Starting phenix.real_space_refine on Sun Feb 8 03:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdt_60008/02_2026/8zdt_60008.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 24783 2.51 5 N 7524 2.21 5 O 8217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40623 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1231 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} 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 Time building chain proxies: 2.44, per 1000 atoms: 0.06 Number of scatterers: 40623 At special positions: 0 Unit cell: (257, 257, 100, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 8217 8.00 N 7524 7.00 C 24783 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: 2.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9900 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 35 sheets defined 29.5% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 229 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 230 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 230 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'D' and resid 230 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 Processing helix chain 'E' and resid 230 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 Processing helix chain 'F' and resid 230 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 Processing helix chain 'G' and resid 230 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 Processing helix chain 'H' and resid 230 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 Processing helix chain 'I' and resid 230 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'J' and resid 230 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 Processing helix chain 'K' and resid 230 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 Processing helix chain 'L' and resid 230 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 Processing helix chain 'M' and resid 230 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 Processing helix chain 'N' and resid 230 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 Processing helix chain 'O' and resid 230 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 Processing helix chain 'P' and resid 230 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 Processing helix chain 'Q' and resid 230 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 Processing helix chain 'R' and resid 230 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 Processing helix chain 'S' and resid 230 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 Processing helix chain 'T' and resid 230 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 230 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 Processing helix chain 'V' and resid 230 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 Processing helix chain 'W' and resid 230 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 Processing helix chain 'X' and resid 230 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 Processing helix chain 'Y' and resid 230 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 Processing helix chain 'Z' and resid 230 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 Processing helix chain 'a' and resid 230 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 Processing helix chain 'b' and resid 230 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 Processing helix chain 'c' and resid 230 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 Processing helix chain 'd' and resid 230 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 Processing helix chain 'e' and resid 230 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 Processing helix chain 'f' and resid 230 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 Processing helix chain 'g' and resid 230 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 282 removed outlier: 3.502A pdb=" N ARG A 370 " --> pdb=" O GLU g 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG g 370 " --> pdb=" O GLU f 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG f 370 " --> pdb=" O GLU e 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG e 370 " --> pdb=" O GLU d 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG d 370 " --> pdb=" O GLU c 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG c 370 " --> pdb=" O GLU b 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG b 370 " --> pdb=" O GLU a 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG a 370 " --> pdb=" O GLU Z 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG Z 370 " --> pdb=" O GLU Y 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG Y 370 " --> pdb=" O GLU X 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG X 370 " --> pdb=" O GLU W 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG W 370 " --> pdb=" O GLU V 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG V 370 " --> pdb=" O GLU U 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG U 370 " --> pdb=" O GLU T 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG T 370 " --> pdb=" O GLU S 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG S 370 " --> pdb=" O GLU R 280 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG R 370 " --> pdb=" O GLU Q 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG Q 370 " --> pdb=" O GLU P 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 370 " --> pdb=" O GLU O 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG O 370 " --> pdb=" O GLU N 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG N 370 " --> pdb=" O GLU M 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG M 370 " --> pdb=" O GLU L 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG L 370 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG K 370 " --> pdb=" O GLU J 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG J 370 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG I 370 " --> pdb=" O GLU H 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 370 " --> pdb=" O GLU G 280 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG G 370 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 370 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 370 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 370 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 370 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 370 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 303 removed outlier: 4.332A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 298 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 361 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A 300 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 359 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 302 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 357 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 292 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 298 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN B 361 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B 300 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 359 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU B 302 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 357 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR C 292 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 298 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C 361 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 300 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN C 359 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU C 302 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 357 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR D 292 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU D 298 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN D 361 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE D 300 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 359 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU D 302 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER D 357 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR E 292 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE E 300 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN E 359 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 302 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER E 357 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR F 292 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 298 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN F 361 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE F 300 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN F 359 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU F 302 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER F 357 " --> pdb=" O GLU F 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR G 292 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU G 298 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN G 361 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE G 300 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN G 359 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU G 302 " --> pdb=" O SER G 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER G 357 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR H 292 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE H 300 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN H 359 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU H 302 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER H 357 " --> pdb=" O GLU H 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR I 292 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU I 298 " --> pdb=" O ASN I 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN I 361 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE I 300 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN I 359 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU I 302 " --> pdb=" O SER I 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER I 357 " --> pdb=" O GLU I 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR J 292 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU J 298 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN J 361 " --> pdb=" O LEU J 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE J 300 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN J 359 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU J 302 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER J 357 " --> pdb=" O GLU J 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR K 292 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU K 298 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN K 361 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE K 300 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN K 359 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU K 302 " --> pdb=" O SER K 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER K 357 " --> pdb=" O GLU K 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR L 292 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU L 298 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN L 361 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE L 300 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN L 359 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU L 302 " --> pdb=" O SER L 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER L 357 " --> pdb=" O GLU L 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR M 292 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU M 298 " --> pdb=" O ASN M 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN M 361 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE M 300 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN M 359 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU M 302 " --> pdb=" O SER M 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER M 357 " --> pdb=" O GLU M 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR N 292 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU N 298 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN N 361 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE N 300 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN N 359 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU N 302 " --> pdb=" O SER N 357 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER N 357 " --> pdb=" O GLU N 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR O 292 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU O 298 " --> pdb=" O ASN O 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN O 361 " --> pdb=" O LEU O 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE O 300 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN O 359 " --> pdb=" O ILE O 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU O 302 " --> pdb=" O SER O 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER O 357 " --> pdb=" O GLU O 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR P 292 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU P 298 " --> pdb=" O ASN P 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN P 361 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE P 300 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN P 359 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU P 302 " --> pdb=" O SER P 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER P 357 " --> pdb=" O GLU P 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR Q 292 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU Q 298 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN Q 361 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE Q 300 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN Q 359 " --> pdb=" O ILE Q 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU Q 302 " --> pdb=" O SER Q 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER Q 357 " --> pdb=" O GLU Q 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU R 298 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN R 361 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE R 300 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN R 359 " --> pdb=" O ILE R 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU R 302 " --> pdb=" O SER R 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER R 357 " --> pdb=" O GLU R 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR S 292 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU S 298 " --> pdb=" O ASN S 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN S 361 " --> pdb=" O LEU S 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE S 300 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN S 359 " --> pdb=" O ILE S 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU S 302 " --> pdb=" O SER S 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER S 357 " --> pdb=" O GLU S 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR T 292 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE T 300 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN T 359 " --> pdb=" O ILE T 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU T 302 " --> pdb=" O SER T 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER T 357 " --> pdb=" O GLU T 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR U 292 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU U 298 " --> pdb=" O ASN U 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN U 361 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE U 300 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN U 359 " --> pdb=" O ILE U 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU U 302 " --> pdb=" O SER U 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER U 357 " --> pdb=" O GLU U 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR V 292 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE V 300 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN V 359 " --> pdb=" O ILE V 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU V 302 " --> pdb=" O SER V 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER V 357 " --> pdb=" O GLU V 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR W 292 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU W 298 " --> pdb=" O ASN W 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN W 361 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE W 300 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN W 359 " --> pdb=" O ILE W 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU W 302 " --> pdb=" O SER W 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER W 357 " --> pdb=" O GLU W 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR X 292 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU X 298 " --> pdb=" O ASN X 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN X 361 " --> pdb=" O LEU X 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE X 300 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN X 359 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU X 302 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER X 357 " --> pdb=" O GLU X 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR Y 292 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE Y 300 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN Y 359 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU Y 302 " --> pdb=" O SER Y 357 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER Y 357 " --> pdb=" O GLU Y 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR Z 292 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU Z 298 " --> pdb=" O ASN Z 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN Z 361 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE Z 300 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN Z 359 " --> pdb=" O ILE Z 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU Z 302 " --> pdb=" O SER Z 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER Z 357 " --> pdb=" O GLU Z 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR a 292 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU a 298 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN a 361 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE a 300 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN a 359 " --> pdb=" O ILE a 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU a 302 " --> pdb=" O SER a 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER a 357 " --> pdb=" O GLU a 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR b 292 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU b 298 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN b 361 " --> pdb=" O LEU b 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE b 300 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN b 359 " --> pdb=" O ILE b 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU b 302 " --> pdb=" O SER b 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER b 357 " --> pdb=" O GLU b 302 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR c 292 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU c 298 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN c 361 " --> pdb=" O LEU c 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE c 300 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN c 359 " --> pdb=" O ILE c 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU c 302 " --> pdb=" O SER c 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER c 357 " --> pdb=" O GLU c 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR d 292 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU d 298 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN d 361 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE d 300 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN d 359 " --> pdb=" O ILE d 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU d 302 " --> pdb=" O SER d 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER d 357 " --> pdb=" O GLU d 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR e 292 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU e 298 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN e 361 " --> pdb=" O LEU e 298 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE e 300 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN e 359 " --> pdb=" O ILE e 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU e 302 " --> pdb=" O SER e 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER e 357 " --> pdb=" O GLU e 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR f 292 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU f 298 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN f 361 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE f 300 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN f 359 " --> pdb=" O ILE f 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU f 302 " --> pdb=" O SER f 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER f 357 " --> pdb=" O GLU f 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR g 292 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU g 298 " --> pdb=" O ASN g 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN g 361 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE g 300 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN g 359 " --> pdb=" O ILE g 300 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU g 302 " --> pdb=" O SER g 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER g 357 " --> pdb=" O GLU g 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.874A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) 2212 hydrogen bonds defined for protein. 6438 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: 7.25 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14553 1.34 - 1.46: 6274 1.46 - 1.57: 20027 1.57 - 1.69: 0 1.69 - 1.80: 198 Bond restraints: 41052 Sorted by residual: bond pdb=" C VAL M 241 " pdb=" O VAL M 241 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.38e-01 bond pdb=" C VAL V 241 " pdb=" O VAL V 241 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.25e-01 bond pdb=" C VAL X 241 " pdb=" O VAL X 241 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.24e-01 bond pdb=" C VAL J 241 " pdb=" O VAL J 241 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.17e-01 bond pdb=" C VAL I 241 " pdb=" O VAL I 241 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.12e-01 ... (remaining 41047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 53254 0.97 - 1.94: 1768 1.94 - 2.92: 220 2.92 - 3.89: 99 3.89 - 4.86: 33 Bond angle restraints: 55374 Sorted by residual: angle pdb=" CA ARG C 356 " pdb=" CB ARG C 356 " pdb=" CG ARG C 356 " ideal model delta sigma weight residual 114.10 117.41 -3.31 2.00e+00 2.50e-01 2.74e+00 angle pdb=" CA ARG c 356 " pdb=" CB ARG c 356 " pdb=" CG ARG c 356 " ideal model delta sigma weight residual 114.10 117.40 -3.30 2.00e+00 2.50e-01 2.72e+00 angle pdb=" CA ARG e 356 " pdb=" CB ARG e 356 " pdb=" CG ARG e 356 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.71e+00 angle pdb=" CA ARG P 356 " pdb=" CB ARG P 356 " pdb=" CG ARG P 356 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.70e+00 angle pdb=" CA ARG a 356 " pdb=" CB ARG a 356 " pdb=" CG ARG a 356 " ideal model delta sigma weight residual 114.10 117.38 -3.28 2.00e+00 2.50e-01 2.69e+00 ... (remaining 55369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 22145 17.65 - 35.30: 2576 35.30 - 52.94: 656 52.94 - 70.59: 231 70.59 - 88.24: 66 Dihedral angle restraints: 25674 sinusoidal: 10626 harmonic: 15048 Sorted by residual: dihedral pdb=" CB GLU S 383 " pdb=" CG GLU S 383 " pdb=" CD GLU S 383 " pdb=" OE1 GLU S 383 " ideal model delta sinusoidal sigma weight residual 0.00 -88.24 88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU P 383 " pdb=" CG GLU P 383 " pdb=" CD GLU P 383 " pdb=" OE1 GLU P 383 " ideal model delta sinusoidal sigma weight residual 0.00 -88.22 88.22 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU X 383 " pdb=" CG GLU X 383 " pdb=" CD GLU X 383 " pdb=" OE1 GLU X 383 " ideal model delta sinusoidal sigma weight residual 0.00 -88.22 88.22 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 25671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3804 0.024 - 0.047: 1684 0.047 - 0.071: 390 0.071 - 0.094: 158 0.094 - 0.118: 366 Chirality restraints: 6402 Sorted by residual: chirality pdb=" CA ILE J 382 " pdb=" N ILE J 382 " pdb=" C ILE J 382 " pdb=" CB ILE J 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE f 382 " pdb=" N ILE f 382 " pdb=" C ILE f 382 " pdb=" CB ILE f 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA ILE g 382 " pdb=" N ILE g 382 " pdb=" C ILE g 382 " pdb=" CB ILE g 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 6399 not shown) Planarity restraints: 7392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER a 254 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO a 255 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO a 255 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO a 255 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 254 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.29e+00 pdb=" N PRO W 255 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO W 255 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO W 255 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER b 254 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.29e+00 pdb=" N PRO b 255 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO b 255 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO b 255 " 0.016 5.00e-02 4.00e+02 ... (remaining 7389 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 12045 2.84 - 3.35: 32598 3.35 - 3.87: 63439 3.87 - 4.38: 70326 4.38 - 4.90: 126964 Nonbonded interactions: 305372 Sorted by model distance: nonbonded pdb=" NE2 GLN J 246 " pdb=" O ALA J 264 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN X 246 " pdb=" O ALA X 264 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN Z 246 " pdb=" O ALA Z 264 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN Y 246 " pdb=" O ALA Y 264 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN K 246 " pdb=" O ALA K 264 " model vdw 2.319 3.120 ... (remaining 305367 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.270 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.002 0.018 41052 Z= 0.094 Angle : 0.445 4.858 55374 Z= 0.239 Chirality : 0.037 0.118 6402 Planarity : 0.002 0.028 7392 Dihedral : 17.499 88.238 15774 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.72 % Allowed : 23.02 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.12), residues: 4950 helix: 5.30 (0.12), residues: 1386 sheet: 2.34 (0.10), residues: 2442 loop : -0.69 (0.15), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 373 TYR 0.004 0.001 TYR O 282 PHE 0.005 0.001 PHE A 422 HIS 0.001 0.000 HIS J 263 Details of bonding type rmsd covalent geometry : bond 0.00185 (41052) covalent geometry : angle 0.44500 (55374) hydrogen bonds : bond 0.16437 ( 2212) hydrogen bonds : angle 4.16954 ( 6438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1141 time to evaluate : 1.439 Fit side-chains REVERT: A 247 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7402 (mtm110) REVERT: B 247 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.7375 (mtm110) REVERT: B 356 ARG cc_start: 0.6085 (mpp-170) cc_final: 0.5652 (mpp-170) REVERT: B 377 MET cc_start: 0.8574 (mpp) cc_final: 0.8122 (mpp) REVERT: C 410 LYS cc_start: 0.8026 (tttm) cc_final: 0.7719 (ttpt) REVERT: D 247 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7312 (mtm110) REVERT: D 410 LYS cc_start: 0.7779 (tttm) cc_final: 0.7577 (tttm) REVERT: D 413 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6682 (mt-10) REVERT: D 414 ASP cc_start: 0.7307 (m-30) cc_final: 0.7078 (m-30) REVERT: E 247 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7442 (mtm110) REVERT: E 377 MET cc_start: 0.8680 (mpp) cc_final: 0.8084 (mpp) REVERT: E 409 MET cc_start: 0.7467 (mmm) cc_final: 0.6405 (mmp) REVERT: E 413 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6951 (mp0) REVERT: E 414 ASP cc_start: 0.7496 (m-30) cc_final: 0.7265 (m-30) REVERT: F 279 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: F 409 MET cc_start: 0.7480 (mmm) cc_final: 0.6383 (mmp) REVERT: F 410 LYS cc_start: 0.7747 (tttm) cc_final: 0.7508 (ttpt) REVERT: F 417 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7442 (mtt90) REVERT: G 247 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.7110 (mtm110) REVERT: G 279 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: G 413 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6908 (mt-10) REVERT: H 267 THR cc_start: 0.8583 (t) cc_final: 0.8346 (m) REVERT: H 279 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: I 267 THR cc_start: 0.8548 (t) cc_final: 0.8294 (m) REVERT: J 267 THR cc_start: 0.8556 (t) cc_final: 0.8317 (m) REVERT: J 409 MET cc_start: 0.7436 (mmm) cc_final: 0.6327 (mmm) REVERT: J 413 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6780 (mp0) REVERT: K 247 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7178 (mtm-85) REVERT: K 279 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: K 381 ASP cc_start: 0.7792 (m-30) cc_final: 0.7558 (m-30) REVERT: K 410 LYS cc_start: 0.7693 (tttm) cc_final: 0.7456 (ttpt) REVERT: L 232 ASP cc_start: 0.5867 (m-30) cc_final: 0.5440 (t70) REVERT: L 247 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7097 (mtm110) REVERT: L 356 ARG cc_start: 0.5868 (mpp-170) cc_final: 0.5486 (mtp85) REVERT: L 409 MET cc_start: 0.7381 (mmm) cc_final: 0.6408 (mmm) REVERT: L 413 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6876 (mp0) REVERT: M 356 ARG cc_start: 0.6166 (mpp-170) cc_final: 0.5800 (mpt180) REVERT: M 409 MET cc_start: 0.7457 (mmm) cc_final: 0.6425 (mmp) REVERT: M 413 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6920 (mp0) REVERT: M 414 ASP cc_start: 0.7091 (m-30) cc_final: 0.6862 (m-30) REVERT: N 232 ASP cc_start: 0.6090 (m-30) cc_final: 0.5728 (t70) REVERT: N 409 MET cc_start: 0.7479 (mmm) cc_final: 0.6306 (mmm) REVERT: N 414 ASP cc_start: 0.6730 (m-30) cc_final: 0.6409 (m-30) REVERT: N 417 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7617 (mtt90) REVERT: O 409 MET cc_start: 0.7502 (mmm) cc_final: 0.6179 (mmp) REVERT: O 417 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7556 (mtt-85) REVERT: P 287 ASP cc_start: 0.6892 (t0) cc_final: 0.6591 (t70) REVERT: P 413 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6899 (mp0) REVERT: Q 279 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: Q 375 THR cc_start: 0.8108 (t) cc_final: 0.7649 (m) REVERT: Q 413 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7033 (mp0) REVERT: R 409 MET cc_start: 0.7366 (mmm) cc_final: 0.7160 (mmp) REVERT: R 413 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6927 (tt0) REVERT: S 413 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7149 (mp0) REVERT: T 232 ASP cc_start: 0.5952 (m-30) cc_final: 0.5584 (t70) REVERT: T 409 MET cc_start: 0.7555 (mmm) cc_final: 0.6676 (mmp) REVERT: T 413 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7049 (mp0) REVERT: U 247 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7335 (mtm110) REVERT: U 409 MET cc_start: 0.7551 (mmm) cc_final: 0.5976 (mmp) REVERT: U 410 LYS cc_start: 0.7717 (tttm) cc_final: 0.7455 (ttpt) REVERT: U 413 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7104 (mp0) REVERT: W 356 ARG cc_start: 0.5978 (mpp-170) cc_final: 0.5756 (mpp-170) REVERT: W 413 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6921 (tt0) REVERT: X 409 MET cc_start: 0.7806 (mmm) cc_final: 0.7540 (mmp) REVERT: X 414 ASP cc_start: 0.6777 (m-30) cc_final: 0.6474 (m-30) REVERT: Y 279 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: Y 375 THR cc_start: 0.8010 (t) cc_final: 0.7537 (m) REVERT: Y 413 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7155 (mt-10) REVERT: Z 409 MET cc_start: 0.7734 (mmm) cc_final: 0.7492 (mmp) REVERT: a 410 LYS cc_start: 0.7759 (tttm) cc_final: 0.7445 (ttpt) REVERT: b 236 LYS cc_start: 0.6900 (pttp) cc_final: 0.6671 (pptt) REVERT: b 381 ASP cc_start: 0.7880 (m-30) cc_final: 0.7647 (m-30) REVERT: b 409 MET cc_start: 0.7853 (mmm) cc_final: 0.7481 (mmp) REVERT: b 413 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7040 (mt-10) REVERT: c 279 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: c 409 MET cc_start: 0.7779 (mmm) cc_final: 0.6782 (mmm) REVERT: c 413 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6924 (mp0) REVERT: d 247 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7402 (mtm-85) REVERT: d 409 MET cc_start: 0.7729 (mmm) cc_final: 0.7236 (mmp) REVERT: d 413 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7074 (mt-10) REVERT: e 232 ASP cc_start: 0.5568 (m-30) cc_final: 0.5189 (t70) REVERT: e 279 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: e 377 MET cc_start: 0.8697 (mpp) cc_final: 0.8257 (mpt) REVERT: e 410 LYS cc_start: 0.7685 (tttm) cc_final: 0.7311 (ttmt) REVERT: e 413 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6873 (tt0) REVERT: f 247 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7421 (mtm110) REVERT: f 279 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: f 410 LYS cc_start: 0.7868 (tttm) cc_final: 0.7622 (tptp) REVERT: g 236 LYS cc_start: 0.6717 (pttp) cc_final: 0.6497 (pptt) REVERT: g 247 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.7162 (mtm110) REVERT: g 420 MET cc_start: 0.6935 (ptm) cc_final: 0.6522 (ptm) outliers start: 33 outliers final: 0 residues processed: 1142 average time/residue: 0.9171 time to fit residues: 1218.3232 Evaluate side-chains 1079 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1070 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain f residue 279 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN B 374 HIS B 434 ASN C 303 GLN C 434 ASN D 303 GLN D 434 ASN E 303 GLN E 374 HIS E 434 ASN F 303 GLN F 431 ASN F 434 ASN G 303 GLN G 434 ASN H 303 GLN H 374 HIS H 434 ASN I 303 GLN I 434 ASN J 434 ASN K 269 GLN K 431 ASN K 434 ASN L 359 GLN L 434 ASN M 303 GLN M 431 ASN M 434 ASN N 434 ASN O 434 ASN P 434 ASN Q 431 ASN Q 434 ASN R 434 ASN S 434 ASN T 434 ASN U 434 ASN V 374 HIS V 434 ASN W 434 ASN X 431 ASN X 434 ASN Y 374 HIS Y 434 ASN Z 431 ASN Z 434 ASN a 431 ASN a 434 ASN b 431 ASN b 434 ASN c 434 ASN d 431 ASN d 434 ASN e 431 ASN e 434 ASN f 434 ASN g 374 HIS g 434 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147553 restraints weight = 45328.031| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.53 r_work: 0.3626 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41052 Z= 0.114 Angle : 0.484 4.778 55374 Z= 0.268 Chirality : 0.038 0.132 6402 Planarity : 0.002 0.030 7392 Dihedral : 4.301 47.481 5571 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.57 % Allowed : 22.59 % Favored : 75.84 % 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: 4.01 (0.12), residues: 4950 helix: 5.22 (0.12), residues: 1386 sheet: 2.46 (0.11), residues: 2442 loop : -0.69 (0.15), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 370 TYR 0.006 0.001 TYR T 282 PHE 0.005 0.001 PHE L 422 HIS 0.005 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00212 (41052) covalent geometry : angle 0.48371 (55374) hydrogen bonds : bond 0.05247 ( 2212) hydrogen bonds : angle 3.70876 ( 6438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1102 time to evaluate : 1.554 Fit side-chains REVERT: A 247 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7503 (mtm110) REVERT: A 279 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: B 247 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7607 (mtm110) REVERT: B 279 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: B 356 ARG cc_start: 0.6073 (mpp-170) cc_final: 0.5790 (mpp-170) REVERT: B 413 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: C 410 LYS cc_start: 0.8056 (tttm) cc_final: 0.7701 (ttpt) REVERT: D 247 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7416 (mtm110) REVERT: D 279 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: D 377 MET cc_start: 0.8735 (mpp) cc_final: 0.8007 (mpt) REVERT: D 410 LYS cc_start: 0.7799 (tttm) cc_final: 0.7240 (ttpt) REVERT: D 413 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6758 (mp0) REVERT: D 414 ASP cc_start: 0.7372 (m-30) cc_final: 0.7158 (m-30) REVERT: E 232 ASP cc_start: 0.6230 (m-30) cc_final: 0.5697 (t70) REVERT: E 247 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7596 (mtm110) REVERT: E 377 MET cc_start: 0.8751 (mpp) cc_final: 0.8040 (mpp) REVERT: E 409 MET cc_start: 0.7366 (mmm) cc_final: 0.7103 (mmp) REVERT: F 232 ASP cc_start: 0.6247 (m-30) cc_final: 0.5878 (t70) REVERT: F 236 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7234 (pttp) REVERT: F 279 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6889 (mp0) REVERT: F 409 MET cc_start: 0.7130 (mmm) cc_final: 0.6248 (mmp) REVERT: F 410 LYS cc_start: 0.7714 (tttm) cc_final: 0.7441 (ttpt) REVERT: G 232 ASP cc_start: 0.6149 (m-30) cc_final: 0.5809 (t70) REVERT: G 236 LYS cc_start: 0.7969 (mttm) cc_final: 0.7353 (pttp) REVERT: G 247 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7242 (mtm110) REVERT: G 279 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6901 (mp0) REVERT: G 413 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6820 (mt-10) REVERT: H 232 ASP cc_start: 0.6291 (m-30) cc_final: 0.5858 (t70) REVERT: H 267 THR cc_start: 0.8691 (t) cc_final: 0.8338 (m) REVERT: H 410 LYS cc_start: 0.7550 (tttm) cc_final: 0.7059 (tptp) REVERT: I 267 THR cc_start: 0.8505 (t) cc_final: 0.8126 (m) REVERT: I 375 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7697 (t) REVERT: I 413 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6947 (mp0) REVERT: J 232 ASP cc_start: 0.6392 (m-30) cc_final: 0.5881 (t70) REVERT: J 279 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: K 410 LYS cc_start: 0.7739 (tttm) cc_final: 0.7433 (ttpt) REVERT: L 232 ASP cc_start: 0.6333 (m-30) cc_final: 0.5870 (t70) REVERT: L 247 ARG cc_start: 0.7755 (ttp-110) cc_final: 0.7422 (mtm110) REVERT: L 279 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6619 (mt-10) REVERT: L 356 ARG cc_start: 0.6004 (mpp-170) cc_final: 0.5455 (mtp85) REVERT: L 409 MET cc_start: 0.7483 (mmm) cc_final: 0.6390 (mmm) REVERT: L 413 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6971 (mp0) REVERT: M 236 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7360 (pttp) REVERT: M 279 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: M 356 ARG cc_start: 0.6088 (mpp-170) cc_final: 0.5851 (mpt180) REVERT: N 232 ASP cc_start: 0.6486 (m-30) cc_final: 0.6078 (t70) REVERT: N 279 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6697 (mt-10) REVERT: N 375 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7844 (t) REVERT: N 409 MET cc_start: 0.7157 (mmm) cc_final: 0.6204 (mmp) REVERT: N 414 ASP cc_start: 0.7087 (m-30) cc_final: 0.6775 (m-30) REVERT: O 279 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: O 409 MET cc_start: 0.7222 (mmm) cc_final: 0.6477 (mmp) REVERT: O 410 LYS cc_start: 0.7711 (tttm) cc_final: 0.7488 (tttt) REVERT: P 287 ASP cc_start: 0.7002 (t0) cc_final: 0.6755 (t0) REVERT: P 413 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6836 (mp0) REVERT: Q 375 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7454 (m) REVERT: Q 413 GLU cc_start: 0.7496 (tm-30) cc_final: 0.6897 (mp0) REVERT: R 413 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6932 (tt0) REVERT: S 247 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7457 (mtm-85) REVERT: S 290 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8260 (mmtm) REVERT: S 410 LYS cc_start: 0.7517 (tttm) cc_final: 0.7131 (ttpt) REVERT: S 413 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7024 (mp0) REVERT: T 232 ASP cc_start: 0.6335 (m-30) cc_final: 0.5924 (t70) REVERT: T 377 MET cc_start: 0.8704 (mpp) cc_final: 0.8308 (mpt) REVERT: T 409 MET cc_start: 0.7334 (mmm) cc_final: 0.5974 (mmp) REVERT: T 413 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6946 (mp0) REVERT: U 247 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7555 (mtm110) REVERT: U 409 MET cc_start: 0.7365 (mmm) cc_final: 0.6578 (mmp) REVERT: U 413 GLU cc_start: 0.7622 (tm-30) cc_final: 0.6971 (mt-10) REVERT: W 409 MET cc_start: 0.7378 (mmm) cc_final: 0.7091 (mmp) REVERT: W 413 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6933 (tt0) REVERT: X 232 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5745 (t70) REVERT: X 297 GLN cc_start: 0.7802 (tt0) cc_final: 0.7584 (tt0) REVERT: X 409 MET cc_start: 0.7513 (mmm) cc_final: 0.7084 (mmp) REVERT: X 413 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6886 (mt-10) REVERT: X 414 ASP cc_start: 0.6949 (m-30) cc_final: 0.6637 (m-30) REVERT: Z 247 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7434 (mtm-85) REVERT: Z 377 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8248 (mpp) REVERT: Z 409 MET cc_start: 0.7511 (mmm) cc_final: 0.7297 (mmp) REVERT: a 279 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: a 410 LYS cc_start: 0.7697 (tttm) cc_final: 0.7377 (ttpt) REVERT: b 232 ASP cc_start: 0.6329 (m-30) cc_final: 0.5884 (t70) REVERT: b 247 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7406 (mtm110) REVERT: b 279 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: b 375 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7573 (m) REVERT: b 413 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7127 (tt0) REVERT: c 279 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7077 (mp0) REVERT: c 409 MET cc_start: 0.7636 (mmm) cc_final: 0.6770 (mmm) REVERT: c 413 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6811 (mp0) REVERT: d 247 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7388 (mtm110) REVERT: d 409 MET cc_start: 0.7581 (mmm) cc_final: 0.6450 (mmp) REVERT: d 413 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6846 (mp0) REVERT: e 232 ASP cc_start: 0.6053 (m-30) cc_final: 0.5677 (t70) REVERT: e 377 MET cc_start: 0.8835 (mpp) cc_final: 0.8373 (mpt) REVERT: e 410 LYS cc_start: 0.7646 (tttm) cc_final: 0.7271 (ttmt) REVERT: e 413 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6783 (tt0) REVERT: f 247 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7426 (mtm110) outliers start: 72 outliers final: 18 residues processed: 1106 average time/residue: 0.9168 time to fit residues: 1181.8025 Evaluate side-chains 1093 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1056 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain Q residue 375 THR Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 407 ASP Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 323 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 439 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 389 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 246 GLN H 374 HIS I 303 GLN J 246 GLN Y 374 HIS Z 374 HIS b 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139098 restraints weight = 45005.540| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.57 r_work: 0.3539 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 41052 Z= 0.211 Angle : 0.620 4.919 55374 Z= 0.348 Chirality : 0.042 0.132 6402 Planarity : 0.003 0.035 7392 Dihedral : 4.224 18.252 5544 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.57 % Allowed : 19.97 % Favored : 77.46 % 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: 3.52 (0.12), residues: 4950 helix: 4.61 (0.12), residues: 1386 sheet: 2.32 (0.11), residues: 2442 loop : -1.00 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 426 TYR 0.010 0.001 TYR d 282 PHE 0.012 0.002 PHE D 422 HIS 0.006 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00442 (41052) covalent geometry : angle 0.61959 (55374) hydrogen bonds : bond 0.08419 ( 2212) hydrogen bonds : angle 3.93252 ( 6438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1058 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7615 (mtm110) REVERT: B 247 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7623 (mtm110) REVERT: B 356 ARG cc_start: 0.6004 (mpp-170) cc_final: 0.5755 (ttt-90) REVERT: B 377 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8440 (mpp) REVERT: C 232 ASP cc_start: 0.6911 (m-30) cc_final: 0.6622 (t70) REVERT: C 236 LYS cc_start: 0.8128 (mttp) cc_final: 0.7557 (pttp) REVERT: C 279 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: C 410 LYS cc_start: 0.7756 (tttm) cc_final: 0.7470 (ttpt) REVERT: D 247 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7517 (mtm110) REVERT: D 279 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: D 410 LYS cc_start: 0.7769 (tttm) cc_final: 0.7538 (tttp) REVERT: D 413 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6676 (mp0) REVERT: D 414 ASP cc_start: 0.7359 (m-30) cc_final: 0.7152 (m-30) REVERT: E 247 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7609 (mtm180) REVERT: E 383 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7799 (mt-10) REVERT: E 413 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6966 (mp0) REVERT: F 232 ASP cc_start: 0.6850 (m-30) cc_final: 0.6460 (t70) REVERT: F 236 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7577 (pttp) REVERT: F 247 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7562 (mtm180) REVERT: F 279 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: F 410 LYS cc_start: 0.7727 (tttm) cc_final: 0.7468 (ttpt) REVERT: G 232 ASP cc_start: 0.6728 (m-30) cc_final: 0.6440 (t70) REVERT: G 236 LYS cc_start: 0.8370 (mttm) cc_final: 0.7818 (pttp) REVERT: G 247 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7455 (mtm180) REVERT: G 279 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: G 413 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6786 (mt-10) REVERT: H 247 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7604 (mtm180) REVERT: H 267 THR cc_start: 0.8688 (t) cc_final: 0.8351 (m) REVERT: H 279 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: H 410 LYS cc_start: 0.7652 (tttm) cc_final: 0.7146 (tptp) REVERT: I 267 THR cc_start: 0.8567 (t) cc_final: 0.8210 (m) REVERT: I 279 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6425 (mt-10) REVERT: I 413 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6956 (mp0) REVERT: J 267 THR cc_start: 0.8609 (t) cc_final: 0.8347 (m) REVERT: J 410 LYS cc_start: 0.7845 (tttm) cc_final: 0.7381 (ttpt) REVERT: J 413 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7020 (mp0) REVERT: K 279 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: K 290 LYS cc_start: 0.8446 (mttp) cc_final: 0.8213 (mttt) REVERT: K 410 LYS cc_start: 0.7903 (tttm) cc_final: 0.7613 (ttpt) REVERT: L 232 ASP cc_start: 0.6980 (m-30) cc_final: 0.6476 (t70) REVERT: L 247 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7553 (mtm180) REVERT: L 279 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: L 356 ARG cc_start: 0.6037 (mpp-170) cc_final: 0.5544 (mtp85) REVERT: L 409 MET cc_start: 0.7563 (mmm) cc_final: 0.6582 (mmm) REVERT: L 413 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6977 (mp0) REVERT: M 279 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: M 356 ARG cc_start: 0.6040 (mpp-170) cc_final: 0.5553 (mtp85) REVERT: N 409 MET cc_start: 0.7273 (mmm) cc_final: 0.6692 (mmp) REVERT: N 414 ASP cc_start: 0.7313 (m-30) cc_final: 0.6962 (m-30) REVERT: O 247 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7539 (mtm-85) REVERT: O 279 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: O 409 MET cc_start: 0.7209 (mmm) cc_final: 0.6714 (mmp) REVERT: P 413 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6777 (mt-10) REVERT: Q 236 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7595 (pttt) REVERT: Q 247 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7580 (mtm180) REVERT: Q 279 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: R 274 ASN cc_start: 0.8350 (m-40) cc_final: 0.8065 (m110) REVERT: R 279 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: R 413 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6984 (tt0) REVERT: S 247 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7591 (mtm180) REVERT: S 290 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: S 356 ARG cc_start: 0.5832 (mpp-170) cc_final: 0.5518 (mpt90) REVERT: S 410 LYS cc_start: 0.7608 (tttm) cc_final: 0.7215 (ttpt) REVERT: S 413 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7003 (mp0) REVERT: T 232 ASP cc_start: 0.6780 (m-30) cc_final: 0.6403 (t70) REVERT: T 409 MET cc_start: 0.7300 (mmm) cc_final: 0.5991 (mmp) REVERT: T 410 LYS cc_start: 0.7652 (tttm) cc_final: 0.7450 (tttm) REVERT: T 413 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6953 (mp0) REVERT: U 232 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6395 (t0) REVERT: U 247 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7555 (mtm110) REVERT: U 279 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: U 409 MET cc_start: 0.7410 (mmm) cc_final: 0.6891 (mmp) REVERT: U 413 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6784 (mt-10) REVERT: W 409 MET cc_start: 0.7290 (mmm) cc_final: 0.6887 (mmp) REVERT: W 413 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6759 (mt-10) REVERT: X 232 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6275 (t70) REVERT: X 236 LYS cc_start: 0.7901 (pttp) cc_final: 0.7664 (pptt) REVERT: X 297 GLN cc_start: 0.7838 (tt0) cc_final: 0.7628 (tt0) REVERT: X 409 MET cc_start: 0.7466 (mmm) cc_final: 0.7099 (mmp) REVERT: X 413 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6874 (mt-10) REVERT: X 414 ASP cc_start: 0.7290 (m-30) cc_final: 0.6951 (m-30) REVERT: Y 279 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6576 (mt-10) REVERT: Y 356 ARG cc_start: 0.6105 (mpp-170) cc_final: 0.5605 (mpp-170) REVERT: Z 236 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7553 (pttt) REVERT: Z 247 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7309 (mtm110) REVERT: Z 409 MET cc_start: 0.7512 (mmm) cc_final: 0.6264 (mmp) REVERT: Z 413 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6562 (mp0) REVERT: a 232 ASP cc_start: 0.6848 (m-30) cc_final: 0.6390 (t70) REVERT: a 279 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: a 356 ARG cc_start: 0.6385 (mpp-170) cc_final: 0.6100 (mpp-170) REVERT: a 410 LYS cc_start: 0.7694 (tttm) cc_final: 0.7363 (ttpt) REVERT: b 247 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7539 (mtm180) REVERT: b 279 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: b 413 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6605 (mp0) REVERT: c 279 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7097 (mp0) REVERT: c 413 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6706 (mp0) REVERT: d 232 ASP cc_start: 0.6979 (m-30) cc_final: 0.6589 (t70) REVERT: d 409 MET cc_start: 0.7537 (mmm) cc_final: 0.6413 (mmp) REVERT: d 413 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6775 (mp0) REVERT: e 232 ASP cc_start: 0.6711 (m-30) cc_final: 0.6353 (t70) REVERT: e 410 LYS cc_start: 0.7641 (tttm) cc_final: 0.7332 (ttpt) REVERT: e 413 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6672 (mt-10) REVERT: f 247 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7489 (mtm180) REVERT: f 279 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: g 267 THR cc_start: 0.8534 (t) cc_final: 0.8252 (m) REVERT: g 279 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: g 413 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6650 (mp0) outliers start: 118 outliers final: 43 residues processed: 1080 average time/residue: 1.0003 time to fit residues: 1252.4256 Evaluate side-chains 1100 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1032 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 413 GLU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 377 MET Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain Q residue 236 LYS Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 407 ASP Chi-restraints excluded: chain d residue 236 LYS Chi-restraints excluded: chain d residue 254 SER Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 198 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 419 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 370 optimal weight: 10.0000 chunk 483 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 368 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN H 374 HIS S 303 GLN V 303 GLN Y 303 GLN Y 374 HIS Z 274 ASN g 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139879 restraints weight = 44845.512| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.57 r_work: 0.3547 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 41052 Z= 0.180 Angle : 0.578 5.184 55374 Z= 0.323 Chirality : 0.041 0.128 6402 Planarity : 0.003 0.031 7392 Dihedral : 4.207 18.080 5544 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.64 % Allowed : 19.38 % Favored : 77.98 % 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: 3.37 (0.12), residues: 4950 helix: 4.41 (0.12), residues: 1386 sheet: 2.30 (0.11), residues: 2442 loop : -1.15 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 370 TYR 0.010 0.001 TYR d 282 PHE 0.011 0.002 PHE L 422 HIS 0.007 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00367 (41052) covalent geometry : angle 0.57813 (55374) hydrogen bonds : bond 0.07535 ( 2212) hydrogen bonds : angle 3.89861 ( 6438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1045 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7551 (mtm180) REVERT: A 279 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: B 247 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7575 (mtm110) REVERT: C 232 ASP cc_start: 0.6769 (m-30) cc_final: 0.6422 (t70) REVERT: C 279 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: C 410 LYS cc_start: 0.7788 (tttm) cc_final: 0.7442 (ttpt) REVERT: C 413 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: D 247 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7433 (mtm180) REVERT: D 279 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: D 356 ARG cc_start: 0.6194 (mpp-170) cc_final: 0.5853 (mpt180) REVERT: D 377 MET cc_start: 0.8789 (mpp) cc_final: 0.8104 (mpt) REVERT: D 410 LYS cc_start: 0.7835 (tttm) cc_final: 0.7573 (tttp) REVERT: D 413 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6670 (mp0) REVERT: D 414 ASP cc_start: 0.7384 (m-30) cc_final: 0.7174 (m-30) REVERT: E 247 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7555 (mtm180) REVERT: E 383 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 413 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6956 (mp0) REVERT: F 232 ASP cc_start: 0.6670 (m-30) cc_final: 0.6125 (t70) REVERT: F 247 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7588 (mtm180) REVERT: F 279 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: G 232 ASP cc_start: 0.6609 (m-30) cc_final: 0.6286 (t70) REVERT: G 247 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7421 (mtm180) REVERT: G 279 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7028 (mp0) REVERT: G 356 ARG cc_start: 0.6250 (mpp-170) cc_final: 0.5987 (mpp-170) REVERT: G 413 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6835 (mt-10) REVERT: H 267 THR cc_start: 0.8690 (t) cc_final: 0.8363 (m) REVERT: H 279 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: H 410 LYS cc_start: 0.7641 (tttm) cc_final: 0.7081 (tptp) REVERT: H 413 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6817 (mp0) REVERT: I 267 THR cc_start: 0.8573 (t) cc_final: 0.8212 (m) REVERT: I 279 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: I 370 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7907 (ttm170) REVERT: I 413 GLU cc_start: 0.7579 (tm-30) cc_final: 0.6941 (mp0) REVERT: J 267 THR cc_start: 0.8619 (t) cc_final: 0.8318 (m) REVERT: J 377 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8460 (mpp) REVERT: J 410 LYS cc_start: 0.7849 (tttm) cc_final: 0.7391 (ttpt) REVERT: J 413 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7031 (mp0) REVERT: K 279 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: K 290 LYS cc_start: 0.8464 (mttp) cc_final: 0.8235 (mttt) REVERT: K 410 LYS cc_start: 0.7896 (tttm) cc_final: 0.7608 (ttpt) REVERT: L 232 ASP cc_start: 0.6899 (m-30) cc_final: 0.6398 (t70) REVERT: L 247 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7513 (mtm180) REVERT: L 279 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: L 356 ARG cc_start: 0.5955 (mpp-170) cc_final: 0.5526 (mtp85) REVERT: L 409 MET cc_start: 0.7560 (mmm) cc_final: 0.6582 (mmm) REVERT: L 413 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6851 (mp0) REVERT: M 279 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: M 356 ARG cc_start: 0.5994 (mpp-170) cc_final: 0.5543 (mtp85) REVERT: M 394 LYS cc_start: 0.6959 (ttpt) cc_final: 0.6679 (ttpt) REVERT: N 279 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: N 409 MET cc_start: 0.7265 (mmm) cc_final: 0.6608 (mmp) REVERT: N 414 ASP cc_start: 0.7256 (m-30) cc_final: 0.6837 (m-30) REVERT: O 247 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7478 (mtm-85) REVERT: O 409 MET cc_start: 0.7106 (mmm) cc_final: 0.6702 (mmp) REVERT: P 413 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6843 (mt-10) REVERT: Q 236 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7528 (pttt) REVERT: Q 247 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7496 (mtm180) REVERT: Q 279 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6673 (mt-10) REVERT: Q 394 LYS cc_start: 0.6935 (ttpt) cc_final: 0.6731 (ttpt) REVERT: R 279 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: R 356 ARG cc_start: 0.5841 (mpt180) cc_final: 0.5638 (ttt-90) REVERT: R 413 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6914 (tt0) REVERT: S 236 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7416 (pttt) REVERT: S 247 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7652 (mtm180) REVERT: S 290 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: S 410 LYS cc_start: 0.7596 (tttm) cc_final: 0.7233 (ttpt) REVERT: S 413 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7003 (mp0) REVERT: T 232 ASP cc_start: 0.6659 (m-30) cc_final: 0.6277 (t70) REVERT: T 409 MET cc_start: 0.7317 (mmm) cc_final: 0.5955 (mmp) REVERT: T 413 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6963 (mp0) REVERT: U 247 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7502 (mtm110) REVERT: U 279 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: U 409 MET cc_start: 0.7404 (mmm) cc_final: 0.6878 (mmp) REVERT: U 413 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6774 (mt-10) REVERT: W 279 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: W 356 ARG cc_start: 0.6372 (mpp-170) cc_final: 0.5951 (mpp-170) REVERT: W 409 MET cc_start: 0.7268 (mmm) cc_final: 0.6036 (mmp) REVERT: W 413 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6735 (mp0) REVERT: X 232 ASP cc_start: 0.6496 (m-30) cc_final: 0.6136 (t70) REVERT: X 297 GLN cc_start: 0.7815 (tt0) cc_final: 0.7593 (tt0) REVERT: X 409 MET cc_start: 0.7444 (mmm) cc_final: 0.6153 (mmp) REVERT: X 413 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6906 (mp0) REVERT: X 414 ASP cc_start: 0.7295 (m-30) cc_final: 0.7029 (m-30) REVERT: Y 279 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: Y 356 ARG cc_start: 0.6086 (mpp-170) cc_final: 0.5765 (mpp-170) REVERT: Y 394 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6701 (ttpt) REVERT: Z 236 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7527 (pttt) REVERT: Z 247 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7379 (mtm-85) REVERT: Z 409 MET cc_start: 0.7438 (mmm) cc_final: 0.6094 (mmp) REVERT: Z 413 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6544 (mp0) REVERT: a 232 ASP cc_start: 0.6785 (m-30) cc_final: 0.6316 (t70) REVERT: a 259 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6477 (m-40) REVERT: a 279 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: a 410 LYS cc_start: 0.7666 (tttm) cc_final: 0.7302 (ttpt) REVERT: b 247 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7493 (mtm180) REVERT: b 279 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: b 413 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6670 (mp0) REVERT: c 279 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: c 413 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6695 (mp0) REVERT: d 232 ASP cc_start: 0.6822 (m-30) cc_final: 0.6443 (t70) REVERT: d 356 ARG cc_start: 0.6077 (mpp-170) cc_final: 0.5767 (mpp-170) REVERT: d 409 MET cc_start: 0.7536 (mmm) cc_final: 0.6259 (mmp) REVERT: d 413 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6866 (mp0) REVERT: e 232 ASP cc_start: 0.6678 (m-30) cc_final: 0.6284 (t70) REVERT: e 410 LYS cc_start: 0.7607 (tttm) cc_final: 0.7315 (ttpt) REVERT: e 413 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6719 (mt-10) REVERT: f 247 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7430 (mtm180) REVERT: f 279 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: f 356 ARG cc_start: 0.6373 (mpp-170) cc_final: 0.6132 (mpp-170) REVERT: g 279 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: g 377 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8350 (mpt) REVERT: g 413 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6651 (mp0) outliers start: 121 outliers final: 57 residues processed: 1084 average time/residue: 0.9612 time to fit residues: 1209.7497 Evaluate side-chains 1119 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1033 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 377 MET Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 236 LYS Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain S residue 236 LYS Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 410 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 259 ASN Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 407 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 377 MET Chi-restraints excluded: chain g residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 140 optimal weight: 8.9990 chunk 410 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 330 optimal weight: 3.9990 chunk 483 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 426 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 374 HIS I 303 GLN L 374 HIS R 274 ASN S 303 GLN V 303 GLN W 359 GLN Y 374 HIS Z 274 ASN b 246 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.166088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140847 restraints weight = 44948.282| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.57 r_work: 0.3556 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 41052 Z= 0.155 Angle : 0.539 5.489 55374 Z= 0.301 Chirality : 0.040 0.128 6402 Planarity : 0.002 0.023 7392 Dihedral : 4.118 17.521 5544 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.68 % Allowed : 19.03 % Favored : 78.29 % 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: 3.41 (0.12), residues: 4950 helix: 4.49 (0.12), residues: 1386 sheet: 2.33 (0.11), residues: 2442 loop : -1.23 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 426 TYR 0.009 0.001 TYR d 282 PHE 0.009 0.001 PHE L 422 HIS 0.009 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (41052) covalent geometry : angle 0.53926 (55374) hydrogen bonds : bond 0.06823 ( 2212) hydrogen bonds : angle 3.82815 ( 6438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1041 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7511 (mtm180) REVERT: A 279 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: A 356 ARG cc_start: 0.5859 (mpp-170) cc_final: 0.5584 (mtp85) REVERT: A 377 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8104 (mpt) REVERT: B 247 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7509 (mtm180) REVERT: B 279 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: C 232 ASP cc_start: 0.6705 (m-30) cc_final: 0.6208 (t70) REVERT: C 279 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: C 410 LYS cc_start: 0.7776 (tttm) cc_final: 0.7426 (ttpt) REVERT: C 413 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: D 247 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7467 (mtm180) REVERT: D 279 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: D 356 ARG cc_start: 0.6220 (mpp-170) cc_final: 0.5973 (mpt180) REVERT: D 377 MET cc_start: 0.8752 (mpp) cc_final: 0.8080 (mpt) REVERT: D 410 LYS cc_start: 0.7751 (tttm) cc_final: 0.7507 (tttp) REVERT: D 413 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6656 (mp0) REVERT: D 414 ASP cc_start: 0.7356 (m-30) cc_final: 0.7137 (m-30) REVERT: E 247 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7542 (mtm180) REVERT: E 383 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7779 (mt-10) REVERT: E 413 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6980 (mp0) REVERT: F 232 ASP cc_start: 0.6539 (m-30) cc_final: 0.6162 (t70) REVERT: F 236 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7435 (pttp) REVERT: F 247 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7566 (mtm180) REVERT: F 279 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: G 232 ASP cc_start: 0.6489 (m-30) cc_final: 0.6221 (t70) REVERT: G 236 LYS cc_start: 0.8265 (mttm) cc_final: 0.7701 (pttp) REVERT: G 247 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7385 (mtm180) REVERT: G 279 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: G 290 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8349 (mtmt) REVERT: G 356 ARG cc_start: 0.6323 (mpp-170) cc_final: 0.6026 (mpp-170) REVERT: G 413 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6825 (mt-10) REVERT: H 267 THR cc_start: 0.8655 (t) cc_final: 0.8322 (m) REVERT: H 279 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: H 410 LYS cc_start: 0.7617 (tttm) cc_final: 0.7104 (tptp) REVERT: I 267 THR cc_start: 0.8545 (t) cc_final: 0.8161 (m) REVERT: I 279 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6407 (mt-10) REVERT: I 356 ARG cc_start: 0.5821 (mpp-170) cc_final: 0.5601 (mtp85) REVERT: I 370 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7869 (ttm170) REVERT: I 375 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7766 (t) REVERT: I 413 GLU cc_start: 0.7574 (tm-30) cc_final: 0.6907 (mp0) REVERT: J 377 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8490 (mpp) REVERT: J 410 LYS cc_start: 0.7830 (tttm) cc_final: 0.7371 (ttpt) REVERT: J 413 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7054 (mp0) REVERT: K 279 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: K 290 LYS cc_start: 0.8552 (mttp) cc_final: 0.8315 (mttt) REVERT: K 410 LYS cc_start: 0.7877 (tttm) cc_final: 0.7571 (ttpt) REVERT: L 232 ASP cc_start: 0.6676 (m-30) cc_final: 0.6245 (t70) REVERT: L 247 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7454 (mtm180) REVERT: L 279 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: L 356 ARG cc_start: 0.5881 (mpp-170) cc_final: 0.5487 (mtp85) REVERT: L 409 MET cc_start: 0.7551 (mmm) cc_final: 0.6567 (mmm) REVERT: L 413 GLU cc_start: 0.7677 (tm-30) cc_final: 0.6931 (mp0) REVERT: M 236 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7601 (pttt) REVERT: M 279 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: M 356 ARG cc_start: 0.5967 (mpp-170) cc_final: 0.5546 (mtp85) REVERT: M 394 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6683 (ttpt) REVERT: N 279 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: N 409 MET cc_start: 0.7258 (mmm) cc_final: 0.6529 (mmp) REVERT: N 413 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: N 414 ASP cc_start: 0.7205 (m-30) cc_final: 0.6791 (m-30) REVERT: O 247 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7577 (mtm-85) REVERT: O 279 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: O 409 MET cc_start: 0.7008 (mmm) cc_final: 0.6476 (mmp) REVERT: P 413 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6834 (mt-10) REVERT: Q 236 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7430 (pttt) REVERT: Q 279 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: Q 394 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6731 (ttpt) REVERT: R 413 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6878 (tt0) REVERT: S 247 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7629 (mtm180) REVERT: S 290 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8212 (mmtm) REVERT: S 410 LYS cc_start: 0.7581 (tttm) cc_final: 0.7215 (ttpt) REVERT: S 413 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6983 (mp0) REVERT: T 232 ASP cc_start: 0.6626 (m-30) cc_final: 0.6241 (t70) REVERT: T 409 MET cc_start: 0.7239 (mmm) cc_final: 0.5884 (mmp) REVERT: T 413 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6933 (mp0) REVERT: U 247 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7492 (mtm110) REVERT: U 279 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: U 290 LYS cc_start: 0.8777 (mttp) cc_final: 0.8572 (mttt) REVERT: U 356 ARG cc_start: 0.6129 (mpp-170) cc_final: 0.5518 (ttt-90) REVERT: U 409 MET cc_start: 0.7415 (mmm) cc_final: 0.6785 (mmp) REVERT: U 413 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6762 (mt-10) REVERT: W 279 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: W 356 ARG cc_start: 0.6309 (mpp-170) cc_final: 0.6027 (mpp-170) REVERT: W 409 MET cc_start: 0.7293 (mmm) cc_final: 0.6050 (mmp) REVERT: W 413 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6656 (mp0) REVERT: X 232 ASP cc_start: 0.6386 (m-30) cc_final: 0.6044 (t70) REVERT: X 297 GLN cc_start: 0.7806 (tt0) cc_final: 0.7595 (tt0) REVERT: X 394 LYS cc_start: 0.6859 (ttpt) cc_final: 0.6565 (pttt) REVERT: X 409 MET cc_start: 0.7415 (mmm) cc_final: 0.6131 (mmp) REVERT: X 413 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6901 (mp0) REVERT: X 414 ASP cc_start: 0.7251 (m-30) cc_final: 0.6979 (m-30) REVERT: Y 279 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: Y 394 LYS cc_start: 0.7004 (ttpt) cc_final: 0.6748 (ttpt) REVERT: Y 424 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: Z 247 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7450 (mtm-85) REVERT: Z 409 MET cc_start: 0.7436 (mmm) cc_final: 0.6217 (mmp) REVERT: Z 413 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6487 (mp0) REVERT: a 232 ASP cc_start: 0.6696 (m-30) cc_final: 0.6231 (t70) REVERT: a 279 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: a 410 LYS cc_start: 0.7619 (tttm) cc_final: 0.7241 (ttpt) REVERT: a 413 GLU cc_start: 0.7569 (tm-30) cc_final: 0.6929 (mp0) REVERT: b 236 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7562 (pttt) REVERT: b 247 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7403 (mtm110) REVERT: b 279 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: b 413 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6642 (mp0) REVERT: c 279 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: c 413 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6684 (mp0) REVERT: d 232 ASP cc_start: 0.6701 (m-30) cc_final: 0.6326 (t70) REVERT: d 279 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: d 356 ARG cc_start: 0.5999 (mpp-170) cc_final: 0.5739 (mpp-170) REVERT: d 409 MET cc_start: 0.7529 (mmm) cc_final: 0.6219 (mmp) REVERT: d 413 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6853 (mp0) REVERT: e 232 ASP cc_start: 0.6585 (m-30) cc_final: 0.6133 (t70) REVERT: e 410 LYS cc_start: 0.7564 (tttm) cc_final: 0.7293 (ttpt) REVERT: e 413 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6706 (mt-10) REVERT: f 247 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7390 (mtm180) REVERT: f 279 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: f 394 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6076 (tptm) REVERT: g 267 THR cc_start: 0.8554 (t) cc_final: 0.8237 (m) REVERT: g 279 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: g 377 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8263 (mpt) REVERT: g 413 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6637 (mp0) outliers start: 123 outliers final: 54 residues processed: 1079 average time/residue: 0.9423 time to fit residues: 1179.3286 Evaluate side-chains 1126 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1036 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 413 GLU Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 236 LYS Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 410 LYS Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 407 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 377 MET Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 336 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 392 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 437 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 374 HIS I 303 GLN J 303 GLN P 303 GLN S 303 GLN W 359 GLN Y 374 HIS c 246 GLN d 246 GLN e 246 GLN e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138961 restraints weight = 45200.957| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.59 r_work: 0.3536 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 41052 Z= 0.193 Angle : 0.596 5.684 55374 Z= 0.334 Chirality : 0.041 0.130 6402 Planarity : 0.003 0.029 7392 Dihedral : 4.311 18.187 5544 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.92 % Allowed : 18.44 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.12), residues: 4950 helix: 4.26 (0.13), residues: 1386 sheet: 2.24 (0.11), residues: 2442 loop : -1.38 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 356 TYR 0.009 0.001 TYR d 282 PHE 0.012 0.002 PHE L 422 HIS 0.007 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00396 (41052) covalent geometry : angle 0.59636 (55374) hydrogen bonds : bond 0.08084 ( 2212) hydrogen bonds : angle 3.93218 ( 6438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1041 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7593 (mtm180) REVERT: A 259 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6796 (m-40) REVERT: A 279 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6544 (mt-10) REVERT: B 247 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7581 (mtm110) REVERT: B 279 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: B 377 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8432 (mpp) REVERT: C 232 ASP cc_start: 0.6825 (m-30) cc_final: 0.6483 (t70) REVERT: C 279 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6583 (mt-10) REVERT: C 410 LYS cc_start: 0.7815 (tttm) cc_final: 0.7483 (ttpt) REVERT: C 413 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: D 247 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7469 (mtm180) REVERT: D 279 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: D 356 ARG cc_start: 0.6351 (mpp-170) cc_final: 0.6140 (mpp-170) REVERT: D 410 LYS cc_start: 0.7828 (tttm) cc_final: 0.7592 (tttp) REVERT: D 413 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6693 (mp0) REVERT: E 247 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7569 (mtm180) REVERT: E 274 ASN cc_start: 0.8213 (m-40) cc_final: 0.7904 (m110) REVERT: E 413 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6972 (mp0) REVERT: F 232 ASP cc_start: 0.6700 (m-30) cc_final: 0.6175 (t70) REVERT: F 247 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7610 (mtm180) REVERT: F 279 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: G 232 ASP cc_start: 0.6674 (m-30) cc_final: 0.6385 (t70) REVERT: G 236 LYS cc_start: 0.8340 (mttm) cc_final: 0.7774 (pttp) REVERT: G 247 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7425 (mtm180) REVERT: G 279 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: G 356 ARG cc_start: 0.6319 (mpp-170) cc_final: 0.6009 (mpp-170) REVERT: G 413 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6860 (mt-10) REVERT: H 267 THR cc_start: 0.8700 (t) cc_final: 0.8392 (m) REVERT: H 279 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: H 410 LYS cc_start: 0.7654 (tttm) cc_final: 0.7085 (tptp) REVERT: H 413 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6815 (mp0) REVERT: I 267 THR cc_start: 0.8572 (t) cc_final: 0.8228 (m) REVERT: I 356 ARG cc_start: 0.5856 (mpp-170) cc_final: 0.5647 (mtp85) REVERT: I 370 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7900 (ttm170) REVERT: I 413 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6959 (mp0) REVERT: J 267 THR cc_start: 0.8569 (t) cc_final: 0.8352 (m) REVERT: J 279 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: J 410 LYS cc_start: 0.7862 (tttm) cc_final: 0.7401 (ttpt) REVERT: J 413 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7046 (mp0) REVERT: K 279 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: K 290 LYS cc_start: 0.8503 (mttp) cc_final: 0.8260 (mttt) REVERT: K 410 LYS cc_start: 0.7906 (tttm) cc_final: 0.7607 (ttpt) REVERT: L 232 ASP cc_start: 0.6854 (m-30) cc_final: 0.6413 (t70) REVERT: L 247 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7642 (mtm110) REVERT: L 279 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: L 356 ARG cc_start: 0.5809 (mpp-170) cc_final: 0.5409 (mtp85) REVERT: L 413 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6863 (mp0) REVERT: M 236 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7744 (pttt) REVERT: M 279 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: M 356 ARG cc_start: 0.6062 (mpp-170) cc_final: 0.5627 (mtp85) REVERT: N 279 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6574 (mt-10) REVERT: N 409 MET cc_start: 0.7258 (mmm) cc_final: 0.6587 (mmp) REVERT: N 413 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: N 414 ASP cc_start: 0.7257 (m-30) cc_final: 0.6832 (m-30) REVERT: O 247 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7517 (mtm-85) REVERT: O 413 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7214 (tt0) REVERT: P 413 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6829 (mt-10) REVERT: Q 236 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7547 (pttt) REVERT: Q 247 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7531 (mtm180) REVERT: Q 279 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: Q 394 LYS cc_start: 0.6871 (ttpt) cc_final: 0.6635 (ttpt) REVERT: R 279 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: R 413 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6933 (tt0) REVERT: S 236 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7435 (pttt) REVERT: S 247 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7667 (mtm180) REVERT: S 290 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (mmtm) REVERT: S 356 ARG cc_start: 0.6015 (mpp-170) cc_final: 0.5611 (mpp-170) REVERT: S 410 LYS cc_start: 0.7570 (tttm) cc_final: 0.7200 (ttpt) REVERT: S 413 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6969 (mp0) REVERT: T 232 ASP cc_start: 0.6716 (m-30) cc_final: 0.6371 (t70) REVERT: T 267 THR cc_start: 0.8648 (t) cc_final: 0.8366 (m) REVERT: T 409 MET cc_start: 0.7246 (mmm) cc_final: 0.5923 (mmp) REVERT: T 413 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6960 (mp0) REVERT: U 247 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7506 (mtm180) REVERT: U 279 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6733 (mt-10) REVERT: U 290 LYS cc_start: 0.8776 (mttp) cc_final: 0.8565 (mttt) REVERT: U 356 ARG cc_start: 0.6168 (mpp-170) cc_final: 0.5661 (ttt-90) REVERT: U 409 MET cc_start: 0.7437 (mmm) cc_final: 0.6899 (mmp) REVERT: U 413 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6799 (mt-10) REVERT: W 279 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6482 (mt-10) REVERT: W 356 ARG cc_start: 0.6264 (mpp-170) cc_final: 0.6057 (mpp-170) REVERT: W 409 MET cc_start: 0.7295 (mmm) cc_final: 0.6136 (mmp) REVERT: W 413 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6677 (mp0) REVERT: X 232 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6237 (t70) REVERT: X 409 MET cc_start: 0.7459 (mmm) cc_final: 0.6154 (mmp) REVERT: X 413 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6828 (mp0) REVERT: X 414 ASP cc_start: 0.7316 (m-30) cc_final: 0.7032 (m-30) REVERT: Y 279 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6575 (mt-10) REVERT: Y 356 ARG cc_start: 0.6128 (mpp-170) cc_final: 0.5847 (mpp-170) REVERT: Y 424 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: Z 236 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7545 (pttt) REVERT: Z 247 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7400 (mtm-85) REVERT: Z 409 MET cc_start: 0.7454 (mmm) cc_final: 0.6258 (mmp) REVERT: Z 413 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6556 (mp0) REVERT: a 232 ASP cc_start: 0.6859 (m-30) cc_final: 0.6394 (t70) REVERT: a 279 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: a 410 LYS cc_start: 0.7637 (tttm) cc_final: 0.7247 (ttpt) REVERT: a 413 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6957 (mp0) REVERT: b 247 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7497 (mtm180) REVERT: b 279 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: b 413 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6645 (mp0) REVERT: c 279 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: c 413 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6691 (mp0) REVERT: d 232 ASP cc_start: 0.6918 (m-30) cc_final: 0.6537 (t70) REVERT: d 236 LYS cc_start: 0.7691 (pttp) cc_final: 0.7396 (pptt) REVERT: d 279 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: d 356 ARG cc_start: 0.6084 (mpp-170) cc_final: 0.5829 (mpp-170) REVERT: d 409 MET cc_start: 0.7562 (mmm) cc_final: 0.6278 (mmp) REVERT: d 413 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6867 (mp0) REVERT: e 232 ASP cc_start: 0.6693 (m-30) cc_final: 0.6330 (t70) REVERT: e 356 ARG cc_start: 0.5969 (mpp-170) cc_final: 0.5712 (mpp-170) REVERT: e 410 LYS cc_start: 0.7599 (tttm) cc_final: 0.7340 (ttpt) REVERT: e 413 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6704 (mt-10) REVERT: f 247 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7440 (mtm180) REVERT: f 279 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: g 267 THR cc_start: 0.8580 (t) cc_final: 0.8293 (m) REVERT: g 279 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: g 413 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6649 (mp0) outliers start: 134 outliers final: 68 residues processed: 1086 average time/residue: 1.0103 time to fit residues: 1268.9699 Evaluate side-chains 1137 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1034 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain N residue 413 GLU Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 236 LYS Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 236 LYS Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 259 ASN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 410 LYS Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 259 ASN Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 390 optimal weight: 0.5980 chunk 120 optimal weight: 0.0980 chunk 440 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 451 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 263 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN H 374 HIS I 303 GLN J 303 GLN L 374 HIS N 303 GLN P 303 GLN S 303 GLN S 359 GLN V 303 GLN W 303 GLN W 359 GLN Y 374 HIS e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142544 restraints weight = 45207.435| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.57 r_work: 0.3584 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 41052 Z= 0.123 Angle : 0.495 4.644 55374 Z= 0.275 Chirality : 0.039 0.128 6402 Planarity : 0.002 0.024 7392 Dihedral : 3.986 16.937 5544 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 2.18 % Allowed : 19.03 % Favored : 78.79 % 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: 3.43 (0.12), residues: 4950 helix: 4.60 (0.13), residues: 1386 sheet: 2.32 (0.11), residues: 2442 loop : -1.30 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 356 TYR 0.010 0.001 TYR d 282 PHE 0.008 0.001 PHE L 422 HIS 0.007 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00225 (41052) covalent geometry : angle 0.49528 (55374) hydrogen bonds : bond 0.05636 ( 2212) hydrogen bonds : angle 3.73625 ( 6438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1061 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7561 (mtm110) REVERT: A 279 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: B 279 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: B 413 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6702 (mp0) REVERT: C 232 ASP cc_start: 0.6531 (m-30) cc_final: 0.6053 (t70) REVERT: C 279 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: C 410 LYS cc_start: 0.7747 (tttm) cc_final: 0.7403 (ttpt) REVERT: D 247 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7446 (mtm110) REVERT: D 279 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6651 (mt-10) REVERT: D 377 MET cc_start: 0.8739 (mpp) cc_final: 0.8023 (mpt) REVERT: D 413 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6639 (mp0) REVERT: E 247 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7547 (mtm180) REVERT: E 274 ASN cc_start: 0.8082 (m-40) cc_final: 0.7793 (m110) REVERT: E 413 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6948 (mp0) REVERT: F 232 ASP cc_start: 0.6403 (m-30) cc_final: 0.6034 (t70) REVERT: F 236 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7342 (pttp) REVERT: F 247 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7567 (mtm180) REVERT: F 279 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6949 (mp0) REVERT: F 409 MET cc_start: 0.7010 (mmm) cc_final: 0.6353 (mmp) REVERT: G 232 ASP cc_start: 0.6292 (m-30) cc_final: 0.6040 (t70) REVERT: G 236 LYS cc_start: 0.8137 (mttm) cc_final: 0.7518 (pttp) REVERT: G 247 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7318 (mtm180) REVERT: G 279 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: G 290 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8349 (mtmt) REVERT: G 356 ARG cc_start: 0.6206 (mpp-170) cc_final: 0.5956 (mpp-170) REVERT: G 413 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6921 (mt-10) REVERT: H 267 THR cc_start: 0.8680 (t) cc_final: 0.8327 (m) REVERT: H 279 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: H 410 LYS cc_start: 0.7584 (tttm) cc_final: 0.7059 (tptp) REVERT: H 413 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6832 (mp0) REVERT: I 267 THR cc_start: 0.8529 (t) cc_final: 0.8121 (m) REVERT: I 279 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: I 370 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7860 (ttm170) REVERT: I 413 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6879 (mp0) REVERT: J 232 ASP cc_start: 0.6515 (m-30) cc_final: 0.6023 (t70) REVERT: J 279 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: J 377 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (mpt) REVERT: J 410 LYS cc_start: 0.7840 (tttm) cc_final: 0.7363 (ttpt) REVERT: J 413 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7040 (mp0) REVERT: K 279 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: K 410 LYS cc_start: 0.7720 (tttm) cc_final: 0.7412 (ttpt) REVERT: L 232 ASP cc_start: 0.6416 (m-30) cc_final: 0.6019 (t70) REVERT: L 247 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7457 (mtm180) REVERT: L 279 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: L 413 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6910 (mp0) REVERT: M 236 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7403 (pttt) REVERT: M 279 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: M 356 ARG cc_start: 0.6021 (mpp-170) cc_final: 0.5611 (mtp85) REVERT: N 279 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: N 409 MET cc_start: 0.7232 (mmm) cc_final: 0.6459 (mmp) REVERT: N 414 ASP cc_start: 0.7245 (m-30) cc_final: 0.6891 (m-30) REVERT: O 247 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7497 (mtm-85) REVERT: O 279 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: P 413 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6808 (mt-10) REVERT: Q 279 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: Q 394 LYS cc_start: 0.6843 (ttpt) cc_final: 0.6615 (ttpt) REVERT: R 279 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: R 413 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6890 (tt0) REVERT: S 247 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7543 (mtm180) REVERT: S 290 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (mmtm) REVERT: S 410 LYS cc_start: 0.7552 (tttm) cc_final: 0.7202 (ttpt) REVERT: S 413 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6932 (mp0) REVERT: T 232 ASP cc_start: 0.6344 (m-30) cc_final: 0.5985 (t70) REVERT: T 409 MET cc_start: 0.7260 (mmm) cc_final: 0.5977 (mmp) REVERT: T 413 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6908 (mp0) REVERT: U 247 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7548 (mtm110) REVERT: U 279 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: U 356 ARG cc_start: 0.6219 (mpp-170) cc_final: 0.5593 (ttt-90) REVERT: U 409 MET cc_start: 0.7370 (mmm) cc_final: 0.6749 (mmp) REVERT: U 413 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6757 (mt-10) REVERT: W 279 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: W 409 MET cc_start: 0.7294 (mmm) cc_final: 0.6115 (mmp) REVERT: W 413 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6730 (mp0) REVERT: X 232 ASP cc_start: 0.6207 (m-30) cc_final: 0.5873 (t70) REVERT: X 409 MET cc_start: 0.7396 (mmm) cc_final: 0.6065 (mmp) REVERT: X 413 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6890 (mp0) REVERT: X 414 ASP cc_start: 0.7098 (m-30) cc_final: 0.6826 (m-30) REVERT: Y 279 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: Y 356 ARG cc_start: 0.6062 (mpp-170) cc_final: 0.5837 (mpp-170) REVERT: Y 424 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: Z 236 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7340 (pttt) REVERT: Z 247 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7375 (mtm-85) REVERT: Z 409 MET cc_start: 0.7392 (mmm) cc_final: 0.6141 (mmp) REVERT: Z 413 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6472 (mp0) REVERT: a 232 ASP cc_start: 0.6502 (m-30) cc_final: 0.6028 (t70) REVERT: a 279 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: a 410 LYS cc_start: 0.7561 (tttm) cc_final: 0.7237 (ttpt) REVERT: a 413 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6904 (mp0) REVERT: b 236 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7435 (pttt) REVERT: b 247 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7328 (mtm110) REVERT: b 279 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: b 356 ARG cc_start: 0.6176 (mpp-170) cc_final: 0.5855 (mpp-170) REVERT: b 413 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6614 (mp0) REVERT: c 247 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7379 (mtm180) REVERT: c 279 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: c 413 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6698 (mp0) REVERT: d 236 LYS cc_start: 0.7468 (pttp) cc_final: 0.7172 (pptt) REVERT: d 279 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: d 409 MET cc_start: 0.7495 (mmm) cc_final: 0.6164 (mmp) REVERT: d 413 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6812 (mp0) REVERT: e 232 ASP cc_start: 0.6421 (m-30) cc_final: 0.5978 (t70) REVERT: e 356 ARG cc_start: 0.6023 (mpp-170) cc_final: 0.5796 (mpp-170) REVERT: e 410 LYS cc_start: 0.7573 (tttm) cc_final: 0.7281 (ttpt) REVERT: e 413 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6655 (mt-10) REVERT: f 247 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7339 (mtm180) REVERT: f 279 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: f 394 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6066 (tptm) REVERT: g 279 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6555 (mt-10) REVERT: g 413 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6616 (mp0) outliers start: 100 outliers final: 46 residues processed: 1086 average time/residue: 0.9340 time to fit residues: 1176.8699 Evaluate side-chains 1125 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1048 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 410 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 376 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 301 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 chunk 100 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 374 HIS I 303 GLN J 303 GLN L 374 HIS P 303 GLN P 359 GLN S 303 GLN U 246 GLN V 246 GLN W 303 GLN W 359 GLN Y 374 HIS Z 374 HIS e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140611 restraints weight = 44551.111| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.56 r_work: 0.3534 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 41052 Z= 0.221 Angle : 0.633 5.340 55374 Z= 0.355 Chirality : 0.043 0.136 6402 Planarity : 0.003 0.045 7392 Dihedral : 4.411 18.269 5544 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.75 % Allowed : 18.16 % Favored : 79.09 % 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: 3.05 (0.12), residues: 4950 helix: 4.15 (0.13), residues: 1386 sheet: 2.17 (0.11), residues: 2442 loop : -1.51 (0.13), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 370 TYR 0.009 0.001 TYR d 282 PHE 0.013 0.002 PHE L 422 HIS 0.010 0.002 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00469 (41052) covalent geometry : angle 0.63281 (55374) hydrogen bonds : bond 0.08718 ( 2212) hydrogen bonds : angle 3.96665 ( 6438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1029 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7624 (mtm180) REVERT: A 259 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6785 (m-40) REVERT: A 279 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: B 247 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7590 (mtm110) REVERT: B 279 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: B 377 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8472 (mpp) REVERT: B 413 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6724 (mp0) REVERT: C 232 ASP cc_start: 0.6952 (m-30) cc_final: 0.6594 (t70) REVERT: C 279 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: C 410 LYS cc_start: 0.7835 (tttm) cc_final: 0.7512 (ttpt) REVERT: D 247 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7559 (mtm110) REVERT: D 279 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: D 413 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6821 (mp0) REVERT: E 247 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7586 (mtm180) REVERT: E 274 ASN cc_start: 0.8200 (m-40) cc_final: 0.7907 (m110) REVERT: F 232 ASP cc_start: 0.6787 (m-30) cc_final: 0.6395 (t70) REVERT: F 247 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7651 (mtm180) REVERT: F 279 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6964 (mp0) REVERT: G 232 ASP cc_start: 0.6757 (m-30) cc_final: 0.6487 (t70) REVERT: G 236 LYS cc_start: 0.8412 (mttm) cc_final: 0.7872 (pttp) REVERT: G 247 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7634 (mtm110) REVERT: G 279 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: G 290 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8387 (mtmt) REVERT: G 356 ARG cc_start: 0.6244 (mpp-170) cc_final: 0.5810 (mtp85) REVERT: G 413 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6794 (mt-10) REVERT: H 267 THR cc_start: 0.8725 (t) cc_final: 0.8412 (m) REVERT: H 279 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: H 410 LYS cc_start: 0.7717 (tttm) cc_final: 0.7156 (tptp) REVERT: H 413 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6873 (mp0) REVERT: I 267 THR cc_start: 0.8586 (t) cc_final: 0.8250 (m) REVERT: I 413 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6947 (mp0) REVERT: J 267 THR cc_start: 0.8595 (t) cc_final: 0.8382 (m) REVERT: J 279 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: J 413 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7109 (mp0) REVERT: K 279 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: K 290 LYS cc_start: 0.8617 (mttp) cc_final: 0.8377 (mttt) REVERT: K 410 LYS cc_start: 0.7939 (tttm) cc_final: 0.7631 (ttpt) REVERT: L 232 ASP cc_start: 0.6929 (m-30) cc_final: 0.6505 (t70) REVERT: L 247 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7712 (mtm110) REVERT: L 279 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: L 413 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6887 (mp0) REVERT: M 236 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7777 (pttt) REVERT: M 279 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: M 356 ARG cc_start: 0.6071 (mpp-170) cc_final: 0.5645 (mtp85) REVERT: M 370 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7780 (ttp80) REVERT: N 279 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: N 409 MET cc_start: 0.7386 (mmm) cc_final: 0.6987 (mmp) REVERT: O 247 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7573 (mtm-85) REVERT: O 356 ARG cc_start: 0.6055 (mpp-170) cc_final: 0.5805 (mpp-170) REVERT: O 413 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: P 413 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6937 (mp0) REVERT: Q 279 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: R 279 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: R 413 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6968 (tt0) REVERT: S 247 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7635 (mtm180) REVERT: S 290 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8221 (mmtm) REVERT: S 410 LYS cc_start: 0.7579 (tttm) cc_final: 0.7206 (ttpt) REVERT: S 413 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7013 (mp0) REVERT: T 232 ASP cc_start: 0.6808 (m-30) cc_final: 0.6473 (t70) REVERT: T 267 THR cc_start: 0.8643 (t) cc_final: 0.8388 (m) REVERT: T 409 MET cc_start: 0.7338 (mmm) cc_final: 0.5943 (mmp) REVERT: T 413 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7022 (mp0) REVERT: U 247 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7600 (mtm180) REVERT: U 279 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: U 356 ARG cc_start: 0.6193 (mpp-170) cc_final: 0.5717 (ttt-90) REVERT: U 409 MET cc_start: 0.7469 (mmm) cc_final: 0.6981 (mmp) REVERT: U 413 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6869 (mt-10) REVERT: W 279 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6468 (mt-10) REVERT: W 356 ARG cc_start: 0.6107 (mpp-170) cc_final: 0.5858 (mtp85) REVERT: W 409 MET cc_start: 0.7340 (mmm) cc_final: 0.6197 (mmp) REVERT: W 413 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6691 (mp0) REVERT: X 232 ASP cc_start: 0.6751 (m-30) cc_final: 0.6389 (t70) REVERT: X 409 MET cc_start: 0.7556 (mmm) cc_final: 0.6255 (mmp) REVERT: X 413 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6877 (mp0) REVERT: X 414 ASP cc_start: 0.7392 (m-30) cc_final: 0.7136 (m-30) REVERT: Y 279 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6524 (mt-10) REVERT: Y 356 ARG cc_start: 0.6123 (mpp-170) cc_final: 0.5911 (mpp-170) REVERT: Y 424 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: Z 236 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7621 (pttt) REVERT: Z 247 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7441 (mtm-85) REVERT: Z 409 MET cc_start: 0.7498 (mmm) cc_final: 0.6263 (mmp) REVERT: Z 413 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6584 (mp0) REVERT: a 232 ASP cc_start: 0.6945 (m-30) cc_final: 0.6584 (t70) REVERT: a 279 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: a 410 LYS cc_start: 0.7656 (tttm) cc_final: 0.7261 (ttpt) REVERT: a 413 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6979 (mp0) REVERT: b 247 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7502 (mtm180) REVERT: b 279 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6827 (mt-10) REVERT: b 413 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6631 (mp0) REVERT: c 279 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: c 413 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6820 (mp0) REVERT: d 236 LYS cc_start: 0.7777 (pttp) cc_final: 0.7513 (pptt) REVERT: d 279 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: d 409 MET cc_start: 0.7552 (mmm) cc_final: 0.6255 (mmp) REVERT: d 413 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6909 (mp0) REVERT: e 410 LYS cc_start: 0.7592 (tttm) cc_final: 0.7333 (ttpt) REVERT: e 413 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6722 (mt-10) REVERT: f 236 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7480 (pptt) REVERT: f 247 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7517 (mtm180) REVERT: f 279 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: f 394 LYS cc_start: 0.6861 (ttpt) cc_final: 0.6091 (tptm) REVERT: g 267 THR cc_start: 0.8609 (t) cc_final: 0.8348 (m) REVERT: g 279 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: g 413 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 126 outliers final: 63 residues processed: 1077 average time/residue: 0.9141 time to fit residues: 1139.9806 Evaluate side-chains 1126 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1031 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 386 SER Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain O residue 413 GLU Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 259 ASN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 386 SER Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 429 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 492 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 318 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 443 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 380 optimal weight: 4.9990 chunk 445 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN H 374 HIS I 303 GLN J 303 GLN N 303 GLN P 303 GLN P 359 GLN S 303 GLN S 359 GLN W 303 GLN W 359 GLN Y 374 HIS e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141744 restraints weight = 45051.105| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.57 r_work: 0.3553 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 41052 Z= 0.178 Angle : 0.578 5.866 55374 Z= 0.323 Chirality : 0.041 0.129 6402 Planarity : 0.003 0.022 7392 Dihedral : 4.293 17.998 5544 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.38 % Allowed : 18.55 % Favored : 79.07 % 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: 3.08 (0.12), residues: 4950 helix: 4.21 (0.13), residues: 1386 sheet: 2.18 (0.11), residues: 2442 loop : -1.51 (0.13), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 356 TYR 0.009 0.001 TYR d 282 PHE 0.011 0.002 PHE L 422 HIS 0.008 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00361 (41052) covalent geometry : angle 0.57830 (55374) hydrogen bonds : bond 0.07482 ( 2212) hydrogen bonds : angle 3.87025 ( 6438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1039 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7648 (mtm110) REVERT: A 279 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6514 (mt-10) REVERT: B 247 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7508 (mtm180) REVERT: B 279 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: B 377 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8451 (mpp) REVERT: B 413 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6715 (mp0) REVERT: C 232 ASP cc_start: 0.6821 (m-30) cc_final: 0.6468 (t70) REVERT: C 410 LYS cc_start: 0.7792 (tttm) cc_final: 0.7440 (ttpt) REVERT: C 413 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: D 247 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7512 (mtm180) REVERT: D 279 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: D 377 MET cc_start: 0.8809 (mpp) cc_final: 0.8121 (mpt) REVERT: D 413 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6706 (mp0) REVERT: E 247 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7583 (mtm180) REVERT: E 274 ASN cc_start: 0.8138 (m-40) cc_final: 0.7844 (m110) REVERT: E 413 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7009 (mp0) REVERT: F 232 ASP cc_start: 0.6669 (m-30) cc_final: 0.6284 (t70) REVERT: F 236 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7540 (pttp) REVERT: F 247 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7562 (mtm180) REVERT: F 279 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: F 356 ARG cc_start: 0.6071 (mpp-170) cc_final: 0.5842 (mtp-110) REVERT: F 409 MET cc_start: 0.7018 (mmm) cc_final: 0.6618 (mmp) REVERT: G 232 ASP cc_start: 0.6641 (m-30) cc_final: 0.6375 (t70) REVERT: G 236 LYS cc_start: 0.8356 (mttm) cc_final: 0.7842 (pttp) REVERT: G 247 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7448 (mtm180) REVERT: G 279 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: G 290 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: G 356 ARG cc_start: 0.6226 (mpp-170) cc_final: 0.5786 (mtp85) REVERT: G 413 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6843 (mt-10) REVERT: H 267 THR cc_start: 0.8694 (t) cc_final: 0.8365 (m) REVERT: H 279 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: H 410 LYS cc_start: 0.7670 (tttm) cc_final: 0.7129 (tptp) REVERT: H 413 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6885 (mp0) REVERT: I 267 THR cc_start: 0.8560 (t) cc_final: 0.8182 (m) REVERT: I 279 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: I 413 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6930 (mp0) REVERT: J 267 THR cc_start: 0.8590 (t) cc_final: 0.8340 (m) REVERT: J 279 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: J 377 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8430 (mpt) REVERT: J 413 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7109 (mp0) REVERT: K 279 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: K 410 LYS cc_start: 0.7911 (tttm) cc_final: 0.7605 (ttpt) REVERT: L 232 ASP cc_start: 0.6832 (m-30) cc_final: 0.6390 (t70) REVERT: L 247 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7549 (mtm180) REVERT: L 279 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: L 413 GLU cc_start: 0.7638 (tm-30) cc_final: 0.6894 (mp0) REVERT: M 236 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7750 (pttt) REVERT: M 279 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: M 356 ARG cc_start: 0.6054 (mpp-170) cc_final: 0.5633 (mtp85) REVERT: N 279 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: N 409 MET cc_start: 0.7230 (mmm) cc_final: 0.6855 (mmp) REVERT: N 414 ASP cc_start: 0.7228 (m-30) cc_final: 0.6834 (m-30) REVERT: O 356 ARG cc_start: 0.6045 (mpp-170) cc_final: 0.5806 (mpp-170) REVERT: O 413 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: P 413 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6924 (mt-10) REVERT: Q 279 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: R 279 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: R 413 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6945 (tt0) REVERT: S 247 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7671 (mtm180) REVERT: S 290 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8202 (mmtm) REVERT: S 410 LYS cc_start: 0.7564 (tttm) cc_final: 0.7205 (ttpt) REVERT: S 413 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6991 (mp0) REVERT: T 232 ASP cc_start: 0.6658 (m-30) cc_final: 0.6312 (t70) REVERT: T 409 MET cc_start: 0.7320 (mmm) cc_final: 0.5933 (mmp) REVERT: T 413 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7000 (mp0) REVERT: U 247 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7647 (mtm110) REVERT: U 279 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: U 356 ARG cc_start: 0.6179 (mpp-170) cc_final: 0.5753 (ttt-90) REVERT: U 409 MET cc_start: 0.7472 (mmm) cc_final: 0.6849 (mmp) REVERT: U 413 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6825 (mt-10) REVERT: V 413 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6685 (tt0) REVERT: W 279 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: W 356 ARG cc_start: 0.6108 (mpp-170) cc_final: 0.5849 (mtp85) REVERT: W 377 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8605 (mpt) REVERT: W 409 MET cc_start: 0.7346 (mmm) cc_final: 0.6156 (mmp) REVERT: W 413 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6661 (mp0) REVERT: X 232 ASP cc_start: 0.6602 (m-30) cc_final: 0.6247 (t70) REVERT: X 356 ARG cc_start: 0.6031 (mpp-170) cc_final: 0.5610 (mtp85) REVERT: X 409 MET cc_start: 0.7496 (mmm) cc_final: 0.6254 (mmp) REVERT: X 413 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6871 (mp0) REVERT: X 414 ASP cc_start: 0.7350 (m-30) cc_final: 0.7081 (m-30) REVERT: Y 279 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: Y 424 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: Z 236 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7554 (pttt) REVERT: Z 247 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7400 (mtm-85) REVERT: Z 409 MET cc_start: 0.7435 (mmm) cc_final: 0.6254 (mmp) REVERT: Z 413 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6509 (mp0) REVERT: a 232 ASP cc_start: 0.6856 (m-30) cc_final: 0.6405 (t70) REVERT: a 279 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: a 410 LYS cc_start: 0.7619 (tttm) cc_final: 0.7239 (ttpt) REVERT: a 413 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6961 (mp0) REVERT: b 247 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7465 (mtm180) REVERT: b 279 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: b 356 ARG cc_start: 0.6169 (mpp-170) cc_final: 0.5891 (mpt180) REVERT: b 413 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6618 (mp0) REVERT: c 279 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: c 413 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6805 (mp0) REVERT: d 232 ASP cc_start: 0.6828 (m-30) cc_final: 0.6472 (t70) REVERT: d 236 LYS cc_start: 0.7643 (pttp) cc_final: 0.7380 (pptt) REVERT: d 279 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: d 409 MET cc_start: 0.7528 (mmm) cc_final: 0.6210 (mmp) REVERT: d 413 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6890 (mp0) REVERT: e 232 ASP cc_start: 0.6733 (m-30) cc_final: 0.6360 (t70) REVERT: e 410 LYS cc_start: 0.7584 (tttm) cc_final: 0.7304 (ttpt) REVERT: e 413 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6700 (mt-10) REVERT: f 236 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7425 (pptt) REVERT: f 247 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7483 (mtm180) REVERT: f 279 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: f 394 LYS cc_start: 0.6908 (ttpt) cc_final: 0.6140 (tptm) REVERT: g 267 THR cc_start: 0.8596 (t) cc_final: 0.8306 (m) REVERT: g 279 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: g 356 ARG cc_start: 0.5983 (mpp-170) cc_final: 0.5406 (mpp-170) REVERT: g 413 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6687 (mp0) outliers start: 109 outliers final: 65 residues processed: 1078 average time/residue: 1.0034 time to fit residues: 1250.0467 Evaluate side-chains 1137 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1037 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain O residue 413 GLU Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 259 ASN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 413 GLU Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 420 MET Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 236 LYS Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 259 ASN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 11 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 479 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 246 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN B 303 GLN H 374 HIS I 303 GLN J 303 GLN N 303 GLN P 303 GLN P 359 GLN S 303 GLN S 359 GLN W 303 GLN W 359 GLN Y 374 HIS Z 374 HIS e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138925 restraints weight = 44536.259| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.59 r_work: 0.3531 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 41052 Z= 0.212 Angle : 0.634 5.985 55374 Z= 0.354 Chirality : 0.043 0.136 6402 Planarity : 0.003 0.055 7392 Dihedral : 4.431 18.262 5544 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.46 % Allowed : 18.42 % Favored : 79.11 % 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: 2.88 (0.12), residues: 4950 helix: 4.01 (0.13), residues: 1386 sheet: 2.09 (0.11), residues: 2442 loop : -1.61 (0.13), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 356 TYR 0.009 0.001 TYR d 282 PHE 0.014 0.002 PHE L 422 HIS 0.009 0.002 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00445 (41052) covalent geometry : angle 0.63399 (55374) hydrogen bonds : bond 0.08529 ( 2212) hydrogen bonds : angle 3.96990 ( 6438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9900 Ramachandran restraints generated. 4950 Oldfield, 0 Emsley, 4950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1040 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7616 (mtm180) REVERT: A 259 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6663 (m-40) REVERT: A 279 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: B 247 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7565 (mtm110) REVERT: B 274 ASN cc_start: 0.8229 (m-40) cc_final: 0.7876 (m110) REVERT: B 279 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: B 377 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8432 (mpp) REVERT: B 413 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6645 (mp0) REVERT: C 232 ASP cc_start: 0.6908 (m-30) cc_final: 0.6557 (t70) REVERT: C 356 ARG cc_start: 0.6180 (mpp-170) cc_final: 0.5977 (mpp-170) REVERT: C 410 LYS cc_start: 0.7828 (tttm) cc_final: 0.7489 (ttpt) REVERT: C 413 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: D 247 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7542 (mtm110) REVERT: D 279 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: D 413 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6678 (mp0) REVERT: D 425 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7159 (tptp) REVERT: E 247 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7591 (mtm180) REVERT: E 274 ASN cc_start: 0.8190 (m-40) cc_final: 0.7889 (m110) REVERT: E 413 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6934 (mp0) REVERT: F 232 ASP cc_start: 0.6790 (m-30) cc_final: 0.6293 (t70) REVERT: F 247 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7637 (mtm180) REVERT: F 279 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: F 409 MET cc_start: 0.7034 (mmm) cc_final: 0.6609 (mmp) REVERT: G 232 ASP cc_start: 0.6734 (m-30) cc_final: 0.6467 (t70) REVERT: G 236 LYS cc_start: 0.8398 (mttm) cc_final: 0.7832 (pttp) REVERT: G 247 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7492 (mtm110) REVERT: G 279 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: G 290 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8399 (mtmt) REVERT: G 356 ARG cc_start: 0.6212 (mpp-170) cc_final: 0.5809 (mtp85) REVERT: G 413 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6829 (mt-10) REVERT: H 267 THR cc_start: 0.8723 (t) cc_final: 0.8416 (m) REVERT: H 279 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: H 410 LYS cc_start: 0.7671 (tttm) cc_final: 0.7117 (tptp) REVERT: H 413 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6848 (mp0) REVERT: I 267 THR cc_start: 0.8570 (t) cc_final: 0.8212 (m) REVERT: I 279 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: I 413 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6937 (mp0) REVERT: J 267 THR cc_start: 0.8593 (t) cc_final: 0.8372 (m) REVERT: J 279 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: J 377 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (mpp) REVERT: J 413 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7084 (mp0) REVERT: K 279 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: K 410 LYS cc_start: 0.7921 (tttm) cc_final: 0.7613 (ttpt) REVERT: L 232 ASP cc_start: 0.6884 (m-30) cc_final: 0.6455 (t70) REVERT: L 247 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7691 (mtm110) REVERT: L 279 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: L 413 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6836 (mp0) REVERT: M 236 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7788 (pttt) REVERT: M 279 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: M 356 ARG cc_start: 0.6033 (mpp-170) cc_final: 0.5586 (mtp85) REVERT: N 279 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: N 409 MET cc_start: 0.7245 (mmm) cc_final: 0.7031 (mmp) REVERT: O 247 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7532 (mtm-85) REVERT: O 356 ARG cc_start: 0.6032 (mpp-170) cc_final: 0.5774 (mpp-170) REVERT: O 413 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: P 413 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6877 (mp0) REVERT: Q 279 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: R 279 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: R 413 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6932 (tt0) REVERT: S 247 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7640 (mtm180) REVERT: S 290 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8200 (mmtm) REVERT: S 410 LYS cc_start: 0.7591 (tttm) cc_final: 0.7219 (ttpt) REVERT: S 413 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6985 (mp0) REVERT: T 232 ASP cc_start: 0.6769 (m-30) cc_final: 0.6434 (t70) REVERT: T 267 THR cc_start: 0.8659 (t) cc_final: 0.8404 (m) REVERT: T 409 MET cc_start: 0.7305 (mmm) cc_final: 0.5940 (mmp) REVERT: T 413 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6989 (mp0) REVERT: U 247 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7654 (mtm110) REVERT: U 279 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: U 356 ARG cc_start: 0.6172 (mpp-170) cc_final: 0.5741 (ttt-90) REVERT: U 409 MET cc_start: 0.7469 (mmm) cc_final: 0.6962 (mmp) REVERT: U 413 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6826 (mt-10) REVERT: V 413 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: W 279 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6497 (mt-10) REVERT: W 356 ARG cc_start: 0.6135 (mpp-170) cc_final: 0.5870 (mtp85) REVERT: W 377 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8620 (mpt) REVERT: W 409 MET cc_start: 0.7293 (mmm) cc_final: 0.6083 (mmp) REVERT: W 413 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6646 (mp0) REVERT: X 232 ASP cc_start: 0.6680 (m-30) cc_final: 0.6312 (t70) REVERT: X 356 ARG cc_start: 0.5996 (mpp-170) cc_final: 0.5623 (mtp85) REVERT: X 409 MET cc_start: 0.7495 (mmm) cc_final: 0.6198 (mmp) REVERT: X 413 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6837 (mp0) REVERT: X 414 ASP cc_start: 0.7356 (m-30) cc_final: 0.7081 (m-30) REVERT: Y 279 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: Y 356 ARG cc_start: 0.6229 (mpp-170) cc_final: 0.5816 (mpp-170) REVERT: Y 424 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: Z 236 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7606 (pttt) REVERT: Z 247 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7423 (mtm-85) REVERT: Z 409 MET cc_start: 0.7436 (mmm) cc_final: 0.6258 (mmp) REVERT: Z 413 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6531 (mp0) REVERT: a 232 ASP cc_start: 0.6908 (m-30) cc_final: 0.6474 (t70) REVERT: a 279 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: a 410 LYS cc_start: 0.7637 (tttm) cc_final: 0.7245 (ttpt) REVERT: a 413 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6961 (mp0) REVERT: b 247 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7451 (mtm180) REVERT: b 279 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: b 356 ARG cc_start: 0.6226 (mpp-170) cc_final: 0.5778 (mpp-170) REVERT: b 394 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6563 (ttpt) REVERT: b 413 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6618 (mp0) REVERT: c 279 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: c 413 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6809 (mp0) REVERT: d 232 ASP cc_start: 0.6943 (m-30) cc_final: 0.6624 (t70) REVERT: d 236 LYS cc_start: 0.7706 (pttp) cc_final: 0.7441 (pptt) REVERT: d 279 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6435 (mt-10) REVERT: d 409 MET cc_start: 0.7522 (mmm) cc_final: 0.6183 (mmp) REVERT: d 413 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6868 (mp0) REVERT: e 232 ASP cc_start: 0.6809 (m-30) cc_final: 0.6507 (t70) REVERT: e 410 LYS cc_start: 0.7586 (tttm) cc_final: 0.7320 (ttpt) REVERT: e 413 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6703 (mt-10) REVERT: f 236 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (pptt) REVERT: f 247 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7470 (mtm180) REVERT: f 279 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: f 394 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6075 (tptm) REVERT: g 267 THR cc_start: 0.8624 (t) cc_final: 0.8354 (m) REVERT: g 279 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: g 413 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6660 (mp0) outliers start: 113 outliers final: 65 residues processed: 1080 average time/residue: 1.0187 time to fit residues: 1270.6929 Evaluate side-chains 1137 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1034 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 396 LEU Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 386 SER Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 279 GLU Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain O residue 413 GLU Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 375 THR Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 259 ASN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 236 LYS Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 413 GLU Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 279 GLU Chi-restraints excluded: chain W residue 375 THR Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 375 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 236 LYS Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 279 GLU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 394 LYS Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 375 THR Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 375 THR Chi-restraints excluded: chain f residue 236 LYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 210 optimal weight: 3.9990 chunk 381 optimal weight: 0.6980 chunk 397 optimal weight: 4.9990 chunk 456 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 463 optimal weight: 3.9990 chunk 240 optimal weight: 0.5980 chunk 412 optimal weight: 3.9990 chunk 405 optimal weight: 0.0170 chunk 197 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN H 303 GLN H 374 HIS I 303 GLN J 303 GLN N 303 GLN P 303 GLN P 359 GLN S 303 GLN S 359 GLN W 303 GLN W 359 GLN Y 374 HIS Z 303 GLN e 303 GLN f 359 GLN g 374 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143782 restraints weight = 45024.275| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.59 r_work: 0.3584 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 41052 Z= 0.121 Angle : 0.507 6.305 55374 Z= 0.280 Chirality : 0.039 0.127 6402 Planarity : 0.002 0.060 7392 Dihedral : 4.043 17.033 5544 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 2.16 % Allowed : 18.79 % Favored : 79.05 % 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: 3.28 (0.12), residues: 4950 helix: 4.51 (0.13), residues: 1386 sheet: 2.22 (0.11), residues: 2442 loop : -1.40 (0.14), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 356 TYR 0.011 0.001 TYR B 282 PHE 0.007 0.001 PHE L 422 HIS 0.006 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00222 (41052) covalent geometry : angle 0.50664 (55374) hydrogen bonds : bond 0.05626 ( 2212) hydrogen bonds : angle 3.74564 ( 6438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26678.74 seconds wall clock time: 451 minutes 3.51 seconds (27063.51 seconds total)