Starting phenix.real_space_refine on Sat Mar 7 08:02:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.map" model { file = "/net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cg7_30351/03_2026/7cg7_30351.cif" } resolution = 3.61 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= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 24548 2.51 5 N 7514 2.21 5 O 8126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40290 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} 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, c, b, d, e, f, g, h Time building chain proxies: 2.91, per 1000 atoms: 0.07 Number of scatterers: 40290 At special positions: 0 Unit cell: (254.865, 253.558, 100.639, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 8126 8.00 N 7514 7.00 C 24548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9792 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 64 sheets defined 28.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 233 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 233 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 233 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 233 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 233 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP A 271 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 382 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR A 429 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 385 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN A 431 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 387 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 433 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 389 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG A 373 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 302 removed outlier: 6.754A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 298 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 361 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 300 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN A 359 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 302 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 298 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN B 361 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE B 300 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN B 359 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 302 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 298 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN C 361 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE C 300 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN C 359 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 302 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 298 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN D 361 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE D 300 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN D 359 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 302 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE E 300 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN E 359 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 302 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU F 298 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN F 361 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE F 300 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN F 359 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU G 302 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 362 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU G 298 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN G 361 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE G 300 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN G 359 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 302 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE H 300 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN H 359 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU I 302 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU I 298 " --> pdb=" O ASN I 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 361 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE I 300 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN I 359 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU J 302 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU J 298 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN J 361 " --> pdb=" O LEU J 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE J 300 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN J 359 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU K 302 " --> pdb=" O THR J 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU K 298 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN K 361 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE K 300 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN K 359 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU L 302 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU L 298 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN L 361 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE L 300 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN L 359 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU M 302 " --> pdb=" O THR L 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU M 298 " --> pdb=" O ASN M 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN M 361 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE M 300 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN M 359 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU N 302 " --> pdb=" O THR M 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 362 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU N 298 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN N 361 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE N 300 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN N 359 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU O 302 " --> pdb=" O THR N 358 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU O 298 " --> pdb=" O ASN O 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN O 361 " --> pdb=" O LEU O 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE O 300 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN O 359 " --> pdb=" O ILE O 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU P 302 " --> pdb=" O THR O 358 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU O 362 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU P 298 " --> pdb=" O ASN P 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN P 361 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE P 300 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN P 359 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU Q 302 " --> pdb=" O THR P 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU Q 298 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Q 361 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE Q 300 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Q 359 " --> pdb=" O ILE Q 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU R 302 " --> pdb=" O THR Q 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 362 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU R 298 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN R 361 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE R 300 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN R 359 " --> pdb=" O ILE R 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU S 302 " --> pdb=" O THR R 358 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU S 298 " --> pdb=" O ASN S 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN S 361 " --> pdb=" O LEU S 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE S 300 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN S 359 " --> pdb=" O ILE S 300 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU T 302 " --> pdb=" O THR S 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU S 362 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE T 300 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN T 359 " --> pdb=" O ILE T 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU U 302 " --> pdb=" O THR T 358 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU U 298 " --> pdb=" O ASN U 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN U 361 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE U 300 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN U 359 " --> pdb=" O ILE U 300 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU V 302 " --> pdb=" O THR U 358 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU U 362 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE V 300 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN V 359 " --> pdb=" O ILE V 300 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU W 302 " --> pdb=" O THR V 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU W 298 " --> pdb=" O ASN W 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN W 361 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE W 300 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN W 359 " --> pdb=" O ILE W 300 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU X 302 " --> pdb=" O THR W 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU X 298 " --> pdb=" O ASN X 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN X 361 " --> pdb=" O LEU X 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE X 300 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN X 359 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU Y 302 " --> pdb=" O THR X 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Y 300 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Y 359 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU Z 302 " --> pdb=" O THR Y 358 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU Z 298 " --> pdb=" O ASN Z 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Z 361 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE Z 300 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Z 359 " --> pdb=" O ILE Z 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU a 302 " --> pdb=" O THR Z 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU Z 362 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU a 298 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN a 361 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE a 300 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN a 359 " --> pdb=" O ILE a 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU b 302 " --> pdb=" O THR a 358 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU b 298 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN b 361 " --> pdb=" O LEU b 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE b 300 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN b 359 " --> pdb=" O ILE b 300 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU c 302 " --> pdb=" O THR b 358 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU c 298 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN c 361 " --> pdb=" O LEU c 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE c 300 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN c 359 " --> pdb=" O ILE c 300 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU d 302 " --> pdb=" O THR c 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU c 362 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU d 298 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN d 361 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE d 300 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN d 359 " --> pdb=" O ILE d 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU e 302 " --> pdb=" O THR d 358 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU e 298 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN e 361 " --> pdb=" O LEU e 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE e 300 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN e 359 " --> pdb=" O ILE e 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU f 302 " --> pdb=" O THR e 358 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU f 298 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN f 361 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE f 300 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN f 359 " --> pdb=" O ILE f 300 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU g 302 " --> pdb=" O THR f 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU f 362 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU g 298 " --> pdb=" O ASN g 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN g 361 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE g 300 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN g 359 " --> pdb=" O ILE g 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU h 302 " --> pdb=" O THR g 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU g 362 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU h 298 " --> pdb=" O ASN h 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN h 361 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE h 300 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN h 359 " --> pdb=" O ILE h 300 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 302 " --> pdb=" O THR h 358 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU h 362 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER h 364 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP B 271 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 382 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR B 429 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 385 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN B 431 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 387 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 433 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 389 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG B 373 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR C 429 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 385 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN C 431 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 387 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL C 433 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 389 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG C 373 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP D 271 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 382 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR D 429 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 385 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN D 431 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 387 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 433 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 389 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG D 373 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP E 271 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE E 382 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR E 429 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 385 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN E 431 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 387 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 433 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 389 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG E 373 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP F 271 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 382 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR F 429 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU F 385 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN F 431 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 387 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL F 433 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL F 389 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG F 373 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP G 271 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE G 382 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR G 429 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 385 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN G 431 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 387 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL G 433 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL G 389 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG G 373 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP H 271 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE H 382 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR H 429 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU H 385 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN H 431 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL H 387 " --> pdb=" O ASN H 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL H 433 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL H 389 " --> pdb=" O VAL H 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG H 373 " --> pdb=" O GLU H 279 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP I 271 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 382 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR I 429 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU I 385 " --> pdb=" O THR I 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN I 431 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL I 387 " --> pdb=" O ASN I 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL I 433 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL I 389 " --> pdb=" O VAL I 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 371 through 373 removed outlier: 3.731A pdb=" N ARG I 373 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 372 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG J 373 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR J 429 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU J 385 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN J 431 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL J 387 " --> pdb=" O ASN J 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL J 433 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL J 389 " --> pdb=" O VAL J 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR K 429 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU K 385 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN K 431 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL K 387 " --> pdb=" O ASN K 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL K 433 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL K 389 " --> pdb=" O VAL K 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG K 373 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP L 271 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE L 382 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR L 429 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU L 385 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN L 431 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 387 " --> pdb=" O ASN L 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL L 433 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL L 389 " --> pdb=" O VAL L 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG L 373 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR M 429 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU M 385 " --> pdb=" O THR M 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN M 431 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL M 387 " --> pdb=" O ASN M 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL M 433 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 389 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG M 373 " --> pdb=" O GLU M 279 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP N 271 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE N 382 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR N 429 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU N 385 " --> pdb=" O THR N 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN N 431 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL N 387 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL N 433 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL N 389 " --> pdb=" O VAL N 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG N 373 " --> pdb=" O GLU N 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR O 429 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU O 385 " --> pdb=" O THR O 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN O 431 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL O 387 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL O 433 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL O 389 " --> pdb=" O VAL O 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG O 373 " --> pdb=" O GLU O 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG P 373 " --> pdb=" O GLU P 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE Q 372 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG Q 373 " --> pdb=" O GLU Q 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR P 429 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU P 385 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN P 431 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL P 387 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL P 433 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL P 389 " --> pdb=" O VAL P 433 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP Q 271 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Q 382 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Q 429 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU Q 385 " --> pdb=" O THR Q 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN Q 431 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL Q 387 " --> pdb=" O ASN Q 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL Q 433 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL Q 389 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP R 271 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE R 382 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR R 429 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU R 385 " --> pdb=" O THR R 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN R 431 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL R 387 " --> pdb=" O ASN R 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL R 433 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL R 389 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG R 373 " --> pdb=" O GLU R 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP S 271 " --> pdb=" O ILE S 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE S 382 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR S 429 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU S 385 " --> pdb=" O THR S 429 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN S 431 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL S 387 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL S 433 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL S 389 " --> pdb=" O VAL S 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG S 373 " --> pdb=" O GLU S 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE T 372 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG T 373 " --> pdb=" O GLU T 279 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR T 429 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU T 385 " --> pdb=" O THR T 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN T 431 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL T 387 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL T 433 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL T 389 " --> pdb=" O VAL T 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP U 271 " --> pdb=" O ILE U 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE U 382 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR U 429 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU U 385 " --> pdb=" O THR U 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN U 431 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL U 387 " --> pdb=" O ASN U 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL U 433 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL U 389 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG U 373 " --> pdb=" O GLU U 279 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP V 271 " --> pdb=" O ILE V 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE V 382 " --> pdb=" O ASP V 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR V 429 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU V 385 " --> pdb=" O THR V 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN V 431 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL V 387 " --> pdb=" O ASN V 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL V 433 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL V 389 " --> pdb=" O VAL V 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG V 373 " --> pdb=" O GLU V 279 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP W 271 " --> pdb=" O ILE W 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE W 382 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR W 429 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU W 385 " --> pdb=" O THR W 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN W 431 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL W 387 " --> pdb=" O ASN W 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL W 433 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL W 389 " --> pdb=" O VAL W 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG W 373 " --> pdb=" O GLU W 279 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP X 271 " --> pdb=" O ILE X 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE X 382 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR X 429 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU X 385 " --> pdb=" O THR X 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN X 431 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL X 387 " --> pdb=" O ASN X 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL X 433 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL X 389 " --> pdb=" O VAL X 433 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG X 373 " --> pdb=" O GLU X 279 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP Y 271 " --> pdb=" O ILE Y 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Y 382 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Y 429 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU Y 385 " --> pdb=" O THR Y 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN Y 431 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL Y 387 " --> pdb=" O ASN Y 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL Y 433 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Y 389 " --> pdb=" O VAL Y 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG Y 373 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP Z 271 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Z 382 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Z 429 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU Z 385 " --> pdb=" O THR Z 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN Z 431 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL Z 387 " --> pdb=" O ASN Z 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL Z 433 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Z 389 " --> pdb=" O VAL Z 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG Z 373 " --> pdb=" O GLU Z 279 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP a 271 " --> pdb=" O ILE a 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE a 382 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR a 429 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU a 385 " --> pdb=" O THR a 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN a 431 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL a 387 " --> pdb=" O ASN a 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL a 433 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL a 389 " --> pdb=" O VAL a 433 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG a 373 " --> pdb=" O GLU a 279 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP c 271 " --> pdb=" O ILE c 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE c 382 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR c 429 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU c 385 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN c 431 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL c 387 " --> pdb=" O ASN c 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL c 433 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL c 389 " --> pdb=" O VAL c 433 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG c 373 " --> pdb=" O GLU c 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP b 271 " --> pdb=" O ILE b 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE b 382 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR b 429 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU b 385 " --> pdb=" O THR b 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN b 431 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL b 387 " --> pdb=" O ASN b 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL b 433 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL b 389 " --> pdb=" O VAL b 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG b 373 " --> pdb=" O GLU b 279 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP d 271 " --> pdb=" O ILE d 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE d 382 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR d 429 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU d 385 " --> pdb=" O THR d 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN d 431 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL d 387 " --> pdb=" O ASN d 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL d 433 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL d 389 " --> pdb=" O VAL d 433 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG d 373 " --> pdb=" O GLU d 279 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP e 271 " --> pdb=" O ILE e 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE e 382 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR e 429 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU e 385 " --> pdb=" O THR e 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN e 431 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL e 387 " --> pdb=" O ASN e 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL e 433 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL e 389 " --> pdb=" O VAL e 433 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG e 373 " --> pdb=" O GLU e 279 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP f 271 " --> pdb=" O ILE f 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE f 382 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR f 429 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU f 385 " --> pdb=" O THR f 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN f 431 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL f 387 " --> pdb=" O ASN f 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL f 433 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL f 389 " --> pdb=" O VAL f 433 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG f 373 " --> pdb=" O GLU f 279 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP g 271 " --> pdb=" O ILE g 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE g 382 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR g 429 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU g 385 " --> pdb=" O THR g 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN g 431 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL g 387 " --> pdb=" O ASN g 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL g 433 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL g 389 " --> pdb=" O VAL g 433 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG g 373 " --> pdb=" O GLU g 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG h 373 " --> pdb=" O GLU h 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP h 271 " --> pdb=" O ILE h 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE h 382 " --> pdb=" O ASP h 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR h 429 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU h 385 " --> pdb=" O THR h 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN h 431 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL h 387 " --> pdb=" O ASN h 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL h 433 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL h 389 " --> pdb=" O VAL h 433 " (cutoff:3.500A) 1739 hydrogen bonds defined for protein. 4911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 4.15 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: 14450 1.34 - 1.46: 6419 1.46 - 1.57: 19625 1.57 - 1.69: 0 1.69 - 1.80: 204 Bond restraints: 40698 Sorted by residual: bond pdb=" CB LEU T 415 " pdb=" CG LEU T 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.79e-01 bond pdb=" CB LEU L 415 " pdb=" CG LEU L 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.66e-01 bond pdb=" N SER V 254 " pdb=" CA SER V 254 " ideal model delta sigma weight residual 1.462 1.455 0.007 8.50e-03 1.38e+04 6.58e-01 bond pdb=" CB LEU K 415 " pdb=" CG LEU K 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.56e-01 bond pdb=" CB LEU N 415 " pdb=" CG LEU N 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.55e-01 ... (remaining 40693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 50378 1.15 - 2.30: 3901 2.30 - 3.45: 427 3.45 - 4.60: 68 4.60 - 5.75: 68 Bond angle restraints: 54842 Sorted by residual: angle pdb=" N GLY h 421 " pdb=" CA GLY h 421 " pdb=" C GLY h 421 " ideal model delta sigma weight residual 113.18 107.43 5.75 2.37e+00 1.78e-01 5.88e+00 angle pdb=" N GLY R 421 " pdb=" CA GLY R 421 " pdb=" C GLY R 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.87e+00 angle pdb=" N GLY e 421 " pdb=" CA GLY e 421 " pdb=" C GLY e 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.86e+00 angle pdb=" N GLY O 421 " pdb=" CA GLY O 421 " pdb=" C GLY O 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.86e+00 angle pdb=" N GLY Z 421 " pdb=" CA GLY Z 421 " pdb=" C GLY Z 421 " ideal model delta sigma weight residual 113.18 107.45 5.73 2.37e+00 1.78e-01 5.85e+00 ... (remaining 54837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 21332 11.63 - 23.26: 2740 23.26 - 34.89: 1012 34.89 - 46.53: 246 46.53 - 58.16: 102 Dihedral angle restraints: 25432 sinusoidal: 10540 harmonic: 14892 Sorted by residual: dihedral pdb=" CA MET E 420 " pdb=" C MET E 420 " pdb=" N GLY E 421 " pdb=" CA GLY E 421 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET K 420 " pdb=" C MET K 420 " pdb=" N GLY K 421 " pdb=" CA GLY K 421 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET Q 420 " pdb=" C MET Q 420 " pdb=" N GLY Q 421 " pdb=" CA GLY Q 421 " ideal model delta harmonic sigma weight residual 180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 25429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2930 0.023 - 0.046: 2139 0.046 - 0.069: 656 0.069 - 0.092: 262 0.092 - 0.115: 303 Chirality restraints: 6290 Sorted by residual: chirality pdb=" CA PRO K 255 " pdb=" N PRO K 255 " pdb=" C PRO K 255 " pdb=" CB PRO K 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.31e-01 chirality pdb=" CA PRO L 255 " pdb=" N PRO L 255 " pdb=" C PRO L 255 " pdb=" CB PRO L 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO S 255 " pdb=" N PRO S 255 " pdb=" C PRO S 255 " pdb=" CB PRO S 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 6287 not shown) Planarity restraints: 7344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 435 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.87e-01 pdb=" N PRO J 436 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO J 436 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO J 436 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 435 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.83e-01 pdb=" N PRO M 436 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO M 436 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO M 436 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 435 " 0.015 5.00e-02 4.00e+02 2.35e-02 8.81e-01 pdb=" N PRO c 436 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO c 436 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO c 436 " 0.013 5.00e-02 4.00e+02 ... (remaining 7341 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 577 2.60 - 3.18: 34081 3.18 - 3.75: 54523 3.75 - 4.33: 77579 4.33 - 4.90: 136174 Nonbonded interactions: 302934 Sorted by model distance: nonbonded pdb=" OD2 ASP A 414 " pdb=" ND2 ASN h 431 " model vdw 2.027 3.120 nonbonded pdb=" ND2 ASN g 431 " pdb=" OD2 ASP h 414 " model vdw 2.043 3.120 nonbonded pdb=" ND2 ASN N 431 " pdb=" OD2 ASP O 414 " model vdw 2.047 3.120 nonbonded pdb=" ND2 ASN c 431 " pdb=" OD2 ASP d 414 " model vdw 2.061 3.120 nonbonded pdb=" ND2 ASN Q 431 " pdb=" OD2 ASP R 414 " model vdw 2.063 3.120 ... (remaining 302929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 'c' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.005 0.027 40698 Z= 0.252 Angle : 0.665 5.747 54842 Z= 0.409 Chirality : 0.039 0.115 6290 Planarity : 0.003 0.024 7344 Dihedral : 12.606 58.158 15640 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 5.26 % Favored : 92.48 % 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: -2.97 (0.11), residues: 4896 helix: 0.99 (0.15), residues: 1292 sheet: -2.82 (0.10), residues: 2312 loop : -2.93 (0.11), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 248 TYR 0.011 0.002 TYR B 393 PHE 0.006 0.001 PHE R 422 HIS 0.002 0.001 HIS S 374 Details of bonding type rmsd covalent geometry : bond 0.00528 (40698) covalent geometry : angle 0.66480 (54842) hydrogen bonds : bond 0.19115 ( 1739) hydrogen bonds : angle 6.77084 ( 4911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1223 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 GLN cc_start: 0.7966 (tt0) cc_final: 0.7701 (tt0) REVERT: A 409 MET cc_start: 0.7116 (tmm) cc_final: 0.6673 (tmm) REVERT: A 410 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8275 (ttpt) REVERT: B 290 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8254 (mtmm) REVERT: B 373 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7549 (mtp85) REVERT: B 385 LEU cc_start: 0.9012 (mt) cc_final: 0.8681 (mt) REVERT: B 394 LYS cc_start: 0.7017 (ttpt) cc_final: 0.6763 (ttpp) REVERT: B 410 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8042 (ttpt) REVERT: B 428 ASP cc_start: 0.8511 (m-30) cc_final: 0.8139 (m-30) REVERT: B 431 ASN cc_start: 0.7194 (t0) cc_final: 0.6721 (t0) REVERT: C 385 LEU cc_start: 0.9108 (mt) cc_final: 0.8765 (mt) REVERT: C 413 GLU cc_start: 0.8140 (tt0) cc_final: 0.7807 (tm-30) REVERT: C 428 ASP cc_start: 0.8336 (m-30) cc_final: 0.8106 (m-30) REVERT: C 431 ASN cc_start: 0.6915 (t0) cc_final: 0.6578 (t0) REVERT: D 240 ASP cc_start: 0.7759 (m-30) cc_final: 0.7515 (m-30) REVERT: D 359 GLN cc_start: 0.8142 (tt0) cc_final: 0.7811 (tt0) REVERT: E 367 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8280 (mm-30) REVERT: F 295 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8070 (t) REVERT: F 418 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7957 (mm-30) REVERT: G 295 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8420 (t) REVERT: G 409 MET cc_start: 0.6934 (tmm) cc_final: 0.6595 (tmm) REVERT: G 410 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8113 (ttpt) REVERT: G 413 GLU cc_start: 0.7890 (tt0) cc_final: 0.7522 (tm-30) REVERT: G 431 ASN cc_start: 0.7611 (t0) cc_final: 0.7223 (t0) REVERT: H 290 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7882 (mtmm) REVERT: H 410 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8019 (ttpt) REVERT: H 431 ASN cc_start: 0.7235 (t0) cc_final: 0.6950 (t0) REVERT: I 290 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7451 (mtmm) REVERT: I 294 ARG cc_start: 0.8907 (tpp-160) cc_final: 0.8663 (ttm-80) REVERT: I 418 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7685 (mm-30) REVERT: J 383 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8123 (mm-30) REVERT: J 413 GLU cc_start: 0.8121 (tt0) cc_final: 0.7668 (tm-30) REVERT: K 295 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8304 (t) REVERT: K 431 ASN cc_start: 0.7025 (t0) cc_final: 0.6474 (t0) REVERT: L 410 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8090 (ttpp) REVERT: L 431 ASN cc_start: 0.7177 (t0) cc_final: 0.6703 (t0) REVERT: M 280 GLU cc_start: 0.7986 (tt0) cc_final: 0.7733 (tt0) REVERT: M 359 GLN cc_start: 0.8042 (tt0) cc_final: 0.7735 (tt0) REVERT: N 280 GLU cc_start: 0.8277 (tt0) cc_final: 0.8041 (tt0) REVERT: N 290 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8254 (mtmm) REVERT: N 295 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8456 (t) REVERT: N 359 GLN cc_start: 0.8236 (tt0) cc_final: 0.7916 (tt0) REVERT: N 367 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7822 (mm-30) REVERT: N 383 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8268 (mm-30) REVERT: O 303 GLN cc_start: 0.7925 (mt0) cc_final: 0.7530 (mp10) REVERT: P 247 ARG cc_start: 0.7825 (ppt170) cc_final: 0.7580 (ppt170) REVERT: P 252 ILE cc_start: 0.8390 (tp) cc_final: 0.8173 (tt) REVERT: P 359 GLN cc_start: 0.8188 (tt0) cc_final: 0.7901 (mt0) REVERT: P 418 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7784 (mt-10) REVERT: P 431 ASN cc_start: 0.7346 (t0) cc_final: 0.7119 (t0) REVERT: Q 377 MET cc_start: 0.8247 (mmt) cc_final: 0.8022 (mmm) REVERT: Q 410 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8433 (ttpt) REVERT: Q 418 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7669 (mm-30) REVERT: Q 425 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8436 (ttpt) REVERT: R 431 ASN cc_start: 0.7255 (t0) cc_final: 0.6941 (t0) REVERT: S 303 GLN cc_start: 0.8111 (mt0) cc_final: 0.7910 (mp10) REVERT: S 410 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7954 (ttpp) REVERT: S 428 ASP cc_start: 0.8157 (m-30) cc_final: 0.7927 (m-30) REVERT: T 431 ASN cc_start: 0.7093 (t0) cc_final: 0.6280 (t0) REVERT: U 410 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8134 (ttpp) REVERT: U 418 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7574 (mm-30) REVERT: U 425 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8388 (ttpt) REVERT: V 429 THR cc_start: 0.8538 (p) cc_final: 0.8331 (p) REVERT: V 431 ASN cc_start: 0.7221 (t0) cc_final: 0.6743 (t0) REVERT: W 418 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7819 (mm-30) REVERT: W 431 ASN cc_start: 0.7482 (t0) cc_final: 0.6915 (t0) REVERT: X 290 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8141 (mtmm) REVERT: X 409 MET cc_start: 0.7028 (tmm) cc_final: 0.6762 (tmm) REVERT: X 425 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8460 (ttpt) REVERT: X 428 ASP cc_start: 0.8388 (m-30) cc_final: 0.8187 (m-30) REVERT: X 431 ASN cc_start: 0.7322 (t0) cc_final: 0.6824 (t0) REVERT: Z 294 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8626 (ttm-80) REVERT: Z 295 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8506 (m) REVERT: Z 410 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7965 (ttpt) REVERT: a 431 ASN cc_start: 0.6753 (t0) cc_final: 0.6515 (t0) REVERT: c 274 ASN cc_start: 0.7773 (t0) cc_final: 0.7474 (t0) REVERT: c 373 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7510 (ttm110) REVERT: c 409 MET cc_start: 0.6260 (tmm) cc_final: 0.5962 (tmm) REVERT: c 431 ASN cc_start: 0.7451 (t0) cc_final: 0.7136 (t0) REVERT: b 431 ASN cc_start: 0.7435 (t0) cc_final: 0.7000 (t0) REVERT: d 373 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7548 (mtp85) REVERT: d 409 MET cc_start: 0.6608 (tmm) cc_final: 0.6367 (tmm) REVERT: d 425 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8418 (ttpt) REVERT: e 250 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7865 (mt-10) REVERT: e 280 GLU cc_start: 0.8083 (tt0) cc_final: 0.7552 (tt0) REVERT: e 290 LYS cc_start: 0.8224 (ptpp) cc_final: 0.8014 (mtmm) REVERT: e 360 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7451 (ttm-80) REVERT: f 270 LEU cc_start: 0.9453 (mt) cc_final: 0.9247 (mt) REVERT: f 303 GLN cc_start: 0.7796 (mt0) cc_final: 0.7464 (mp10) REVERT: f 407 ASP cc_start: 0.7675 (p0) cc_final: 0.7403 (p0) REVERT: f 410 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8228 (ttpt) REVERT: f 418 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7554 (mm-30) REVERT: g 303 GLN cc_start: 0.7730 (mt0) cc_final: 0.7413 (mp10) REVERT: g 367 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7844 (mm-30) REVERT: g 383 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8064 (mm-30) REVERT: g 431 ASN cc_start: 0.7227 (t0) cc_final: 0.6700 (t0) REVERT: h 418 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7953 (mm-30) REVERT: h 431 ASN cc_start: 0.6870 (t0) cc_final: 0.6426 (t0) outliers start: 102 outliers final: 1 residues processed: 1317 average time/residue: 0.3084 time to fit residues: 594.8869 Evaluate side-chains 955 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 945 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain S residue 425 LYS Chi-restraints excluded: chain U residue 425 LYS Chi-restraints excluded: chain X residue 425 LYS Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain d residue 425 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.0770 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 361 ASN D 261 ASN D 361 ASN G 265 GLN J 365 ASN M 261 ASN M 361 ASN N 361 ASN O 265 GLN O 361 ASN P 265 GLN P 361 ASN S 361 ASN T 361 ASN U 361 ASN V 361 ASN W 361 ASN X 361 ASN Y 265 GLN Y 431 ASN c 361 ASN b 361 ASN d 361 ASN e 261 ASN e 361 ASN f 361 ASN g 361 ASN h 361 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.121921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.109520 restraints weight = 67041.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112484 restraints weight = 33771.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114406 restraints weight = 20519.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115693 restraints weight = 14124.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116510 restraints weight = 10515.713| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40698 Z= 0.150 Angle : 0.561 7.645 54842 Z= 0.291 Chirality : 0.039 0.120 6290 Planarity : 0.003 0.050 7344 Dihedral : 5.224 59.902 5533 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.64 % Allowed : 13.27 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.12), residues: 4896 helix: 2.61 (0.14), residues: 1326 sheet: -2.14 (0.10), residues: 2414 loop : -2.23 (0.14), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 417 TYR 0.009 0.001 TYR d 282 PHE 0.009 0.001 PHE V 422 HIS 0.003 0.001 HIS S 374 Details of bonding type rmsd covalent geometry : bond 0.00345 (40698) covalent geometry : angle 0.56051 (54842) hydrogen bonds : bond 0.04692 ( 1739) hydrogen bonds : angle 4.43052 ( 4911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 916 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6944 (tmm) cc_final: 0.6617 (tmm) REVERT: A 410 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8018 (ttpt) REVERT: A 418 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7559 (mt-10) REVERT: B 394 LYS cc_start: 0.7044 (ttpt) cc_final: 0.6767 (ttpp) REVERT: B 417 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8015 (ttp80) REVERT: C 383 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8228 (mm-30) REVERT: D 240 ASP cc_start: 0.7724 (m-30) cc_final: 0.7440 (m-30) REVERT: D 267 THR cc_start: 0.8516 (m) cc_final: 0.8221 (p) REVERT: D 367 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7684 (mm-30) REVERT: E 367 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8257 (mm-30) REVERT: E 383 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8213 (mm-30) REVERT: E 418 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7943 (mm-30) REVERT: F 295 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8296 (t) REVERT: F 367 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7822 (mt-10) REVERT: F 409 MET cc_start: 0.7042 (tmm) cc_final: 0.6766 (tmm) REVERT: G 295 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (t) REVERT: G 410 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8107 (ttpt) REVERT: H 410 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7970 (ttpt) REVERT: I 383 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8102 (mm-30) REVERT: J 244 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7989 (ttm170) REVERT: J 383 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8359 (mm-30) REVERT: J 417 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7804 (ttp80) REVERT: K 414 ASP cc_start: 0.7907 (t0) cc_final: 0.7482 (t0) REVERT: L 367 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8122 (mm-30) REVERT: L 385 LEU cc_start: 0.8959 (mt) cc_final: 0.8731 (mt) REVERT: L 414 ASP cc_start: 0.8181 (t0) cc_final: 0.7876 (t0) REVERT: M 267 THR cc_start: 0.8554 (m) cc_final: 0.8350 (p) REVERT: M 414 ASP cc_start: 0.7772 (t0) cc_final: 0.7504 (t0) REVERT: M 418 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7719 (mt-10) REVERT: P 247 ARG cc_start: 0.7796 (ppt170) cc_final: 0.7516 (ppt170) REVERT: P 385 LEU cc_start: 0.9003 (mt) cc_final: 0.8773 (mt) REVERT: P 431 ASN cc_start: 0.7112 (t0) cc_final: 0.6822 (t0) REVERT: Q 377 MET cc_start: 0.8244 (mmt) cc_final: 0.8030 (mmm) REVERT: R 367 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8020 (mt-10) REVERT: S 410 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7727 (ttpp) REVERT: T 409 MET cc_start: 0.7512 (tmm) cc_final: 0.7253 (tmm) REVERT: U 356 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6889 (ptp90) REVERT: X 250 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7706 (mt-10) REVERT: Y 414 ASP cc_start: 0.7482 (t0) cc_final: 0.7174 (t0) REVERT: Z 267 THR cc_start: 0.8637 (m) cc_final: 0.8401 (p) REVERT: Z 409 MET cc_start: 0.7185 (tmm) cc_final: 0.6916 (tmm) REVERT: a 428 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8014 (t0) REVERT: c 409 MET cc_start: 0.6047 (tmm) cc_final: 0.5817 (tmm) REVERT: b 250 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: d 267 THR cc_start: 0.8554 (m) cc_final: 0.8239 (p) REVERT: d 385 LEU cc_start: 0.8988 (mt) cc_final: 0.8715 (mt) REVERT: d 414 ASP cc_start: 0.7368 (t0) cc_final: 0.6839 (t0) REVERT: e 239 ASN cc_start: 0.8418 (t0) cc_final: 0.8190 (t0) REVERT: e 280 GLU cc_start: 0.8020 (tt0) cc_final: 0.7588 (tt0) REVERT: g 269 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7561 (mp10) REVERT: g 367 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7891 (mm-30) REVERT: g 377 MET cc_start: 0.8047 (mmm) cc_final: 0.7625 (mmm) outliers start: 74 outliers final: 53 residues processed: 959 average time/residue: 0.2625 time to fit residues: 387.9432 Evaluate side-chains 846 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 789 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 428 ASP Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 246 GLN Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 405 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 433 optimal weight: 0.7980 chunk 426 optimal weight: 2.9990 chunk 253 optimal weight: 0.7980 chunk 445 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 367 optimal weight: 0.3980 chunk 354 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 374 HIS D 261 ASN F 365 ASN F 374 HIS G 374 HIS H 365 ASN J 374 HIS K 374 HIS L 411 GLN N 365 ASN O 365 ASN P 265 GLN P 374 HIS Q 261 ASN S 374 HIS T 374 HIS X 365 ASN X 374 HIS Y 365 ASN Z 374 HIS a 361 ASN a 411 GLN d 365 ASN d 374 HIS f 374 HIS g 374 HIS h 374 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107582 restraints weight = 67975.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110536 restraints weight = 34134.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112442 restraints weight = 20689.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113705 restraints weight = 14206.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114526 restraints weight = 10661.626| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 40698 Z= 0.210 Angle : 0.585 6.134 54842 Z= 0.301 Chirality : 0.040 0.126 6290 Planarity : 0.003 0.037 7344 Dihedral : 4.696 19.798 5510 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.92 % Allowed : 17.14 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.12), residues: 4896 helix: 2.93 (0.13), residues: 1326 sheet: -2.00 (0.10), residues: 2414 loop : -1.91 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 417 TYR 0.013 0.002 TYR B 282 PHE 0.015 0.001 PHE T 422 HIS 0.003 0.000 HIS S 374 Details of bonding type rmsd covalent geometry : bond 0.00487 (40698) covalent geometry : angle 0.58466 (54842) hydrogen bonds : bond 0.05085 ( 1739) hydrogen bonds : angle 4.37426 ( 4911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 815 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6964 (tmm) cc_final: 0.6664 (tmm) REVERT: C 247 ARG cc_start: 0.7676 (ppt170) cc_final: 0.7445 (ppt170) REVERT: D 240 ASP cc_start: 0.7606 (m-30) cc_final: 0.7271 (m-30) REVERT: D 267 THR cc_start: 0.8475 (m) cc_final: 0.8224 (p) REVERT: D 367 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7754 (mm-30) REVERT: E 236 LYS cc_start: 0.8538 (mptt) cc_final: 0.8283 (mptt) REVERT: F 367 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7984 (mt-10) REVERT: F 383 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8109 (mm-30) REVERT: F 409 MET cc_start: 0.7117 (tmm) cc_final: 0.6886 (tmm) REVERT: I 243 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9134 (p) REVERT: I 367 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8152 (mt-10) REVERT: I 383 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8150 (mm-30) REVERT: J 244 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7969 (ttm170) REVERT: J 269 GLN cc_start: 0.8317 (mp10) cc_final: 0.7965 (mp10) REVERT: J 383 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8418 (mm-30) REVERT: J 418 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7725 (mt-10) REVERT: L 367 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8204 (mm-30) REVERT: P 247 ARG cc_start: 0.7717 (ppt170) cc_final: 0.7460 (ppt170) REVERT: P 418 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7575 (mt-10) REVERT: Q 367 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7916 (mt-10) REVERT: R 280 GLU cc_start: 0.8068 (tt0) cc_final: 0.7813 (tt0) REVERT: R 367 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8137 (mt-10) REVERT: S 410 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7893 (ttpp) REVERT: W 269 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8249 (mp10) REVERT: X 250 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7695 (mt-10) REVERT: Y 414 ASP cc_start: 0.7227 (t0) cc_final: 0.7003 (t0) REVERT: Z 409 MET cc_start: 0.7155 (tmm) cc_final: 0.6797 (tmm) REVERT: c 269 GLN cc_start: 0.8468 (mp10) cc_final: 0.8020 (mt0) REVERT: c 409 MET cc_start: 0.6127 (tmm) cc_final: 0.5898 (tmm) REVERT: c 424 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (t0) REVERT: b 250 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: d 409 MET cc_start: 0.6773 (tmm) cc_final: 0.6461 (tmm) REVERT: d 418 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7781 (mm-30) REVERT: e 239 ASN cc_start: 0.8430 (t0) cc_final: 0.8216 (t0) REVERT: e 280 GLU cc_start: 0.8066 (tt0) cc_final: 0.7663 (tt0) REVERT: g 269 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7588 (mp10) REVERT: g 367 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8033 (mm-30) outliers start: 132 outliers final: 85 residues processed: 897 average time/residue: 0.2631 time to fit residues: 362.8962 Evaluate side-chains 852 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 764 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 252 ILE Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 246 GLN Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 252 ILE Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 252 ILE Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain c residue 424 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 385 LEU Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 295 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 409 optimal weight: 1.9990 chunk 479 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 363 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN P 365 ASN Q 239 ASN V 365 ASN Y 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108060 restraints weight = 67281.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111190 restraints weight = 33452.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113144 restraints weight = 19840.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114440 restraints weight = 13365.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115334 restraints weight = 9860.030| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 40698 Z= 0.205 Angle : 0.579 6.496 54842 Z= 0.300 Chirality : 0.040 0.126 6290 Planarity : 0.003 0.027 7344 Dihedral : 4.646 18.471 5508 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.27 % Allowed : 17.91 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4896 helix: 3.09 (0.13), residues: 1326 sheet: -1.92 (0.10), residues: 2414 loop : -1.68 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 248 TYR 0.013 0.002 TYR B 282 PHE 0.029 0.001 PHE D 422 HIS 0.003 0.001 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00473 (40698) covalent geometry : angle 0.57934 (54842) hydrogen bonds : bond 0.04912 ( 1739) hydrogen bonds : angle 4.28250 ( 4911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 826 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6917 (tmm) cc_final: 0.6646 (tmm) REVERT: A 431 ASN cc_start: 0.7003 (m110) cc_final: 0.6563 (m-40) REVERT: B 279 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 414 ASP cc_start: 0.7605 (t0) cc_final: 0.7246 (t0) REVERT: D 240 ASP cc_start: 0.7574 (m-30) cc_final: 0.7282 (m-30) REVERT: D 267 THR cc_start: 0.8651 (m) cc_final: 0.8309 (p) REVERT: E 383 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 418 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7655 (mt-10) REVERT: F 367 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8065 (mt-10) REVERT: F 409 MET cc_start: 0.7100 (tmm) cc_final: 0.6870 (tmm) REVERT: G 431 ASN cc_start: 0.7204 (t0) cc_final: 0.6969 (t0) REVERT: I 243 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9123 (p) REVERT: I 367 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8118 (mt-10) REVERT: I 383 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8097 (mm-30) REVERT: J 269 GLN cc_start: 0.8346 (mp10) cc_final: 0.8050 (mp10) REVERT: J 431 ASN cc_start: 0.6347 (m-40) cc_final: 0.6094 (t0) REVERT: L 279 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: L 367 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8161 (mm-30) REVERT: L 418 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7804 (mt-10) REVERT: N 367 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7859 (mm-30) REVERT: N 383 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8359 (mm-30) REVERT: P 247 ARG cc_start: 0.7763 (ppt170) cc_final: 0.7534 (ppt170) REVERT: Q 367 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7998 (mt-10) REVERT: Q 393 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.5765 (m-80) REVERT: R 279 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: R 280 GLU cc_start: 0.8028 (tt0) cc_final: 0.7705 (tt0) REVERT: R 367 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8092 (mt-10) REVERT: S 410 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7854 (ttpp) REVERT: T 393 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: T 409 MET cc_start: 0.7603 (tmm) cc_final: 0.7327 (tmm) REVERT: U 418 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7517 (mt-10) REVERT: V 356 ARG cc_start: 0.7593 (ptt-90) cc_final: 0.7134 (ptp90) REVERT: W 420 MET cc_start: 0.8543 (ttm) cc_final: 0.8342 (ttp) REVERT: X 247 ARG cc_start: 0.7978 (tmm-80) cc_final: 0.7713 (ptt180) REVERT: X 250 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7653 (mt-10) REVERT: X 367 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8033 (mm-30) REVERT: Z 409 MET cc_start: 0.7132 (tmm) cc_final: 0.6780 (tmm) REVERT: a 393 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: c 269 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: c 409 MET cc_start: 0.6072 (tmm) cc_final: 0.5828 (tmm) REVERT: b 250 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: d 409 MET cc_start: 0.6714 (tmm) cc_final: 0.6307 (tmm) REVERT: e 280 GLU cc_start: 0.8044 (tt0) cc_final: 0.7642 (tt0) REVERT: f 393 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: g 269 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7660 (mp10) REVERT: g 367 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8066 (mm-30) outliers start: 148 outliers final: 105 residues processed: 922 average time/residue: 0.2598 time to fit residues: 368.9146 Evaluate side-chains 887 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 772 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 252 ILE Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 246 GLN Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 252 ILE Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 252 ILE Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 430 LEU Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 162 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 234 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 362 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN I 365 ASN K 261 ASN K 365 ASN M 261 ASN O 378 ASN P 374 HIS Q 261 ASN Q 365 ASN W 365 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113301 restraints weight = 65464.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116287 restraints weight = 32347.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118234 restraints weight = 19671.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119474 restraints weight = 13450.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120362 restraints weight = 10136.640| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40698 Z= 0.128 Angle : 0.527 6.990 54842 Z= 0.271 Chirality : 0.039 0.120 6290 Planarity : 0.002 0.025 7344 Dihedral : 4.288 16.937 5508 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 3.01 % Allowed : 18.97 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4896 helix: 3.47 (0.13), residues: 1326 sheet: -1.63 (0.11), residues: 2414 loop : -1.57 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 370 TYR 0.012 0.001 TYR e 393 PHE 0.021 0.001 PHE D 422 HIS 0.002 0.000 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00299 (40698) covalent geometry : angle 0.52703 (54842) hydrogen bonds : bond 0.03983 ( 1739) hydrogen bonds : angle 3.97175 ( 4911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 814 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6892 (tmm) cc_final: 0.6651 (tmm) REVERT: A 431 ASN cc_start: 0.6519 (m110) cc_final: 0.6233 (m-40) REVERT: B 240 ASP cc_start: 0.7653 (m-30) cc_final: 0.7335 (m-30) REVERT: B 414 ASP cc_start: 0.7546 (t0) cc_final: 0.7164 (t0) REVERT: D 240 ASP cc_start: 0.7681 (m-30) cc_final: 0.7410 (m-30) REVERT: D 367 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7742 (mm-30) REVERT: F 367 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8010 (mt-10) REVERT: F 409 MET cc_start: 0.7040 (tmm) cc_final: 0.6755 (tmm) REVERT: G 283 SER cc_start: 0.9215 (m) cc_final: 0.8912 (p) REVERT: G 431 ASN cc_start: 0.6701 (t0) cc_final: 0.6427 (t0) REVERT: I 367 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8051 (mt-10) REVERT: I 383 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8057 (mm-30) REVERT: J 269 GLN cc_start: 0.8302 (mp10) cc_final: 0.8028 (mp10) REVERT: J 383 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8167 (mm-30) REVERT: J 393 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: J 418 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7673 (mt-10) REVERT: K 414 ASP cc_start: 0.7807 (t0) cc_final: 0.7448 (t0) REVERT: L 418 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7752 (mt-10) REVERT: N 383 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8529 (mm-30) REVERT: O 236 LYS cc_start: 0.7731 (mptt) cc_final: 0.7448 (mmtm) REVERT: Q 367 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7849 (mt-10) REVERT: Q 393 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: Q 394 LYS cc_start: 0.6923 (tppt) cc_final: 0.6520 (ttmm) REVERT: R 280 GLU cc_start: 0.7866 (tt0) cc_final: 0.7559 (tt0) REVERT: R 367 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8073 (mt-10) REVERT: R 414 ASP cc_start: 0.7406 (t0) cc_final: 0.7014 (t0) REVERT: R 418 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7298 (mt-10) REVERT: S 412 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8095 (mm) REVERT: T 393 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: T 409 MET cc_start: 0.7579 (tmm) cc_final: 0.7238 (tmm) REVERT: V 356 ARG cc_start: 0.7672 (ptt-90) cc_final: 0.7182 (ptp90) REVERT: X 250 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7506 (mt-10) REVERT: X 269 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7489 (mp10) REVERT: Z 409 MET cc_start: 0.7075 (tmm) cc_final: 0.6721 (tmm) REVERT: c 269 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: c 409 MET cc_start: 0.6160 (tmm) cc_final: 0.5939 (tmm) REVERT: c 414 ASP cc_start: 0.7792 (t0) cc_final: 0.7498 (t0) REVERT: b 250 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: d 409 MET cc_start: 0.6639 (tmm) cc_final: 0.6232 (tmm) REVERT: d 414 ASP cc_start: 0.7078 (t0) cc_final: 0.6731 (t0) REVERT: d 418 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7855 (mm-30) REVERT: e 280 GLU cc_start: 0.7725 (tt0) cc_final: 0.7287 (tt0) REVERT: e 405 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6653 (t) REVERT: f 413 GLU cc_start: 0.8285 (tt0) cc_final: 0.7824 (tm-30) REVERT: g 269 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7782 (mp10) REVERT: g 367 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8030 (mm-30) REVERT: h 418 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7403 (mt-10) outliers start: 136 outliers final: 92 residues processed: 913 average time/residue: 0.2508 time to fit residues: 355.7536 Evaluate side-chains 868 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 769 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 412 ILE Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 430 LEU Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 289 SER Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 483 optimal weight: 0.7980 chunk 444 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 175 optimal weight: 0.8980 chunk 162 optimal weight: 0.3980 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 0.0970 chunk 427 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 157 optimal weight: 0.0970 chunk 77 optimal weight: 0.0570 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN R 365 ASN Z 431 ASN b 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121328 restraints weight = 67591.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124546 restraints weight = 33408.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126841 restraints weight = 20101.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128382 restraints weight = 13305.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129451 restraints weight = 9646.975| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 40698 Z= 0.100 Angle : 0.507 7.227 54842 Z= 0.259 Chirality : 0.039 0.126 6290 Planarity : 0.002 0.037 7344 Dihedral : 3.963 16.321 5508 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 2.43 % Allowed : 20.04 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4896 helix: 3.73 (0.13), residues: 1326 sheet: -1.32 (0.11), residues: 2414 loop : -1.47 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 417 TYR 0.007 0.001 TYR K 393 PHE 0.017 0.001 PHE D 422 HIS 0.002 0.000 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00238 (40698) covalent geometry : angle 0.50712 (54842) hydrogen bonds : bond 0.03307 ( 1739) hydrogen bonds : angle 3.74001 ( 4911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 870 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6831 (tmm) cc_final: 0.6547 (tmm) REVERT: B 240 ASP cc_start: 0.7678 (m-30) cc_final: 0.7393 (m-30) REVERT: B 414 ASP cc_start: 0.7914 (t0) cc_final: 0.7695 (t0) REVERT: C 269 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7544 (mp10) REVERT: D 240 ASP cc_start: 0.7688 (m-30) cc_final: 0.7402 (m-30) REVERT: D 383 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8183 (mm-30) REVERT: D 409 MET cc_start: 0.6779 (tmm) cc_final: 0.6574 (tmm) REVERT: E 414 ASP cc_start: 0.7976 (t0) cc_final: 0.7367 (t0) REVERT: E 418 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7881 (mm-30) REVERT: F 367 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8058 (mt-10) REVERT: F 383 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8146 (mm-30) REVERT: F 409 MET cc_start: 0.6889 (tmm) cc_final: 0.6575 (tmm) REVERT: G 283 SER cc_start: 0.9399 (m) cc_final: 0.8895 (p) REVERT: G 302 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6961 (tm-30) REVERT: G 413 GLU cc_start: 0.7580 (tt0) cc_final: 0.7320 (tm-30) REVERT: H 247 ARG cc_start: 0.7985 (ppt170) cc_final: 0.7697 (ppt170) REVERT: H 269 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7658 (mt0) REVERT: H 431 ASN cc_start: 0.6476 (t0) cc_final: 0.6224 (t0) REVERT: I 236 LYS cc_start: 0.8138 (mptt) cc_final: 0.7920 (mptt) REVERT: J 269 GLN cc_start: 0.8112 (mp10) cc_final: 0.7819 (mp10) REVERT: J 383 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 393 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7436 (m-80) REVERT: J 418 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7279 (mt-10) REVERT: L 418 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7624 (mt-10) REVERT: M 269 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7548 (mt0) REVERT: N 236 LYS cc_start: 0.7870 (mptt) cc_final: 0.7441 (mmtm) REVERT: N 383 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8556 (mm-30) REVERT: O 414 ASP cc_start: 0.7896 (t0) cc_final: 0.7223 (t0) REVERT: P 418 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7383 (mt-10) REVERT: Q 269 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7958 (mp10) REVERT: Q 290 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8021 (mtmm) REVERT: Q 393 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: R 279 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: R 280 GLU cc_start: 0.8023 (tt0) cc_final: 0.7518 (tt0) REVERT: R 418 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7379 (mt-10) REVERT: T 393 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: T 409 MET cc_start: 0.7451 (tmm) cc_final: 0.7075 (tmm) REVERT: V 275 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7935 (mtmm) REVERT: V 356 ARG cc_start: 0.7577 (ptt-90) cc_final: 0.7229 (ptp-170) REVERT: V 429 THR cc_start: 0.8380 (p) cc_final: 0.8128 (t) REVERT: W 269 GLN cc_start: 0.8297 (mp10) cc_final: 0.7202 (mp10) REVERT: W 418 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7782 (mm-30) REVERT: X 250 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7654 (mt-10) REVERT: X 269 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7354 (mp10) REVERT: Z 267 THR cc_start: 0.8583 (m) cc_final: 0.8074 (p) REVERT: Z 290 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7698 (mppt) REVERT: Z 409 MET cc_start: 0.6979 (tmm) cc_final: 0.6635 (tmm) REVERT: a 393 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: c 269 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: b 250 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: b 269 GLN cc_start: 0.7777 (mp10) cc_final: 0.7565 (mp10) REVERT: d 409 MET cc_start: 0.6638 (tmm) cc_final: 0.6251 (tmm) REVERT: d 414 ASP cc_start: 0.7555 (t0) cc_final: 0.7248 (t0) REVERT: d 418 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7146 (mt-10) REVERT: e 253 LEU cc_start: 0.7566 (mt) cc_final: 0.7337 (mt) REVERT: e 280 GLU cc_start: 0.7837 (tt0) cc_final: 0.7313 (tt0) REVERT: e 282 TYR cc_start: 0.8333 (m-10) cc_final: 0.7867 (m-10) REVERT: e 414 ASP cc_start: 0.7882 (t0) cc_final: 0.7419 (t0) REVERT: f 393 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: g 269 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7658 (mp10) REVERT: g 290 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8181 (pttm) REVERT: g 367 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8137 (mm-30) REVERT: g 377 MET cc_start: 0.8287 (mmm) cc_final: 0.7914 (mmm) REVERT: h 418 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7312 (mt-10) outliers start: 110 outliers final: 81 residues processed: 949 average time/residue: 0.2532 time to fit residues: 374.1633 Evaluate side-chains 870 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 780 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 289 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 282 optimal weight: 0.5980 chunk 399 optimal weight: 0.0570 chunk 371 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN G 265 GLN P 378 ASN f 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113604 restraints weight = 62064.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115895 restraints weight = 32357.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117617 restraints weight = 20745.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119210 restraints weight = 15700.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120055 restraints weight = 12524.779| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40698 Z= 0.138 Angle : 0.546 7.926 54842 Z= 0.276 Chirality : 0.039 0.134 6290 Planarity : 0.003 0.058 7344 Dihedral : 4.048 16.247 5508 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.90 % Allowed : 20.41 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4896 helix: 3.54 (0.13), residues: 1326 sheet: -1.26 (0.11), residues: 2414 loop : -1.40 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG a 417 TYR 0.012 0.001 TYR D 393 PHE 0.015 0.001 PHE D 422 HIS 0.002 0.000 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00325 (40698) covalent geometry : angle 0.54594 (54842) hydrogen bonds : bond 0.03941 ( 1739) hydrogen bonds : angle 3.81530 ( 4911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 790 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6654 (tmm) cc_final: 0.6306 (tmm) REVERT: B 236 LYS cc_start: 0.7285 (mptt) cc_final: 0.6923 (mptt) REVERT: B 240 ASP cc_start: 0.7790 (m-30) cc_final: 0.7491 (m-30) REVERT: B 247 ARG cc_start: 0.8150 (ppt170) cc_final: 0.7880 (ppt170) REVERT: C 269 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7338 (mp10) REVERT: D 240 ASP cc_start: 0.7760 (m-30) cc_final: 0.7473 (m-30) REVERT: D 367 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 383 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8274 (mm-30) REVERT: E 393 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: F 367 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8093 (mt-10) REVERT: F 409 MET cc_start: 0.6907 (tmm) cc_final: 0.6570 (tmm) REVERT: G 261 ASN cc_start: 0.8867 (m-40) cc_final: 0.8643 (m110) REVERT: G 283 SER cc_start: 0.9363 (m) cc_final: 0.8997 (p) REVERT: G 393 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: H 247 ARG cc_start: 0.8005 (ppt170) cc_final: 0.7748 (ppt170) REVERT: H 431 ASN cc_start: 0.6670 (t0) cc_final: 0.6462 (t0) REVERT: I 367 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8126 (mt-10) REVERT: J 269 GLN cc_start: 0.7930 (mp10) cc_final: 0.7626 (mp10) REVERT: J 393 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: J 418 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7239 (mt-10) REVERT: L 418 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7653 (mt-10) REVERT: M 269 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7368 (mt0) REVERT: M 356 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6317 (ptp-170) REVERT: M 367 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: N 383 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8432 (mm-30) REVERT: O 414 ASP cc_start: 0.7973 (t0) cc_final: 0.7756 (t0) REVERT: Q 269 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7909 (mp10) REVERT: Q 290 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8126 (mtmm) REVERT: Q 393 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: R 269 GLN cc_start: 0.8041 (mp10) cc_final: 0.7796 (mp10) REVERT: R 279 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: R 280 GLU cc_start: 0.8094 (tt0) cc_final: 0.7610 (tt0) REVERT: R 418 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7200 (mt-10) REVERT: S 370 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: S 393 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: T 393 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: T 409 MET cc_start: 0.7468 (tmm) cc_final: 0.7063 (tmm) REVERT: V 275 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7658 (mttp) REVERT: V 356 ARG cc_start: 0.7584 (ptt-90) cc_final: 0.7238 (ptp-170) REVERT: V 393 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: V 429 THR cc_start: 0.8360 (p) cc_final: 0.8130 (t) REVERT: W 269 GLN cc_start: 0.8073 (mp10) cc_final: 0.6896 (mp10) REVERT: W 418 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7715 (mm-30) REVERT: X 250 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7769 (mt-10) REVERT: X 290 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8315 (mtmm) REVERT: Y 236 LYS cc_start: 0.8040 (mptt) cc_final: 0.7820 (mppt) REVERT: Z 267 THR cc_start: 0.8579 (m) cc_final: 0.8063 (p) REVERT: Z 290 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7713 (mppt) REVERT: Z 409 MET cc_start: 0.7021 (tmm) cc_final: 0.6633 (tmm) REVERT: a 393 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: c 269 GLN cc_start: 0.8228 (mp10) cc_final: 0.7698 (mt0) REVERT: b 250 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: b 269 GLN cc_start: 0.7878 (mp10) cc_final: 0.7629 (mp10) REVERT: d 269 GLN cc_start: 0.7969 (mp10) cc_final: 0.7585 (mp10) REVERT: d 409 MET cc_start: 0.6479 (tmm) cc_final: 0.6266 (tmm) REVERT: d 418 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7284 (mt-10) REVERT: e 279 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: e 280 GLU cc_start: 0.7906 (tt0) cc_final: 0.7353 (tt0) REVERT: e 282 TYR cc_start: 0.8437 (m-10) cc_final: 0.8080 (m-10) REVERT: f 393 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: f 428 ASP cc_start: 0.8672 (m-30) cc_final: 0.8448 (t70) REVERT: g 269 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7579 (mp10) REVERT: g 367 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8221 (mm-30) REVERT: h 418 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7160 (mt-10) outliers start: 131 outliers final: 95 residues processed: 880 average time/residue: 0.2582 time to fit residues: 352.3792 Evaluate side-chains 879 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 769 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 393 TYR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain f residue 250 GLU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 441 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 337 optimal weight: 0.0870 chunk 508 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 280 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN G 431 ASN O 411 GLN W 411 GLN b 411 GLN h 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114464 restraints weight = 61604.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116836 restraints weight = 32393.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118707 restraints weight = 20583.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120246 restraints weight = 15522.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121008 restraints weight = 12349.108| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40698 Z= 0.134 Angle : 0.546 8.602 54842 Z= 0.277 Chirality : 0.039 0.125 6290 Planarity : 0.003 0.049 7344 Dihedral : 4.033 16.128 5508 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.96 % Allowed : 20.81 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4896 helix: 3.49 (0.13), residues: 1326 sheet: -1.21 (0.11), residues: 2414 loop : -1.36 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 417 TYR 0.011 0.001 TYR e 393 PHE 0.022 0.001 PHE Z 422 HIS 0.002 0.000 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (40698) covalent geometry : angle 0.54558 (54842) hydrogen bonds : bond 0.03883 ( 1739) hydrogen bonds : angle 3.78893 ( 4911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 798 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6670 (tmm) cc_final: 0.6340 (tmm) REVERT: B 247 ARG cc_start: 0.8179 (ppt170) cc_final: 0.7866 (ppt170) REVERT: C 269 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7324 (mp10) REVERT: D 240 ASP cc_start: 0.7723 (m-30) cc_final: 0.7449 (m-30) REVERT: D 367 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7773 (mm-30) REVERT: D 383 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8281 (mm-30) REVERT: E 356 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6333 (ptp-170) REVERT: E 393 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: F 367 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8076 (mt-10) REVERT: F 383 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8422 (mm-30) REVERT: F 409 MET cc_start: 0.6850 (tmm) cc_final: 0.6519 (tmm) REVERT: G 283 SER cc_start: 0.9344 (m) cc_final: 0.8987 (p) REVERT: G 393 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.5571 (m-80) REVERT: G 431 ASN cc_start: 0.7140 (OUTLIER) cc_final: 0.6560 (p0) REVERT: H 247 ARG cc_start: 0.8078 (ppt170) cc_final: 0.7786 (ppt170) REVERT: H 431 ASN cc_start: 0.6628 (t0) cc_final: 0.6409 (t0) REVERT: I 367 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8107 (mt-10) REVERT: J 269 GLN cc_start: 0.8054 (mp10) cc_final: 0.7745 (mp10) REVERT: J 383 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8360 (mm-30) REVERT: J 393 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: J 418 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7308 (mt-10) REVERT: L 418 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7633 (mt-10) REVERT: M 269 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7332 (mt0) REVERT: M 356 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6375 (ptp-170) REVERT: N 383 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8394 (mm-30) REVERT: O 414 ASP cc_start: 0.7955 (t0) cc_final: 0.7722 (t0) REVERT: Q 269 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7851 (mp10) REVERT: Q 290 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8173 (mtmm) REVERT: Q 393 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.5668 (m-80) REVERT: R 279 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: R 280 GLU cc_start: 0.8023 (tt0) cc_final: 0.7560 (tt0) REVERT: R 414 ASP cc_start: 0.7576 (t0) cc_final: 0.7157 (t0) REVERT: R 418 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7196 (mt-10) REVERT: T 393 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: T 409 MET cc_start: 0.7457 (tmm) cc_final: 0.7239 (tmm) REVERT: V 356 ARG cc_start: 0.7704 (ptt-90) cc_final: 0.7327 (ptp-170) REVERT: V 393 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: V 429 THR cc_start: 0.8366 (p) cc_final: 0.8128 (t) REVERT: W 269 GLN cc_start: 0.8054 (mp10) cc_final: 0.6865 (mp10) REVERT: W 418 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7710 (mm-30) REVERT: X 250 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7755 (mt-10) REVERT: X 269 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7074 (mp10) REVERT: Y 236 LYS cc_start: 0.8052 (mptt) cc_final: 0.7841 (mppt) REVERT: Y 431 ASN cc_start: 0.6222 (m110) cc_final: 0.6003 (m-40) REVERT: Z 290 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7831 (mppt) REVERT: Z 409 MET cc_start: 0.7028 (tmm) cc_final: 0.6633 (tmm) REVERT: a 393 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: c 269 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: b 244 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8017 (ttm170) REVERT: b 250 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: b 269 GLN cc_start: 0.7921 (mp10) cc_final: 0.7657 (mp10) REVERT: d 269 GLN cc_start: 0.8039 (mp10) cc_final: 0.7214 (mt0) REVERT: d 409 MET cc_start: 0.6481 (tmm) cc_final: 0.6192 (tmm) REVERT: e 279 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: e 280 GLU cc_start: 0.7929 (tt0) cc_final: 0.7349 (tt0) REVERT: e 282 TYR cc_start: 0.8451 (m-10) cc_final: 0.8111 (m-10) REVERT: f 393 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: g 269 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7590 (mp10) REVERT: g 367 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8149 (mm-30) REVERT: h 418 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7137 (mt-10) outliers start: 134 outliers final: 104 residues processed: 889 average time/residue: 0.2518 time to fit residues: 346.8203 Evaluate side-chains 886 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 767 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 289 SER Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 289 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain d residue 430 LEU Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain f residue 250 GLU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 224 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 497 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 419 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN D 431 ASN G 265 GLN K 269 GLN T 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113393 restraints weight = 61937.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115608 restraints weight = 32239.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117513 restraints weight = 20720.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118501 restraints weight = 15540.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119471 restraints weight = 13161.875| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 40698 Z= 0.159 Angle : 0.567 9.348 54842 Z= 0.288 Chirality : 0.040 0.130 6290 Planarity : 0.003 0.044 7344 Dihedral : 4.155 18.574 5508 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.99 % Allowed : 21.25 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4896 helix: 3.33 (0.13), residues: 1326 sheet: -1.27 (0.11), residues: 2414 loop : -1.38 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 417 TYR 0.014 0.002 TYR N 393 PHE 0.023 0.001 PHE Z 422 HIS 0.002 0.000 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00374 (40698) covalent geometry : angle 0.56732 (54842) hydrogen bonds : bond 0.04234 ( 1739) hydrogen bonds : angle 3.88868 ( 4911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 788 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6759 (tmm) cc_final: 0.6419 (tmm) REVERT: B 247 ARG cc_start: 0.8162 (ppt170) cc_final: 0.7839 (ppt170) REVERT: B 279 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: B 418 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7526 (mm-30) REVERT: D 240 ASP cc_start: 0.7746 (m-30) cc_final: 0.7469 (m-30) REVERT: D 367 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7778 (mm-30) REVERT: D 383 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8245 (mm-30) REVERT: E 356 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6398 (ptp-170) REVERT: E 393 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: F 269 GLN cc_start: 0.8312 (mp10) cc_final: 0.7852 (mp10) REVERT: F 367 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8035 (mt-10) REVERT: F 383 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8455 (mm-30) REVERT: F 409 MET cc_start: 0.6879 (tmm) cc_final: 0.6543 (tmm) REVERT: G 283 SER cc_start: 0.9326 (m) cc_final: 0.8944 (p) REVERT: G 393 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.5614 (m-80) REVERT: H 431 ASN cc_start: 0.6839 (t0) cc_final: 0.6602 (t0) REVERT: I 367 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8105 (mt-10) REVERT: J 269 GLN cc_start: 0.8061 (mp10) cc_final: 0.7754 (mp10) REVERT: J 383 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8343 (mm-30) REVERT: J 393 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: J 418 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7362 (mt-10) REVERT: K 247 ARG cc_start: 0.7960 (ppt170) cc_final: 0.7749 (ppt170) REVERT: K 269 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: L 418 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7680 (mt-10) REVERT: M 269 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7322 (mt0) REVERT: M 356 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6426 (ptp-170) REVERT: M 367 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: N 383 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8401 (mm-30) REVERT: O 414 ASP cc_start: 0.7976 (t0) cc_final: 0.7731 (t0) REVERT: Q 236 LYS cc_start: 0.8547 (mptt) cc_final: 0.8286 (mmtm) REVERT: Q 269 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7884 (mp10) REVERT: Q 367 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7920 (mt-10) REVERT: Q 393 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: R 269 GLN cc_start: 0.8235 (mp10) cc_final: 0.7783 (mt0) REVERT: R 279 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: R 280 GLU cc_start: 0.8126 (tt0) cc_final: 0.7694 (tt0) REVERT: R 414 ASP cc_start: 0.7599 (t0) cc_final: 0.7196 (t0) REVERT: R 418 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7219 (mt-10) REVERT: S 393 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: T 385 LEU cc_start: 0.8546 (mt) cc_final: 0.8242 (tp) REVERT: T 393 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: U 269 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7478 (mp10) REVERT: V 356 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.7010 (ptp90) REVERT: V 393 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: V 429 THR cc_start: 0.8358 (p) cc_final: 0.8112 (t) REVERT: W 418 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7717 (mm-30) REVERT: X 236 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7909 (mppt) REVERT: X 250 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7758 (mt-10) REVERT: X 269 GLN cc_start: 0.7909 (mm-40) cc_final: 0.6885 (mp10) REVERT: X 289 SER cc_start: 0.8592 (p) cc_final: 0.8356 (p) REVERT: Y 431 ASN cc_start: 0.6284 (m110) cc_final: 0.6021 (m-40) REVERT: Z 409 MET cc_start: 0.7042 (tmm) cc_final: 0.6629 (tmm) REVERT: a 393 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: c 269 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: b 247 ARG cc_start: 0.8046 (ppt170) cc_final: 0.7765 (ppt170) REVERT: b 250 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: b 269 GLN cc_start: 0.7974 (mp10) cc_final: 0.7680 (mp10) REVERT: d 409 MET cc_start: 0.6443 (tmm) cc_final: 0.6139 (tmm) REVERT: d 418 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7612 (mm-30) REVERT: e 279 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: e 280 GLU cc_start: 0.7999 (tt0) cc_final: 0.7429 (tt0) REVERT: f 393 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: f 428 ASP cc_start: 0.8712 (m-30) cc_final: 0.8449 (t70) REVERT: g 269 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7622 (mp10) REVERT: g 289 SER cc_start: 0.8921 (p) cc_final: 0.7976 (t) REVERT: g 367 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8164 (mm-30) REVERT: h 418 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7142 (mt-10) outliers start: 135 outliers final: 103 residues processed: 886 average time/residue: 0.2529 time to fit residues: 348.9387 Evaluate side-chains 896 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 775 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 393 TYR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 289 SER Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain d residue 430 LEU Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 289 SER Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain f residue 250 GLU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 430 LEU Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 276 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 314 optimal weight: 0.3980 chunk 414 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 325 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 478 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN D 431 ASN G 265 GLN h 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114928 restraints weight = 61222.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117331 restraints weight = 31777.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119451 restraints weight = 20123.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120738 restraints weight = 15005.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120749 restraints weight = 11739.559| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40698 Z= 0.125 Angle : 0.559 10.832 54842 Z= 0.283 Chirality : 0.039 0.128 6290 Planarity : 0.002 0.043 7344 Dihedral : 4.042 16.081 5508 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.74 % Allowed : 21.74 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4896 helix: 3.45 (0.13), residues: 1326 sheet: -1.18 (0.11), residues: 2414 loop : -1.35 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 417 TYR 0.010 0.001 TYR e 393 PHE 0.019 0.001 PHE Z 422 HIS 0.001 0.000 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (40698) covalent geometry : angle 0.55904 (54842) hydrogen bonds : bond 0.03770 ( 1739) hydrogen bonds : angle 3.76496 ( 4911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 790 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6626 (tmm) cc_final: 0.6298 (tmm) REVERT: B 240 ASP cc_start: 0.7786 (m-30) cc_final: 0.7477 (m-30) REVERT: B 418 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 269 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7256 (mp10) REVERT: D 240 ASP cc_start: 0.7715 (m-30) cc_final: 0.7445 (m-30) REVERT: D 367 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7778 (mm-30) REVERT: D 383 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8260 (mm-30) REVERT: D 409 MET cc_start: 0.6730 (tmm) cc_final: 0.6365 (tmm) REVERT: E 356 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6353 (ptp-170) REVERT: E 393 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: E 410 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8191 (ttpt) REVERT: F 269 GLN cc_start: 0.8321 (mp10) cc_final: 0.7904 (mp10) REVERT: F 367 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8070 (mt-10) REVERT: F 383 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8414 (mm-30) REVERT: F 409 MET cc_start: 0.6804 (tmm) cc_final: 0.6471 (tmm) REVERT: F 418 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7655 (mt-10) REVERT: G 283 SER cc_start: 0.9330 (m) cc_final: 0.8980 (p) REVERT: G 393 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: H 431 ASN cc_start: 0.6669 (t0) cc_final: 0.6436 (t0) REVERT: I 236 LYS cc_start: 0.8136 (mptt) cc_final: 0.7892 (mppt) REVERT: I 383 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8117 (mm-30) REVERT: J 269 GLN cc_start: 0.8047 (mp10) cc_final: 0.7759 (mp10) REVERT: J 383 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8337 (mm-30) REVERT: J 393 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: J 418 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7370 (mt-10) REVERT: K 247 ARG cc_start: 0.7910 (ppt170) cc_final: 0.7679 (ppt170) REVERT: K 269 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: L 418 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7694 (mt-10) REVERT: M 269 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7348 (mt0) REVERT: M 356 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6455 (ptp-170) REVERT: M 367 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: N 269 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7759 (mp10) REVERT: N 383 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8395 (mm-30) REVERT: O 414 ASP cc_start: 0.7993 (t0) cc_final: 0.7194 (t0) REVERT: Q 269 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7879 (mp10) REVERT: Q 393 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.5616 (m-80) REVERT: R 269 GLN cc_start: 0.8191 (mp10) cc_final: 0.7904 (mt0) REVERT: R 279 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: R 280 GLU cc_start: 0.8018 (tt0) cc_final: 0.7545 (tt0) REVERT: R 414 ASP cc_start: 0.7648 (t0) cc_final: 0.7252 (t0) REVERT: R 418 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7200 (mt-10) REVERT: S 393 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: T 385 LEU cc_start: 0.8486 (mt) cc_final: 0.8266 (tp) REVERT: T 393 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: T 428 ASP cc_start: 0.8803 (t70) cc_final: 0.8375 (t70) REVERT: V 356 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7111 (ptp90) REVERT: V 393 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: V 429 THR cc_start: 0.8341 (p) cc_final: 0.8094 (t) REVERT: W 269 GLN cc_start: 0.8043 (mp10) cc_final: 0.6873 (mp10) REVERT: W 418 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7581 (mm-30) REVERT: X 236 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7865 (mppt) REVERT: X 250 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7666 (mt-10) REVERT: X 269 GLN cc_start: 0.8003 (mm-40) cc_final: 0.6928 (mp10) REVERT: Y 431 ASN cc_start: 0.6219 (m110) cc_final: 0.5954 (m-40) REVERT: Z 409 MET cc_start: 0.7009 (tmm) cc_final: 0.6619 (tmm) REVERT: a 393 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: c 269 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: b 247 ARG cc_start: 0.8034 (ppt170) cc_final: 0.7745 (ppt170) REVERT: b 250 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: b 269 GLN cc_start: 0.7920 (mp10) cc_final: 0.7655 (mp10) REVERT: d 409 MET cc_start: 0.6386 (tmm) cc_final: 0.6128 (tmm) REVERT: d 418 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7824 (mm-30) REVERT: e 279 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: e 280 GLU cc_start: 0.7933 (tt0) cc_final: 0.7549 (tt0) REVERT: f 393 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: g 269 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7607 (mp10) REVERT: g 367 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8160 (mm-30) REVERT: g 377 MET cc_start: 0.8342 (mmm) cc_final: 0.7979 (mmm) REVERT: h 418 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7107 (mt-10) outliers start: 124 outliers final: 99 residues processed: 879 average time/residue: 0.2561 time to fit residues: 348.6759 Evaluate side-chains 893 residues out of total 4522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 777 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 393 TYR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 289 SER Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain d residue 430 LEU Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain f residue 250 GLU Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 226 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 287 optimal weight: 0.0970 chunk 163 optimal weight: 0.0170 chunk 145 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 335 optimal weight: 2.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 378 ASN D 431 ASN G 265 GLN ** N 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119944 restraints weight = 62781.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122725 restraints weight = 33041.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124764 restraints weight = 20947.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125971 restraints weight = 15379.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126506 restraints weight = 12248.295| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40698 Z= 0.108 Angle : 0.546 9.752 54842 Z= 0.276 Chirality : 0.039 0.134 6290 Planarity : 0.002 0.044 7344 Dihedral : 3.849 15.198 5508 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.43 % Allowed : 22.09 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4896 helix: 3.59 (0.13), residues: 1326 sheet: -1.03 (0.11), residues: 2414 loop : -1.31 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 417 TYR 0.008 0.001 TYR e 393 PHE 0.019 0.001 PHE Z 422 HIS 0.001 0.000 HIS Q 374 Details of bonding type rmsd covalent geometry : bond 0.00262 (40698) covalent geometry : angle 0.54615 (54842) hydrogen bonds : bond 0.03349 ( 1739) hydrogen bonds : angle 3.64209 ( 4911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7811.99 seconds wall clock time: 135 minutes 10.82 seconds (8110.82 seconds total)