.8813 (p) REVERT: E 410 LYS cc_start: 0.8650 (tptp) cc_final: 0.8323 (tptt) REVERT: F 242 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: F 376 LYS cc_start: 0.8509 (tptp) cc_final: 0.8234 (tppp) REVERT: F 377 MET cc_start: 0.8546 (tpt) cc_final: 0.7993 (tpt) REVERT: F 412 ILE cc_start: 0.9424 (mm) cc_final: 0.9064 (mt) REVERT: F 418 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7581 (mt-10) REVERT: F 422 PHE cc_start: 0.8459 (t80) cc_final: 0.8235 (t80) REVERT: G 242 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: G 267 THR cc_start: 0.9209 (m) cc_final: 0.8912 (p) REVERT: G 376 LYS cc_start: 0.8453 (tptp) cc_final: 0.8202 (tppp) REVERT: G 418 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7641 (mt-10) REVERT: H 242 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: H 281 HIS cc_start: 0.7737 (t70) cc_final: 0.7481 (t70) REVERT: H 418 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7732 (mt-10) REVERT: I 246 GLN cc_start: 0.9218 (pt0) cc_final: 0.8824 (pt0) REVERT: I 376 LYS cc_start: 0.8470 (tptp) cc_final: 0.8158 (tppp) REVERT: I 377 MET cc_start: 0.8293 (mmm) cc_final: 0.7935 (mmm) REVERT: I 420 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8468 (ptm) REVERT: I 425 LYS cc_start: 0.9520 (mtmm) cc_final: 0.9184 (mtmt) REVERT: J 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: J 246 GLN cc_start: 0.9154 (pt0) cc_final: 0.8800 (pt0) REVERT: J 302 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6844 (mp0) REVERT: J 418 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7683 (tt0) REVERT: K 242 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: K 246 GLN cc_start: 0.9167 (pt0) cc_final: 0.8859 (pm20) REVERT: K 283 SER cc_start: 0.9109 (m) cc_final: 0.8794 (p) REVERT: L 242 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: L 281 HIS cc_start: 0.7700 (t70) cc_final: 0.7406 (t70) REVERT: M 242 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: M 394 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6953 (pttm) REVERT: M 402 LEU cc_start: 0.8926 (tp) cc_final: 0.8625 (tp) REVERT: M 418 GLU cc_start: 0.8501 (mm-30) cc_final: 0.6990 (mm-30) REVERT: N 242 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: N 267 THR cc_start: 0.9272 (m) cc_final: 0.8981 (p) REVERT: N 281 HIS cc_start: 0.7633 (t70) cc_final: 0.7374 (t70) REVERT: N 302 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6691 (mp0) REVERT: N 429 THR cc_start: 0.7099 (p) cc_final: 0.6874 (t) REVERT: N 431 ASN cc_start: 0.8384 (t0) cc_final: 0.8041 (p0) REVERT: O 242 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: O 280 GLU cc_start: 0.7868 (tt0) cc_final: 0.7118 (tm-30) REVERT: O 410 LYS cc_start: 0.8442 (tptp) cc_final: 0.8153 (tptt) REVERT: O 418 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8010 (mt-10) REVERT: O 425 LYS cc_start: 0.9438 (ttpp) cc_final: 0.9083 (ptpp) REVERT: P 246 GLN cc_start: 0.9331 (pt0) cc_final: 0.9014 (pt0) REVERT: P 376 LYS cc_start: 0.8321 (tppt) cc_final: 0.7879 (tptp) REVERT: P 418 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7822 (mt-10) REVERT: Q 246 GLN cc_start: 0.9183 (pt0) cc_final: 0.8907 (pt0) REVERT: Q 376 LYS cc_start: 0.8521 (tptp) cc_final: 0.8290 (tptp) REVERT: Q 377 MET cc_start: 0.8471 (tpt) cc_final: 0.8124 (tpt) REVERT: Q 418 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7800 (mt-10) REVERT: R 246 GLN cc_start: 0.9275 (pt0) cc_final: 0.8998 (pt0) REVERT: R 280 GLU cc_start: 0.7769 (tt0) cc_final: 0.6855 (tm-30) REVERT: R 410 LYS cc_start: 0.8776 (tptt) cc_final: 0.8547 (tptt) REVERT: S 242 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: S 246 GLN cc_start: 0.9109 (pt0) cc_final: 0.8714 (pm20) REVERT: S 253 LEU cc_start: 0.8771 (mt) cc_final: 0.8442 (mt) REVERT: S 302 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6818 (mp0) REVERT: T 246 GLN cc_start: 0.9095 (pt0) cc_final: 0.8803 (pt0) REVERT: T 376 LYS cc_start: 0.8566 (tptp) cc_final: 0.8127 (tppp) REVERT: T 418 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7637 (mt-10) REVERT: U 242 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: U 280 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: U 394 LYS cc_start: 0.7645 (pttm) cc_final: 0.7415 (pttm) REVERT: U 410 LYS cc_start: 0.9287 (tptp) cc_final: 0.9063 (tptt) REVERT: U 418 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8053 (mt-10) REVERT: V 246 GLN cc_start: 0.9203 (pt0) cc_final: 0.8967 (pt0) REVERT: V 267 THR cc_start: 0.9089 (m) cc_final: 0.8756 (p) REVERT: V 280 GLU cc_start: 0.7689 (tt0) cc_final: 0.6843 (tm-30) REVERT: V 410 LYS cc_start: 0.8760 (tptt) cc_final: 0.8418 (tptt) REVERT: V 413 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8509 (tm-30) REVERT: V 425 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9250 (mtmt) REVERT: W 242 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: W 376 LYS cc_start: 0.8502 (tptp) cc_final: 0.8251 (tppp) REVERT: W 377 MET cc_start: 0.8548 (tpt) cc_final: 0.7978 (tpt) REVERT: W 418 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7635 (mt-10) REVERT: X 232 ASP cc_start: 0.8421 (m-30) cc_final: 0.8098 (m-30) REVERT: X 240 ASP cc_start: 0.9273 (t0) cc_final: 0.9035 (t0) REVERT: X 242 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: X 246 GLN cc_start: 0.9082 (pt0) cc_final: 0.8796 (pt0) REVERT: X 267 THR cc_start: 0.9216 (m) cc_final: 0.8924 (p) REVERT: X 376 LYS cc_start: 0.8464 (tptp) cc_final: 0.8219 (tppp) REVERT: X 418 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7726 (mt-10) REVERT: Y 242 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: Y 281 HIS cc_start: 0.7734 (t70) cc_final: 0.7483 (t70) REVERT: Z 242 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: Z 376 LYS cc_start: 0.8472 (tptp) cc_final: 0.8154 (tppp) REVERT: Z 377 MET cc_start: 0.8296 (mmm) cc_final: 0.7941 (mmm) REVERT: Z 418 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8163 (tt0) REVERT: Z 425 LYS cc_start: 0.9515 (mtmm) cc_final: 0.9167 (mtmt) REVERT: Z 428 ASP cc_start: 0.7540 (m-30) cc_final: 0.6549 (m-30) REVERT: a 242 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: a 302 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6844 (mp0) REVERT: b 242 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: b 246 GLN cc_start: 0.9106 (pt0) cc_final: 0.8812 (pm20) REVERT: b 376 LYS cc_start: 0.8660 (tptp) cc_final: 0.8290 (tppp) REVERT: b 377 MET cc_start: 0.8553 (mmm) cc_final: 0.8221 (mmm) REVERT: b 413 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8567 (tm-30) REVERT: b 418 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7366 (mm-30) REVERT: c 242 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: c 250 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8294 (mt-10) REVERT: c 281 HIS cc_start: 0.7645 (t70) cc_final: 0.7300 (t70) REVERT: c 418 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7555 (mt-10) REVERT: c 425 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9165 (mtmt) REVERT: c 431 ASN cc_start: 0.8341 (t0) cc_final: 0.8078 (p0) REVERT: d 242 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: d 410 LYS cc_start: 0.8434 (tptt) cc_final: 0.8054 (tptt) REVERT: d 418 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7777 (mt-10) REVERT: e 242 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: e 267 THR cc_start: 0.9291 (m) cc_final: 0.9004 (p) REVERT: e 281 HIS cc_start: 0.7636 (t70) cc_final: 0.7388 (t70) REVERT: e 302 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6685 (mp0) REVERT: f 242 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: f 302 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6849 (mp0) REVERT: f 376 LYS cc_start: 0.8596 (tptp) cc_final: 0.8214 (tppp) REVERT: f 377 MET cc_start: 0.8487 (mmm) cc_final: 0.8112 (mmm) REVERT: f 425 LYS cc_start: 0.9414 (ttpp) cc_final: 0.9045 (ptpp) REVERT: g 246 GLN cc_start: 0.9345 (pt0) cc_final: 0.9007 (pt0) REVERT: g 412 ILE cc_start: 0.9306 (mm) cc_final: 0.9040 (mt) REVERT: g 418 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7790 (mt-10) REVERT: h 246 GLN cc_start: 0.9227 (pt0) cc_final: 0.8988 (pt0) REVERT: h 376 LYS cc_start: 0.8517 (tptp) cc_final: 0.8280 (tptp) REVERT: h 377 MET cc_start: 0.8472 (tpt) cc_final: 0.8122 (tpt) REVERT: h 418 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8119 (mm-30) outliers start: 69 outliers final: 26 residues processed: 1071 average time/residue: 0.2916 time to fit residues: 492.7655 Evaluate side-chains 1053 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 1001 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 413 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 280 GLU Chi-restraints excluded: chain V residue 415 LEU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 413 GLU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 413 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 343 optimal weight: 0.8980 chunk 498 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 440 optimal weight: 0.2980 chunk 389 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 486 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 GLN ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN Q 234 GLN ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 281 HIS ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 239 ASN ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 411 GLN ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.203499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.158169 restraints weight = 86229.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.161420 restraints weight = 50309.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.160954 restraints weight = 36126.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.161314 restraints weight = 33984.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.161378 restraints weight = 29161.726| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43146 Z= 0.125 Angle : 0.687 11.987 58174 Z= 0.338 Chirality : 0.042 0.419 6698 Planarity : 0.004 0.049 7786 Dihedral : 4.303 16.136 5848 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.11 % Allowed : 27.74 % Favored : 71.15 % 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: 0.55 (0.12), residues: 5202 helix: 2.38 (0.14), residues: 1428 sheet: -0.10 (0.11), residues: 2516 loop : -0.79 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 244 TYR 0.006 0.001 TYR A 393 PHE 0.033 0.001 PHE Z 422 HIS 0.008 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00294 (43146) covalent geometry : angle 0.68682 (58174) hydrogen bonds : bond 0.02862 ( 2043) hydrogen bonds : angle 4.06554 ( 5718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1083 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.9200 (pt0) cc_final: 0.8793 (pm20) REVERT: A 280 GLU cc_start: 0.7696 (tt0) cc_final: 0.6829 (tm-30) REVERT: A 383 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8195 (mp0) REVERT: B 242 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: B 246 GLN cc_start: 0.9012 (pt0) cc_final: 0.8708 (pm20) REVERT: C 246 GLN cc_start: 0.9085 (pt0) cc_final: 0.8854 (pt0) REVERT: C 280 GLU cc_start: 0.7788 (tt0) cc_final: 0.7404 (tt0) REVERT: C 410 LYS cc_start: 0.8862 (tptt) cc_final: 0.8433 (tptt) REVERT: C 418 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7802 (mt-10) REVERT: D 232 ASP cc_start: 0.8454 (m-30) cc_final: 0.8183 (m-30) REVERT: D 240 ASP cc_start: 0.9205 (t0) cc_final: 0.8954 (t0) REVERT: D 242 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: D 280 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: D 281 HIS cc_start: 0.7423 (t-90) cc_final: 0.6676 (t-90) REVERT: D 377 MET cc_start: 0.8402 (mmm) cc_final: 0.7895 (tpp) REVERT: D 418 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7802 (tt0) REVERT: D 428 ASP cc_start: 0.7614 (m-30) cc_final: 0.6684 (m-30) REVERT: E 267 THR cc_start: 0.9038 (m) cc_final: 0.8696 (p) REVERT: E 381 ASP cc_start: 0.8230 (m-30) cc_final: 0.7983 (m-30) REVERT: E 383 GLU cc_start: 0.8722 (tt0) cc_final: 0.8390 (pm20) REVERT: F 242 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: F 376 LYS cc_start: 0.8499 (tptp) cc_final: 0.8250 (tppp) REVERT: F 377 MET cc_start: 0.8588 (tpt) cc_final: 0.8020 (tpt) REVERT: F 383 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7895 (mt-10) REVERT: F 412 ILE cc_start: 0.9349 (mm) cc_final: 0.8927 (mt) REVERT: F 418 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7071 (mt-10) REVERT: F 422 PHE cc_start: 0.8467 (t80) cc_final: 0.8249 (t80) REVERT: G 242 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: G 246 GLN cc_start: 0.9103 (pt0) cc_final: 0.8748 (pt0) REVERT: G 267 THR cc_start: 0.9214 (m) cc_final: 0.8883 (p) REVERT: G 376 LYS cc_start: 0.8463 (tptp) cc_final: 0.8206 (tppp) REVERT: G 418 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7595 (mt-10) REVERT: G 431 ASN cc_start: 0.7115 (p0) cc_final: 0.6340 (p0) REVERT: H 242 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: H 281 HIS cc_start: 0.7726 (t70) cc_final: 0.7329 (t-90) REVERT: H 418 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7721 (mt-10) REVERT: I 376 LYS cc_start: 0.8429 (tptp) cc_final: 0.8154 (tppp) REVERT: I 377 MET cc_start: 0.8309 (mmm) cc_final: 0.7960 (mmm) REVERT: I 418 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7987 (tt0) REVERT: I 420 MET cc_start: 0.8641 (ttp) cc_final: 0.8301 (ptm) REVERT: I 422 PHE cc_start: 0.8150 (t80) cc_final: 0.7702 (t80) REVERT: I 425 LYS cc_start: 0.9519 (mtmm) cc_final: 0.9232 (mtmt) REVERT: I 428 ASP cc_start: 0.7598 (m-30) cc_final: 0.6612 (m-30) REVERT: J 234 GLN cc_start: 0.8619 (mt0) cc_final: 0.8311 (mt0) REVERT: J 242 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: J 246 GLN cc_start: 0.9145 (pt0) cc_final: 0.8819 (pt0) REVERT: J 418 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7718 (tt0) REVERT: K 242 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: K 246 GLN cc_start: 0.9168 (pt0) cc_final: 0.8881 (pm20) REVERT: K 283 SER cc_start: 0.9107 (m) cc_final: 0.8835 (p) REVERT: K 376 LYS cc_start: 0.8506 (tptp) cc_final: 0.8178 (tppp) REVERT: L 242 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: L 281 HIS cc_start: 0.7723 (t70) cc_final: 0.7364 (t70) REVERT: L 410 LYS cc_start: 0.8157 (tptt) cc_final: 0.7838 (tptt) REVERT: M 242 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: M 402 LEU cc_start: 0.8954 (tp) cc_final: 0.8744 (tp) REVERT: M 410 LYS cc_start: 0.8316 (tptt) cc_final: 0.7964 (tptt) REVERT: M 418 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7424 (mm-30) REVERT: M 425 LYS cc_start: 0.9549 (mtmm) cc_final: 0.9263 (mtmt) REVERT: N 240 ASP cc_start: 0.9229 (t0) cc_final: 0.8933 (t0) REVERT: N 242 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: N 267 THR cc_start: 0.9267 (m) cc_final: 0.8962 (p) REVERT: N 281 HIS cc_start: 0.7629 (t70) cc_final: 0.7393 (t70) REVERT: N 302 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6792 (mp0) REVERT: N 431 ASN cc_start: 0.8336 (t0) cc_final: 0.8045 (p0) REVERT: O 242 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: O 280 GLU cc_start: 0.7845 (tt0) cc_final: 0.7098 (mp0) REVERT: O 383 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8106 (mp0) REVERT: O 410 LYS cc_start: 0.8402 (tptp) cc_final: 0.7846 (tptt) REVERT: O 413 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8478 (tm-30) REVERT: O 418 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8138 (mt-10) REVERT: O 425 LYS cc_start: 0.9454 (ttpp) cc_final: 0.9061 (ptpp) REVERT: P 246 GLN cc_start: 0.9333 (pt0) cc_final: 0.8949 (pt0) REVERT: P 376 LYS cc_start: 0.8325 (tppt) cc_final: 0.7893 (tptp) REVERT: P 383 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8121 (mp0) REVERT: P 418 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7858 (mt-10) REVERT: Q 242 GLU cc_start: 0.7329 (mp0) cc_final: 0.7077 (pm20) REVERT: Q 246 GLN cc_start: 0.9153 (pt0) cc_final: 0.8837 (pt0) REVERT: Q 376 LYS cc_start: 0.8498 (tptp) cc_final: 0.8258 (tptp) REVERT: Q 377 MET cc_start: 0.8467 (tpt) cc_final: 0.8121 (tpt) REVERT: Q 418 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7747 (mt-10) REVERT: R 246 GLN cc_start: 0.9283 (pt0) cc_final: 0.9053 (pt0) REVERT: R 280 GLU cc_start: 0.7700 (tt0) cc_final: 0.6831 (tm-30) REVERT: R 410 LYS cc_start: 0.8769 (tptt) cc_final: 0.8514 (tptt) REVERT: S 242 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: S 246 GLN cc_start: 0.9055 (pt0) cc_final: 0.8714 (pm20) REVERT: S 383 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7947 (mp0) REVERT: T 246 GLN cc_start: 0.9112 (pt0) cc_final: 0.8874 (pt0) REVERT: T 409 MET cc_start: 0.8509 (mmt) cc_final: 0.8293 (tpt) REVERT: T 418 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7664 (mt-10) REVERT: T 425 LYS cc_start: 0.9494 (mtmm) cc_final: 0.9104 (mtmt) REVERT: U 242 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: U 280 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: U 281 HIS cc_start: 0.7391 (t-90) cc_final: 0.6652 (t-90) REVERT: U 394 LYS cc_start: 0.7667 (pttm) cc_final: 0.7432 (pttm) REVERT: U 418 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8122 (mt-10) REVERT: V 246 GLN cc_start: 0.9244 (pt0) cc_final: 0.8920 (pt0) REVERT: V 267 THR cc_start: 0.9058 (m) cc_final: 0.8718 (p) REVERT: V 280 GLU cc_start: 0.7587 (tt0) cc_final: 0.6870 (tm-30) REVERT: V 425 LYS cc_start: 0.9500 (mtmm) cc_final: 0.9255 (mtmt) REVERT: W 242 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: W 376 LYS cc_start: 0.8503 (tptp) cc_final: 0.8259 (tppp) REVERT: W 377 MET cc_start: 0.8584 (tpt) cc_final: 0.7994 (tpt) REVERT: W 383 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7880 (mt-10) REVERT: W 418 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7618 (mt-10) REVERT: X 242 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: X 246 GLN cc_start: 0.9074 (pt0) cc_final: 0.8788 (pt0) REVERT: X 267 THR cc_start: 0.9210 (m) cc_final: 0.8958 (p) REVERT: X 376 LYS cc_start: 0.8455 (tptp) cc_final: 0.8204 (tppp) REVERT: X 418 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7713 (mt-10) REVERT: Y 242 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: Y 281 HIS cc_start: 0.7709 (t70) cc_final: 0.7318 (t-90) REVERT: Z 242 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: Z 376 LYS cc_start: 0.8431 (tptp) cc_final: 0.8153 (tppp) REVERT: Z 377 MET cc_start: 0.8304 (mmm) cc_final: 0.7977 (mmm) REVERT: Z 418 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8255 (tt0) REVERT: Z 420 MET cc_start: 0.8983 (ttp) cc_final: 0.8551 (ptm) REVERT: Z 425 LYS cc_start: 0.9496 (mtmm) cc_final: 0.9164 (mtmt) REVERT: a 242 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: b 242 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: b 246 GLN cc_start: 0.9113 (pt0) cc_final: 0.8821 (pm20) REVERT: b 376 LYS cc_start: 0.8649 (tptp) cc_final: 0.8289 (tppp) REVERT: b 377 MET cc_start: 0.8534 (mmm) cc_final: 0.8233 (mmm) REVERT: b 413 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8600 (tm-30) REVERT: b 418 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7298 (mm-30) REVERT: c 242 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6752 (mt-10) REVERT: c 250 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8306 (mt-10) REVERT: c 281 HIS cc_start: 0.7661 (t70) cc_final: 0.7306 (t70) REVERT: c 381 ASP cc_start: 0.8153 (m-30) cc_final: 0.7859 (m-30) REVERT: c 418 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7428 (mt-10) REVERT: c 425 LYS cc_start: 0.9400 (mtmm) cc_final: 0.9132 (mtmt) REVERT: c 431 ASN cc_start: 0.8315 (t0) cc_final: 0.8083 (p0) REVERT: d 242 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: d 410 LYS cc_start: 0.8174 (tptt) cc_final: 0.7939 (tptt) REVERT: d 418 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7798 (mt-10) REVERT: d 425 LYS cc_start: 0.9470 (mtmm) cc_final: 0.9260 (mtmt) REVERT: e 240 ASP cc_start: 0.9227 (t0) cc_final: 0.8935 (t0) REVERT: e 242 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: e 267 THR cc_start: 0.9261 (m) cc_final: 0.8938 (p) REVERT: e 280 GLU cc_start: 0.7714 (tt0) cc_final: 0.7169 (mp0) REVERT: e 281 HIS cc_start: 0.7628 (t70) cc_final: 0.7390 (t70) REVERT: e 302 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6785 (mp0) REVERT: f 242 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: f 302 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6850 (mp0) REVERT: f 425 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9058 (ptpp) REVERT: g 246 GLN cc_start: 0.9339 (pt0) cc_final: 0.8976 (pt0) REVERT: g 412 ILE cc_start: 0.9252 (mm) cc_final: 0.9003 (mt) REVERT: g 418 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7808 (mt-10) REVERT: h 242 GLU cc_start: 0.7365 (mp0) cc_final: 0.7134 (pm20) REVERT: h 246 GLN cc_start: 0.9198 (pt0) cc_final: 0.8967 (pt0) REVERT: h 376 LYS cc_start: 0.8489 (tptp) cc_final: 0.8240 (tptp) REVERT: h 377 MET cc_start: 0.8461 (tpt) cc_final: 0.8094 (tpt) REVERT: h 418 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8110 (mm-30) outliers start: 53 outliers final: 21 residues processed: 1100 average time/residue: 0.2815 time to fit residues: 490.6039 Evaluate side-chains 1090 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 1044 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 280 GLU Chi-restraints excluded: chain V residue 415 LEU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 413 GLU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain g residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 421 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 411 GLN ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 431 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 239 ASN ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 239 ASN ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.198236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.153073 restraints weight = 86808.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.155453 restraints weight = 57780.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.155672 restraints weight = 44764.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.155999 restraints weight = 39759.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.156065 restraints weight = 35307.785| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43146 Z= 0.196 Angle : 0.737 12.249 58174 Z= 0.369 Chirality : 0.042 0.212 6698 Planarity : 0.004 0.054 7786 Dihedral : 4.537 16.328 5848 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.25 % Allowed : 28.12 % Favored : 70.63 % 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: 0.31 (0.12), residues: 5202 helix: 2.27 (0.13), residues: 1428 sheet: -0.35 (0.11), residues: 2516 loop : -0.79 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.010 0.001 TYR V 366 PHE 0.034 0.002 PHE E 237 HIS 0.004 0.001 HIS Q 281 Details of bonding type rmsd covalent geometry : bond 0.00453 (43146) covalent geometry : angle 0.73735 (58174) hydrogen bonds : bond 0.03312 ( 2043) hydrogen bonds : angle 4.27691 ( 5718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9976.40 seconds wall clock time: 172 minutes 5.01 seconds (10325.01 seconds total)