Starting phenix.real_space_refine on Sun Feb 8 04:33:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5v_39783/02_2026/8z5v_39783.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.084 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 68 5.16 5 C 24446 2.51 5 N 7310 2.21 5 O 7990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39814 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1171 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h Time building chain proxies: 3.06, per 1000 atoms: 0.08 Number of scatterers: 39814 At special positions: 0 Unit cell: (246, 246, 96, 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 68 16.00 O 7990 8.00 N 7310 7.00 C 24446 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9520 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 36 sheets defined 35.2% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 255 through 286 Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY A 432 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'B' and resid 256 through 286 Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY B 432 " --> pdb=" O GLN B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'C' and resid 256 through 286 Proline residue: C 283 - end of helix Processing helix chain 'C' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY C 432 " --> pdb=" O GLN C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'D' and resid 256 through 286 Proline residue: D 283 - end of helix Processing helix chain 'D' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY D 432 " --> pdb=" O GLN D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'E' and resid 256 through 286 Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY E 432 " --> pdb=" O GLN E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'F' and resid 256 through 286 Proline residue: F 283 - end of helix Processing helix chain 'F' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY F 432 " --> pdb=" O GLN F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 441 Processing helix chain 'G' and resid 256 through 286 Proline residue: G 283 - end of helix Processing helix chain 'G' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY G 432 " --> pdb=" O GLN G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 Processing helix chain 'H' and resid 256 through 286 Proline residue: H 283 - end of helix Processing helix chain 'H' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY H 432 " --> pdb=" O GLN H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 441 Processing helix chain 'I' and resid 256 through 286 Proline residue: I 283 - end of helix Processing helix chain 'I' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY I 432 " --> pdb=" O GLN I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 441 Processing helix chain 'J' and resid 256 through 286 Proline residue: J 283 - end of helix Processing helix chain 'J' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY J 432 " --> pdb=" O GLN J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 441 Processing helix chain 'K' and resid 256 through 286 Proline residue: K 283 - end of helix Processing helix chain 'K' and resid 419 through 434 removed outlier: 4.671A pdb=" N GLY K 432 " --> pdb=" O GLN K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 441 Processing helix chain 'L' and resid 256 through 286 Proline residue: L 283 - end of helix Processing helix chain 'L' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY L 432 " --> pdb=" O GLN L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 441 Processing helix chain 'M' and resid 256 through 286 Proline residue: M 283 - end of helix Processing helix chain 'M' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY M 432 " --> pdb=" O GLN M 428 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 441 Processing helix chain 'N' and resid 256 through 286 Proline residue: N 283 - end of helix Processing helix chain 'N' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY N 432 " --> pdb=" O GLN N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 441 Processing helix chain 'O' and resid 256 through 286 Proline residue: O 283 - end of helix Processing helix chain 'O' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY O 432 " --> pdb=" O GLN O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 437 through 441 Processing helix chain 'P' and resid 256 through 286 Proline residue: P 283 - end of helix Processing helix chain 'P' and resid 419 through 434 removed outlier: 4.671A pdb=" N GLY P 432 " --> pdb=" O GLN P 428 " (cutoff:3.500A) Processing helix chain 'P' and resid 437 through 441 Processing helix chain 'Q' and resid 256 through 286 Proline residue: Q 283 - end of helix Processing helix chain 'Q' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY Q 432 " --> pdb=" O GLN Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 441 Processing helix chain 'R' and resid 256 through 286 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY R 432 " --> pdb=" O GLN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 441 Processing helix chain 'S' and resid 256 through 286 Proline residue: S 283 - end of helix Processing helix chain 'S' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY S 432 " --> pdb=" O GLN S 428 " (cutoff:3.500A) Processing helix chain 'S' and resid 437 through 441 Processing helix chain 'T' and resid 256 through 286 Proline residue: T 283 - end of helix Processing helix chain 'T' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY T 432 " --> pdb=" O GLN T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 437 through 441 Processing helix chain 'U' and resid 256 through 286 Proline residue: U 283 - end of helix Processing helix chain 'U' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY U 432 " --> pdb=" O GLN U 428 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 441 Processing helix chain 'V' and resid 256 through 286 Proline residue: V 283 - end of helix Processing helix chain 'V' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY V 432 " --> pdb=" O GLN V 428 " (cutoff:3.500A) Processing helix chain 'V' and resid 437 through 441 Processing helix chain 'W' and resid 256 through 286 Proline residue: W 283 - end of helix Processing helix chain 'W' and resid 419 through 434 removed outlier: 4.671A pdb=" N GLY W 432 " --> pdb=" O GLN W 428 " (cutoff:3.500A) Processing helix chain 'W' and resid 437 through 441 Processing helix chain 'X' and resid 256 through 286 Proline residue: X 283 - end of helix Processing helix chain 'X' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY X 432 " --> pdb=" O GLN X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 437 through 441 Processing helix chain 'Y' and resid 256 through 286 Proline residue: Y 283 - end of helix Processing helix chain 'Y' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY Y 432 " --> pdb=" O GLN Y 428 " (cutoff:3.500A) Processing helix chain 'Y' and resid 437 through 441 Processing helix chain 'Z' and resid 256 through 286 Proline residue: Z 283 - end of helix Processing helix chain 'Z' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY Z 432 " --> pdb=" O GLN Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 437 through 441 Processing helix chain 'a' and resid 256 through 286 Proline residue: a 283 - end of helix Processing helix chain 'a' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY a 432 " --> pdb=" O GLN a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 437 through 441 Processing helix chain 'b' and resid 256 through 286 Proline residue: b 283 - end of helix Processing helix chain 'b' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY b 432 " --> pdb=" O GLN b 428 " (cutoff:3.500A) Processing helix chain 'b' and resid 437 through 441 Processing helix chain 'c' and resid 256 through 286 Proline residue: c 283 - end of helix Processing helix chain 'c' and resid 419 through 434 removed outlier: 4.669A pdb=" N GLY c 432 " --> pdb=" O GLN c 428 " (cutoff:3.500A) Processing helix chain 'c' and resid 437 through 441 Processing helix chain 'd' and resid 256 through 286 Proline residue: d 283 - end of helix Processing helix chain 'd' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY d 432 " --> pdb=" O GLN d 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 437 through 441 Processing helix chain 'e' and resid 256 through 286 Proline residue: e 283 - end of helix Processing helix chain 'e' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY e 432 " --> pdb=" O GLN e 428 " (cutoff:3.500A) Processing helix chain 'e' and resid 437 through 441 Processing helix chain 'f' and resid 256 through 286 Proline residue: f 283 - end of helix Processing helix chain 'f' and resid 419 through 434 removed outlier: 4.671A pdb=" N GLY f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 441 Processing helix chain 'g' and resid 256 through 286 Proline residue: g 283 - end of helix Processing helix chain 'g' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY g 432 " --> pdb=" O GLN g 428 " (cutoff:3.500A) Processing helix chain 'g' and resid 437 through 441 Processing helix chain 'h' and resid 256 through 286 Proline residue: h 283 - end of helix Processing helix chain 'h' and resid 419 through 434 removed outlier: 4.670A pdb=" N GLY h 432 " --> pdb=" O GLN h 428 " (cutoff:3.500A) Processing helix chain 'h' and resid 437 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 290 through 299 removed outlier: 6.221A pdb=" N ASP A 299 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL A 391 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU A 443 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN A 394 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN A 445 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 396 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU A 447 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 398 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 449 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE A 400 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 304 through 310 Processing sheet with id=AA3, first strand: chain 'A' and resid 316 through 326 removed outlier: 5.433A pdb=" N THR A 317 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU A 376 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 319 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 367 " --> pdb=" O TYR B 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 318 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR B 317 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B 376 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 319 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 367 " --> pdb=" O TYR C 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 318 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR C 317 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C 376 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 319 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 367 " --> pdb=" O TYR D 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG D 318 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR D 317 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU D 376 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 319 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 367 " --> pdb=" O TYR E 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG E 318 " --> pdb=" O PHE D 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR E 317 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU E 376 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER E 319 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 367 " --> pdb=" O TYR F 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG F 318 " --> pdb=" O PHE E 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR F 317 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU F 376 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER F 319 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 367 " --> pdb=" O TYR G 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG G 318 " --> pdb=" O PHE F 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR G 317 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU G 376 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER G 319 " --> pdb=" O ASN G 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL G 367 " --> pdb=" O TYR H 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG H 318 " --> pdb=" O PHE G 375 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR H 317 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU H 376 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 319 " --> pdb=" O ASN H 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 367 " --> pdb=" O TYR I 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG I 318 " --> pdb=" O PHE H 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR I 317 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU I 376 " --> pdb=" O THR I 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER I 319 " --> pdb=" O ASN I 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL I 367 " --> pdb=" O TYR J 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG J 318 " --> pdb=" O PHE I 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR J 317 " --> pdb=" O GLU J 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU J 376 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER J 319 " --> pdb=" O ASN J 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL J 367 " --> pdb=" O TYR K 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG K 318 " --> pdb=" O PHE J 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR K 317 " --> pdb=" O GLU K 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU K 376 " --> pdb=" O THR K 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER K 319 " --> pdb=" O ASN K 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL K 367 " --> pdb=" O TYR L 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG L 318 " --> pdb=" O PHE K 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR L 317 " --> pdb=" O GLU L 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU L 376 " --> pdb=" O THR L 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER L 319 " --> pdb=" O ASN L 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL L 367 " --> pdb=" O TYR M 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG M 318 " --> pdb=" O PHE L 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR M 317 " --> pdb=" O GLU M 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU M 376 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER M 319 " --> pdb=" O ASN M 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL M 367 " --> pdb=" O TYR N 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG N 318 " --> pdb=" O PHE M 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR N 317 " --> pdb=" O GLU N 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU N 376 " --> pdb=" O THR N 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 319 " --> pdb=" O ASN N 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL N 367 " --> pdb=" O TYR O 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG O 318 " --> pdb=" O PHE N 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR O 317 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU O 376 " --> pdb=" O THR O 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER O 319 " --> pdb=" O ASN O 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL O 367 " --> pdb=" O TYR P 326 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG P 318 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR P 317 " --> pdb=" O GLU P 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU P 376 " --> pdb=" O THR P 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER P 319 " --> pdb=" O ASN P 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL P 367 " --> pdb=" O TYR Q 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG Q 318 " --> pdb=" O PHE P 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR Q 317 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU Q 376 " --> pdb=" O THR Q 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER Q 319 " --> pdb=" O ASN Q 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Q 367 " --> pdb=" O TYR R 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG R 318 " --> pdb=" O PHE Q 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR R 317 " --> pdb=" O GLU R 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU R 376 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 319 " --> pdb=" O ASN R 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 367 " --> pdb=" O TYR S 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG S 318 " --> pdb=" O PHE R 375 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR S 317 " --> pdb=" O GLU S 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU S 376 " --> pdb=" O THR S 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER S 319 " --> pdb=" O ASN S 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL S 367 " --> pdb=" O TYR T 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG T 318 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR T 317 " --> pdb=" O GLU T 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU T 376 " --> pdb=" O THR T 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER T 319 " --> pdb=" O ASN T 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL T 367 " --> pdb=" O TYR U 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG U 318 " --> pdb=" O PHE T 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR U 317 " --> pdb=" O GLU U 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU U 376 " --> pdb=" O THR U 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER U 319 " --> pdb=" O ASN U 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL U 367 " --> pdb=" O TYR V 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG V 318 " --> pdb=" O PHE U 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR V 317 " --> pdb=" O GLU V 376 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU V 376 " --> pdb=" O THR V 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER V 319 " --> pdb=" O ASN V 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL V 367 " --> pdb=" O TYR W 326 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG W 318 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR W 317 " --> pdb=" O GLU W 376 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU W 376 " --> pdb=" O THR W 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER W 319 " --> pdb=" O ASN W 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL W 367 " --> pdb=" O TYR X 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG X 318 " --> pdb=" O PHE W 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR X 317 " --> pdb=" O GLU X 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU X 376 " --> pdb=" O THR X 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER X 319 " --> pdb=" O ASN X 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL X 367 " --> pdb=" O TYR Y 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG Y 318 " --> pdb=" O PHE X 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR Y 317 " --> pdb=" O GLU Y 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU Y 376 " --> pdb=" O THR Y 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER Y 319 " --> pdb=" O ASN Y 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL Y 367 " --> pdb=" O TYR Z 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG Z 318 " --> pdb=" O PHE Y 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR Z 317 " --> pdb=" O GLU Z 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU Z 376 " --> pdb=" O THR Z 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER Z 319 " --> pdb=" O ASN Z 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL Z 367 " --> pdb=" O TYR a 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG a 318 " --> pdb=" O PHE Z 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR a 317 " --> pdb=" O GLU a 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU a 376 " --> pdb=" O THR a 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER a 319 " --> pdb=" O ASN a 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL a 367 " --> pdb=" O TYR b 326 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG b 318 " --> pdb=" O PHE a 375 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR b 317 " --> pdb=" O GLU b 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU b 376 " --> pdb=" O THR b 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER b 319 " --> pdb=" O ASN b 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL b 367 " --> pdb=" O TYR c 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG c 318 " --> pdb=" O PHE b 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR c 317 " --> pdb=" O GLU c 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU c 376 " --> pdb=" O THR c 317 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER c 319 " --> pdb=" O ASN c 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL c 367 " --> pdb=" O TYR d 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG d 318 " --> pdb=" O PHE c 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR d 317 " --> pdb=" O GLU d 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU d 376 " --> pdb=" O THR d 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER d 319 " --> pdb=" O ASN d 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL d 367 " --> pdb=" O TYR e 326 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG e 318 " --> pdb=" O PHE d 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR e 317 " --> pdb=" O GLU e 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU e 376 " --> pdb=" O THR e 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER e 319 " --> pdb=" O ASN e 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL e 367 " --> pdb=" O TYR f 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG f 318 " --> pdb=" O PHE e 375 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR f 317 " --> pdb=" O GLU f 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU f 376 " --> pdb=" O THR f 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER f 319 " --> pdb=" O ASN f 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL f 367 " --> pdb=" O TYR g 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG g 318 " --> pdb=" O PHE f 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR g 317 " --> pdb=" O GLU g 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU g 376 " --> pdb=" O THR g 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER g 319 " --> pdb=" O ASN g 374 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL g 367 " --> pdb=" O TYR h 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG h 318 " --> pdb=" O PHE g 375 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR h 317 " --> pdb=" O GLU h 376 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU h 376 " --> pdb=" O THR h 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER h 319 " --> pdb=" O ASN h 374 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL h 367 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG A 318 " --> pdb=" O PHE h 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP B 299 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL B 391 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU B 443 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 394 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN B 445 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 396 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU B 447 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 398 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 449 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE B 400 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP C 299 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 391 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU C 443 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN C 394 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN C 445 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 396 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU C 447 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 398 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 449 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 400 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP D 299 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL D 391 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU D 443 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN D 394 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN D 445 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 396 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU D 447 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 398 " --> pdb=" O LEU D 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL D 449 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE D 400 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP E 299 " --> pdb=" O VAL E 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E 391 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU E 443 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN E 394 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN E 445 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 396 " --> pdb=" O ASN E 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU E 447 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 398 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 449 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE E 400 " --> pdb=" O VAL E 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP F 299 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL F 391 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU F 443 " --> pdb=" O ALA F 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN F 394 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN F 445 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 396 " --> pdb=" O ASN F 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU F 447 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL F 398 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL F 449 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE F 400 " --> pdb=" O VAL F 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP G 299 " --> pdb=" O VAL G 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL G 391 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU G 443 " --> pdb=" O ALA G 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN G 394 " --> pdb=" O LEU G 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN G 445 " --> pdb=" O GLN G 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL G 396 " --> pdb=" O ASN G 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU G 447 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL G 398 " --> pdb=" O LEU G 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL G 449 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE G 400 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP H 299 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL H 391 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU H 443 " --> pdb=" O ALA H 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN H 394 " --> pdb=" O LEU H 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN H 445 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL H 396 " --> pdb=" O ASN H 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU H 447 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL H 398 " --> pdb=" O LEU H 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL H 449 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE H 400 " --> pdb=" O VAL H 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP I 299 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL I 391 " --> pdb=" O ASP I 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU I 443 " --> pdb=" O ALA I 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN I 394 " --> pdb=" O LEU I 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN I 445 " --> pdb=" O GLN I 394 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL I 396 " --> pdb=" O ASN I 445 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU I 447 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL I 398 " --> pdb=" O LEU I 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL I 449 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE I 400 " --> pdb=" O VAL I 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP J 299 " --> pdb=" O VAL J 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL J 391 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU J 443 " --> pdb=" O ALA J 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN J 394 " --> pdb=" O LEU J 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN J 445 " --> pdb=" O GLN J 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL J 396 " --> pdb=" O ASN J 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU J 447 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL J 398 " --> pdb=" O LEU J 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL J 449 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE J 400 " --> pdb=" O VAL J 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP K 299 " --> pdb=" O VAL K 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL K 391 " --> pdb=" O ASP K 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU K 443 " --> pdb=" O ALA K 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN K 394 " --> pdb=" O LEU K 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN K 445 " --> pdb=" O GLN K 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL K 396 " --> pdb=" O ASN K 445 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU K 447 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL K 398 " --> pdb=" O LEU K 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL K 449 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE K 400 " --> pdb=" O VAL K 449 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP L 299 " --> pdb=" O VAL L 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL L 391 " --> pdb=" O ASP L 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU L 443 " --> pdb=" O ALA L 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN L 394 " --> pdb=" O LEU L 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN L 445 " --> pdb=" O GLN L 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL L 396 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU L 447 " --> pdb=" O VAL L 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL L 398 " --> pdb=" O LEU L 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL L 449 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE L 400 " --> pdb=" O VAL L 449 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 290 through 299 removed outlier: 6.221A pdb=" N ASP M 299 " --> pdb=" O VAL M 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL M 391 " --> pdb=" O ASP M 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU M 443 " --> pdb=" O ALA M 392 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN M 394 " --> pdb=" O LEU M 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN M 445 " --> pdb=" O GLN M 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL M 396 " --> pdb=" O ASN M 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU M 447 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL M 398 " --> pdb=" O LEU M 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL M 449 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE M 400 " --> pdb=" O VAL M 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP N 299 " --> pdb=" O VAL N 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL N 391 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU N 443 " --> pdb=" O ALA N 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN N 394 " --> pdb=" O LEU N 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN N 445 " --> pdb=" O GLN N 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL N 396 " --> pdb=" O ASN N 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU N 447 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL N 398 " --> pdb=" O LEU N 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL N 449 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE N 400 " --> pdb=" O VAL N 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP O 299 " --> pdb=" O VAL O 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL O 391 " --> pdb=" O ASP O 299 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N LEU O 443 " --> pdb=" O ALA O 392 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN O 394 " --> pdb=" O LEU O 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN O 445 " --> pdb=" O GLN O 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL O 396 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU O 447 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL O 398 " --> pdb=" O LEU O 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL O 449 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE O 400 " --> pdb=" O VAL O 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP P 299 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL P 391 " --> pdb=" O ASP P 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU P 443 " --> pdb=" O ALA P 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN P 394 " --> pdb=" O LEU P 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN P 445 " --> pdb=" O GLN P 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL P 396 " --> pdb=" O ASN P 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU P 447 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL P 398 " --> pdb=" O LEU P 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL P 449 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE P 400 " --> pdb=" O VAL P 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP Q 299 " --> pdb=" O VAL Q 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL Q 391 " --> pdb=" O ASP Q 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU Q 443 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN Q 394 " --> pdb=" O LEU Q 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN Q 445 " --> pdb=" O GLN Q 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL Q 396 " --> pdb=" O ASN Q 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU Q 447 " --> pdb=" O VAL Q 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL Q 398 " --> pdb=" O LEU Q 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL Q 449 " --> pdb=" O VAL Q 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE Q 400 " --> pdb=" O VAL Q 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP R 299 " --> pdb=" O VAL R 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL R 391 " --> pdb=" O ASP R 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU R 443 " --> pdb=" O ALA R 392 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN R 394 " --> pdb=" O LEU R 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN R 445 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL R 396 " --> pdb=" O ASN R 445 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU R 447 " --> pdb=" O VAL R 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL R 398 " --> pdb=" O LEU R 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL R 449 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE R 400 " --> pdb=" O VAL R 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP S 299 " --> pdb=" O VAL S 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL S 391 " --> pdb=" O ASP S 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU S 443 " --> pdb=" O ALA S 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN S 394 " --> pdb=" O LEU S 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN S 445 " --> pdb=" O GLN S 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL S 396 " --> pdb=" O ASN S 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU S 447 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL S 398 " --> pdb=" O LEU S 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL S 449 " --> pdb=" O VAL S 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE S 400 " --> pdb=" O VAL S 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP T 299 " --> pdb=" O VAL T 391 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL T 391 " --> pdb=" O ASP T 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU T 443 " --> pdb=" O ALA T 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN T 394 " --> pdb=" O LEU T 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN T 445 " --> pdb=" O GLN T 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL T 396 " --> pdb=" O ASN T 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU T 447 " --> pdb=" O VAL T 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL T 398 " --> pdb=" O LEU T 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL T 449 " --> pdb=" O VAL T 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE T 400 " --> pdb=" O VAL T 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP U 299 " --> pdb=" O VAL U 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL U 391 " --> pdb=" O ASP U 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU U 443 " --> pdb=" O ALA U 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN U 394 " --> pdb=" O LEU U 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN U 445 " --> pdb=" O GLN U 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL U 396 " --> pdb=" O ASN U 445 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU U 447 " --> pdb=" O VAL U 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL U 398 " --> pdb=" O LEU U 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL U 449 " --> pdb=" O VAL U 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE U 400 " --> pdb=" O VAL U 449 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP V 299 " --> pdb=" O VAL V 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL V 391 " --> pdb=" O ASP V 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU V 443 " --> pdb=" O ALA V 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN V 394 " --> pdb=" O LEU V 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN V 445 " --> pdb=" O GLN V 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL V 396 " --> pdb=" O ASN V 445 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU V 447 " --> pdb=" O VAL V 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL V 398 " --> pdb=" O LEU V 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL V 449 " --> pdb=" O VAL V 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE V 400 " --> pdb=" O VAL V 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP W 299 " --> pdb=" O VAL W 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL W 391 " --> pdb=" O ASP W 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU W 443 " --> pdb=" O ALA W 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN W 394 " --> pdb=" O LEU W 443 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN W 445 " --> pdb=" O GLN W 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL W 396 " --> pdb=" O ASN W 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU W 447 " --> pdb=" O VAL W 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL W 398 " --> pdb=" O LEU W 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL W 449 " --> pdb=" O VAL W 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE W 400 " --> pdb=" O VAL W 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP X 299 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL X 391 " --> pdb=" O ASP X 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU X 443 " --> pdb=" O ALA X 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN X 394 " --> pdb=" O LEU X 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN X 445 " --> pdb=" O GLN X 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL X 396 " --> pdb=" O ASN X 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU X 447 " --> pdb=" O VAL X 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL X 398 " --> pdb=" O LEU X 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL X 449 " --> pdb=" O VAL X 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE X 400 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP Y 299 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL Y 391 " --> pdb=" O ASP Y 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU Y 443 " --> pdb=" O ALA Y 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN Y 394 " --> pdb=" O LEU Y 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN Y 445 " --> pdb=" O GLN Y 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL Y 396 " --> pdb=" O ASN Y 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU Y 447 " --> pdb=" O VAL Y 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL Y 398 " --> pdb=" O LEU Y 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL Y 449 " --> pdb=" O VAL Y 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE Y 400 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP Z 299 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL Z 391 " --> pdb=" O ASP Z 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU Z 443 " --> pdb=" O ALA Z 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN Z 394 " --> pdb=" O LEU Z 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN Z 445 " --> pdb=" O GLN Z 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL Z 396 " --> pdb=" O ASN Z 445 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU Z 447 " --> pdb=" O VAL Z 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL Z 398 " --> pdb=" O LEU Z 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL Z 449 " --> pdb=" O VAL Z 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE Z 400 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP a 299 " --> pdb=" O VAL a 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL a 391 " --> pdb=" O ASP a 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU a 443 " --> pdb=" O ALA a 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN a 394 " --> pdb=" O LEU a 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN a 445 " --> pdb=" O GLN a 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL a 396 " --> pdb=" O ASN a 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU a 447 " --> pdb=" O VAL a 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL a 398 " --> pdb=" O LEU a 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL a 449 " --> pdb=" O VAL a 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE a 400 " --> pdb=" O VAL a 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP b 299 " --> pdb=" O VAL b 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL b 391 " --> pdb=" O ASP b 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU b 443 " --> pdb=" O ALA b 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN b 394 " --> pdb=" O LEU b 443 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASN b 445 " --> pdb=" O GLN b 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL b 396 " --> pdb=" O ASN b 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU b 447 " --> pdb=" O VAL b 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL b 398 " --> pdb=" O LEU b 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL b 449 " --> pdb=" O VAL b 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE b 400 " --> pdb=" O VAL b 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP c 299 " --> pdb=" O VAL c 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL c 391 " --> pdb=" O ASP c 299 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N LEU c 443 " --> pdb=" O ALA c 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN c 394 " --> pdb=" O LEU c 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN c 445 " --> pdb=" O GLN c 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL c 396 " --> pdb=" O ASN c 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU c 447 " --> pdb=" O VAL c 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL c 398 " --> pdb=" O LEU c 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL c 449 " --> pdb=" O VAL c 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE c 400 " --> pdb=" O VAL c 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP d 299 " --> pdb=" O VAL d 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL d 391 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU d 443 " --> pdb=" O ALA d 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN d 394 " --> pdb=" O LEU d 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN d 445 " --> pdb=" O GLN d 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL d 396 " --> pdb=" O ASN d 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU d 447 " --> pdb=" O VAL d 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL d 398 " --> pdb=" O LEU d 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL d 449 " --> pdb=" O VAL d 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE d 400 " --> pdb=" O VAL d 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP e 299 " --> pdb=" O VAL e 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL e 391 " --> pdb=" O ASP e 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU e 443 " --> pdb=" O ALA e 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN e 394 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN e 445 " --> pdb=" O GLN e 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL e 396 " --> pdb=" O ASN e 445 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU e 447 " --> pdb=" O VAL e 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL e 398 " --> pdb=" O LEU e 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL e 449 " --> pdb=" O VAL e 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE e 400 " --> pdb=" O VAL e 449 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP f 299 " --> pdb=" O VAL f 391 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL f 391 " --> pdb=" O ASP f 299 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU f 443 " --> pdb=" O ALA f 392 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN f 394 " --> pdb=" O LEU f 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN f 445 " --> pdb=" O GLN f 394 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL f 396 " --> pdb=" O ASN f 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU f 447 " --> pdb=" O VAL f 396 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL f 398 " --> pdb=" O LEU f 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL f 449 " --> pdb=" O VAL f 398 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE f 400 " --> pdb=" O VAL f 449 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 290 through 299 removed outlier: 6.220A pdb=" N ASP g 299 " --> pdb=" O VAL g 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL g 391 " --> pdb=" O ASP g 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU g 443 " --> pdb=" O ALA g 392 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN g 394 " --> pdb=" O LEU g 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN g 445 " --> pdb=" O GLN g 394 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL g 396 " --> pdb=" O ASN g 445 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU g 447 " --> pdb=" O VAL g 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL g 398 " --> pdb=" O LEU g 447 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL g 449 " --> pdb=" O VAL g 398 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE g 400 " --> pdb=" O VAL g 449 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 290 through 299 removed outlier: 6.219A pdb=" N ASP h 299 " --> pdb=" O VAL h 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL h 391 " --> pdb=" O ASP h 299 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU h 443 " --> pdb=" O ALA h 392 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN h 394 " --> pdb=" O LEU h 443 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN h 445 " --> pdb=" O GLN h 394 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL h 396 " --> pdb=" O ASN h 445 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU h 447 " --> pdb=" O VAL h 396 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL h 398 " --> pdb=" O LEU h 447 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL h 449 " --> pdb=" O VAL h 398 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE h 400 " --> pdb=" O VAL h 449 " (cutoff:3.500A) 2449 hydrogen bonds defined for protein. 6939 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: 8.48 Time building geometry restraints manager: 4.42 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: 14008 1.34 - 1.46: 5687 1.46 - 1.57: 20357 1.57 - 1.69: 0 1.69 - 1.80: 136 Bond restraints: 40188 Sorted by residual: bond pdb=" C LEU V 282 " pdb=" N PRO V 283 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 1.06e+00 bond pdb=" C LEU Y 282 " pdb=" N PRO Y 283 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C LEU T 282 " pdb=" N PRO T 283 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 9.89e-01 bond pdb=" C LEU J 282 " pdb=" N PRO J 283 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 9.89e-01 bond pdb=" C LEU g 282 " pdb=" N PRO g 283 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 9.88e-01 ... (remaining 40183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 51293 0.97 - 1.95: 2330 1.95 - 2.92: 267 2.92 - 3.89: 68 3.89 - 4.87: 34 Bond angle restraints: 53992 Sorted by residual: angle pdb=" C PHE K 375 " pdb=" N GLU K 376 " pdb=" CA GLU K 376 " ideal model delta sigma weight residual 122.94 125.06 -2.12 1.50e+00 4.44e-01 2.00e+00 angle pdb=" C PHE U 375 " pdb=" N GLU U 376 " pdb=" CA GLU U 376 " ideal model delta sigma weight residual 122.94 125.05 -2.11 1.50e+00 4.44e-01 1.99e+00 angle pdb=" C PHE A 375 " pdb=" N GLU A 376 " pdb=" CA GLU A 376 " ideal model delta sigma weight residual 122.94 125.03 -2.09 1.50e+00 4.44e-01 1.95e+00 angle pdb=" C PHE d 375 " pdb=" N GLU d 376 " pdb=" CA GLU d 376 " ideal model delta sigma weight residual 122.94 125.03 -2.09 1.50e+00 4.44e-01 1.94e+00 angle pdb=" C PHE P 375 " pdb=" N GLU P 376 " pdb=" CA GLU P 376 " ideal model delta sigma weight residual 122.94 125.03 -2.09 1.50e+00 4.44e-01 1.94e+00 ... (remaining 53987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 22944 14.69 - 29.38: 1366 29.38 - 44.07: 476 44.07 - 58.75: 170 58.75 - 73.44: 68 Dihedral angle restraints: 25024 sinusoidal: 10438 harmonic: 14586 Sorted by residual: dihedral pdb=" CA ARG V 260 " pdb=" CB ARG V 260 " pdb=" CG ARG V 260 " pdb=" CD ARG V 260 " ideal model delta sinusoidal sigma weight residual 60.00 116.17 -56.17 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG c 260 " pdb=" CB ARG c 260 " pdb=" CG ARG c 260 " pdb=" CD ARG c 260 " ideal model delta sinusoidal sigma weight residual 60.00 116.16 -56.16 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG G 260 " pdb=" CB ARG G 260 " pdb=" CG ARG G 260 " pdb=" CD ARG G 260 " ideal model delta sinusoidal sigma weight residual 60.00 116.15 -56.15 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 25021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3487 0.025 - 0.050: 1603 0.050 - 0.074: 537 0.074 - 0.099: 203 0.099 - 0.124: 324 Chirality restraints: 6154 Sorted by residual: chirality pdb=" CA ILE F 431 " pdb=" N ILE F 431 " pdb=" C ILE F 431 " pdb=" CB ILE F 431 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE K 431 " pdb=" N ILE K 431 " pdb=" C ILE K 431 " pdb=" CB ILE K 431 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 6151 not shown) Planarity restraints: 7140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Q 314 " 0.011 5.00e-02 4.00e+02 1.60e-02 4.10e-01 pdb=" N PRO Q 315 " -0.028 5.00e-02 4.00e+02 pdb=" CA PRO Q 315 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO Q 315 " 0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 314 " -0.011 5.00e-02 4.00e+02 1.59e-02 4.03e-01 pdb=" N PRO G 315 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO G 315 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO G 315 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 314 " 0.011 5.00e-02 4.00e+02 1.58e-02 4.00e-01 pdb=" N PRO N 315 " -0.027 5.00e-02 4.00e+02 pdb=" CA PRO N 315 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO N 315 " 0.009 5.00e-02 4.00e+02 ... (remaining 7137 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7967 2.79 - 3.32: 35362 3.32 - 3.84: 64395 3.84 - 4.37: 77295 4.37 - 4.90: 139704 Nonbonded interactions: 324723 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 324 " pdb=" OH TYR Q 326 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU I 324 " pdb=" OH TYR I 326 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU C 324 " pdb=" OH TYR C 326 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU d 324 " pdb=" OH TYR d 326 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU L 324 " pdb=" OH TYR L 326 " model vdw 2.260 3.040 ... (remaining 324718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 30.830 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 40188 Z= 0.158 Angle : 0.479 4.868 53992 Z= 0.260 Chirality : 0.040 0.124 6154 Planarity : 0.003 0.019 7140 Dihedral : 12.317 73.442 15504 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.91 % Allowed : 6.25 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.13), residues: 4828 helix: 3.53 (0.12), residues: 1326 sheet: 0.08 (0.11), residues: 2244 loop : -1.75 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 385 TYR 0.006 0.001 TYR C 326 PHE 0.008 0.001 PHE c 375 HIS 0.002 0.001 HIS I 383 Details of bonding type rmsd covalent geometry : bond 0.00336 (40188) covalent geometry : angle 0.47858 (53992) hydrogen bonds : bond 0.11922 ( 2449) hydrogen bonds : angle 7.33663 ( 6939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1218 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8382 (tt0) cc_final: 0.8168 (tt0) REVERT: A 320 GLU cc_start: 0.8200 (tt0) cc_final: 0.7925 (tt0) REVERT: A 386 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8232 (mttp) REVERT: A 387 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: A 437 ASP cc_start: 0.8460 (t0) cc_final: 0.8094 (t0) REVERT: B 266 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 290 TYR cc_start: 0.8486 (p90) cc_final: 0.8077 (p90) REVERT: B 386 LYS cc_start: 0.8468 (mmtm) cc_final: 0.7879 (mptt) REVERT: B 387 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: B 445 ASN cc_start: 0.8339 (m110) cc_final: 0.8048 (m110) REVERT: C 266 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 386 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8319 (mmtm) REVERT: D 264 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7423 (mp0) REVERT: D 266 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7083 (mt-10) REVERT: D 386 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8159 (mptp) REVERT: D 387 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: D 445 ASN cc_start: 0.8299 (m110) cc_final: 0.7951 (m110) REVERT: E 266 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7114 (mt-10) REVERT: E 270 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8060 (mt-10) REVERT: E 320 GLU cc_start: 0.8268 (tt0) cc_final: 0.7967 (tt0) REVERT: E 387 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: F 305 GLN cc_start: 0.8489 (tt0) cc_final: 0.8273 (tt0) REVERT: F 320 GLU cc_start: 0.8240 (tt0) cc_final: 0.7998 (tt0) REVERT: F 387 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: G 266 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7111 (mt-10) REVERT: G 305 GLN cc_start: 0.8471 (tt0) cc_final: 0.8259 (tt0) REVERT: G 320 GLU cc_start: 0.8204 (tt0) cc_final: 0.7922 (tt0) REVERT: G 387 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: G 402 ASP cc_start: 0.6813 (m-30) cc_final: 0.6600 (m-30) REVERT: G 422 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6114 (pt0) REVERT: G 445 ASN cc_start: 0.8196 (m110) cc_final: 0.7955 (m110) REVERT: H 264 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7029 (mp0) REVERT: H 266 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7086 (mt-10) REVERT: H 298 MET cc_start: 0.8919 (mtp) cc_final: 0.8564 (mtp) REVERT: H 305 GLN cc_start: 0.8405 (tt0) cc_final: 0.8141 (tt0) REVERT: H 385 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7673 (ttm170) REVERT: H 386 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8463 (mptp) REVERT: H 418 MET cc_start: 0.7319 (ttm) cc_final: 0.6997 (ttm) REVERT: H 422 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6402 (pt0) REVERT: H 445 ASN cc_start: 0.8218 (m110) cc_final: 0.7886 (m110) REVERT: I 280 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8330 (t) REVERT: I 298 MET cc_start: 0.8860 (mtp) cc_final: 0.8582 (mtp) REVERT: I 305 GLN cc_start: 0.8411 (tt0) cc_final: 0.8171 (tt0) REVERT: I 385 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7742 (ttp80) REVERT: I 386 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8420 (mmmt) REVERT: I 387 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: I 422 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: I 445 ASN cc_start: 0.8348 (m110) cc_final: 0.8041 (m110) REVERT: J 298 MET cc_start: 0.8946 (mtp) cc_final: 0.8626 (mtp) REVERT: J 305 GLN cc_start: 0.8475 (tt0) cc_final: 0.8247 (tt0) REVERT: J 320 GLU cc_start: 0.8119 (tt0) cc_final: 0.7873 (tt0) REVERT: J 380 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8352 (m) REVERT: J 386 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8114 (mptt) REVERT: J 387 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: J 445 ASN cc_start: 0.8127 (m110) cc_final: 0.7781 (m110) REVERT: K 262 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6708 (mt-10) REVERT: K 298 MET cc_start: 0.8768 (mtp) cc_final: 0.8483 (mtm) REVERT: K 370 GLU cc_start: 0.8279 (tt0) cc_final: 0.7968 (tt0) REVERT: K 380 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8281 (m) REVERT: K 385 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7598 (ttm170) REVERT: K 387 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: L 305 GLN cc_start: 0.8451 (tt0) cc_final: 0.8174 (tt0) REVERT: L 320 GLU cc_start: 0.8156 (tt0) cc_final: 0.7889 (tt0) REVERT: L 387 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: L 445 ASN cc_start: 0.8247 (m110) cc_final: 0.7921 (m110) REVERT: M 266 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7185 (mt-10) REVERT: M 327 ASN cc_start: 0.7744 (m110) cc_final: 0.7479 (m110) REVERT: M 386 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8307 (mptp) REVERT: M 445 ASN cc_start: 0.8351 (m110) cc_final: 0.8078 (m110) REVERT: N 270 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8097 (mt-10) REVERT: N 305 GLN cc_start: 0.8498 (tt0) cc_final: 0.8184 (tt0) REVERT: N 320 GLU cc_start: 0.8017 (tt0) cc_final: 0.7704 (tt0) REVERT: N 387 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: O 278 ASP cc_start: 0.7651 (m-30) cc_final: 0.7395 (m-30) REVERT: O 298 MET cc_start: 0.8753 (mtp) cc_final: 0.8530 (mtp) REVERT: O 305 GLN cc_start: 0.8419 (tt0) cc_final: 0.8107 (tt0) REVERT: O 387 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: P 262 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7004 (mt-10) REVERT: P 266 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7090 (mt-10) REVERT: P 271 GLN cc_start: 0.8211 (tt0) cc_final: 0.7968 (tp-100) REVERT: P 290 TYR cc_start: 0.8345 (p90) cc_final: 0.8132 (p90) REVERT: P 304 GLU cc_start: 0.7495 (tt0) cc_final: 0.7202 (tt0) REVERT: P 320 GLU cc_start: 0.8231 (tt0) cc_final: 0.7932 (tt0) REVERT: P 422 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6389 (pt0) REVERT: P 445 ASN cc_start: 0.8168 (m110) cc_final: 0.7958 (m110) REVERT: Q 266 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7139 (mt-10) REVERT: Q 298 MET cc_start: 0.8897 (mtp) cc_final: 0.8587 (mtp) REVERT: Q 304 GLU cc_start: 0.7973 (tt0) cc_final: 0.7685 (tt0) REVERT: Q 305 GLN cc_start: 0.8411 (tt0) cc_final: 0.8139 (tt0) REVERT: Q 320 GLU cc_start: 0.8182 (tt0) cc_final: 0.7910 (tt0) REVERT: Q 385 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7816 (ttm170) REVERT: Q 442 ASP cc_start: 0.8495 (m-30) cc_final: 0.8269 (m-30) REVERT: R 305 GLN cc_start: 0.8359 (tt0) cc_final: 0.8139 (tt0) REVERT: R 320 GLU cc_start: 0.8199 (tt0) cc_final: 0.7907 (tt0) REVERT: R 386 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8148 (mttp) REVERT: R 387 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: S 266 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7105 (mt-10) REVERT: S 290 TYR cc_start: 0.8433 (p90) cc_final: 0.8046 (p90) REVERT: S 386 LYS cc_start: 0.8522 (mmtm) cc_final: 0.7947 (mptt) REVERT: S 387 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: S 445 ASN cc_start: 0.8250 (m110) cc_final: 0.7938 (m110) REVERT: T 266 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6787 (mt-10) REVERT: T 320 GLU cc_start: 0.8086 (tt0) cc_final: 0.7852 (tt0) REVERT: T 386 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8327 (mmtm) REVERT: U 264 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7375 (mp0) REVERT: U 266 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7092 (mt-10) REVERT: U 370 GLU cc_start: 0.8177 (tt0) cc_final: 0.7976 (tt0) REVERT: U 386 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8105 (mptp) REVERT: U 387 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: U 445 ASN cc_start: 0.8219 (m110) cc_final: 0.7826 (m110) REVERT: V 266 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7047 (mt-10) REVERT: V 270 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7997 (mt-10) REVERT: V 320 GLU cc_start: 0.8307 (tt0) cc_final: 0.8000 (tt0) REVERT: V 387 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: V 445 ASN cc_start: 0.8346 (m110) cc_final: 0.8139 (m110) REVERT: W 320 GLU cc_start: 0.8218 (tt0) cc_final: 0.7974 (tt0) REVERT: W 418 MET cc_start: 0.7465 (ttm) cc_final: 0.6994 (ttm) REVERT: X 266 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7163 (mt-10) REVERT: X 305 GLN cc_start: 0.8495 (tt0) cc_final: 0.8292 (tt0) REVERT: X 320 GLU cc_start: 0.8252 (tt0) cc_final: 0.8006 (tt0) REVERT: X 387 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: X 422 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6176 (pt0) REVERT: X 445 ASN cc_start: 0.8205 (m110) cc_final: 0.7985 (m110) REVERT: Y 264 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7085 (mp0) REVERT: Y 266 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7185 (mt-10) REVERT: Y 298 MET cc_start: 0.8931 (mtp) cc_final: 0.8560 (mtp) REVERT: Y 305 GLN cc_start: 0.8398 (tt0) cc_final: 0.8184 (tt0) REVERT: Y 385 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7773 (ttm170) REVERT: Y 386 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8012 (mptt) REVERT: Y 445 ASN cc_start: 0.8315 (m110) cc_final: 0.7944 (m110) REVERT: Z 280 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8251 (t) REVERT: Z 298 MET cc_start: 0.8851 (mtp) cc_final: 0.8614 (mtp) REVERT: Z 305 GLN cc_start: 0.8421 (tt0) cc_final: 0.8130 (tt0) REVERT: Z 320 GLU cc_start: 0.8167 (tt0) cc_final: 0.7912 (tt0) REVERT: Z 385 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7771 (ttp80) REVERT: Z 386 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8435 (mmmt) REVERT: Z 387 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: Z 422 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6373 (mt-10) REVERT: Z 445 ASN cc_start: 0.8385 (m110) cc_final: 0.8149 (m110) REVERT: a 262 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6945 (mt-10) REVERT: a 298 MET cc_start: 0.8956 (mtp) cc_final: 0.8723 (mtp) REVERT: a 320 GLU cc_start: 0.8134 (tt0) cc_final: 0.7895 (tt0) REVERT: a 385 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7901 (ttp80) REVERT: a 386 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8098 (mptt) REVERT: a 442 ASP cc_start: 0.8520 (m-30) cc_final: 0.8310 (m-30) REVERT: a 445 ASN cc_start: 0.8172 (m110) cc_final: 0.7843 (m110) REVERT: b 262 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6822 (mt-10) REVERT: b 266 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7249 (mt-10) REVERT: b 298 MET cc_start: 0.8802 (mtp) cc_final: 0.8551 (mtm) REVERT: b 370 GLU cc_start: 0.8225 (tt0) cc_final: 0.7930 (tt0) REVERT: b 385 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7633 (ttm170) REVERT: b 387 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: b 445 ASN cc_start: 0.8489 (m110) cc_final: 0.8169 (m110) REVERT: c 305 GLN cc_start: 0.8495 (tt0) cc_final: 0.8224 (tt0) REVERT: c 320 GLU cc_start: 0.8173 (tt0) cc_final: 0.7920 (tt0) REVERT: c 386 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8418 (mptp) REVERT: c 387 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: c 445 ASN cc_start: 0.8272 (m110) cc_final: 0.8011 (m110) REVERT: d 266 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7185 (mt-10) REVERT: d 327 ASN cc_start: 0.7760 (m110) cc_final: 0.7511 (m110) REVERT: d 386 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8394 (mptp) REVERT: d 445 ASN cc_start: 0.8340 (m110) cc_final: 0.8091 (m110) REVERT: e 270 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8123 (mt-10) REVERT: e 275 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7886 (mt-10) REVERT: e 305 GLN cc_start: 0.8481 (tt0) cc_final: 0.8140 (tt0) REVERT: e 320 GLU cc_start: 0.8017 (tt0) cc_final: 0.7729 (tt0) REVERT: e 387 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: f 298 MET cc_start: 0.8725 (mtp) cc_final: 0.8486 (mtp) REVERT: f 305 GLN cc_start: 0.8428 (tt0) cc_final: 0.8195 (tt0) REVERT: f 386 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8210 (mptt) REVERT: f 387 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7032 (pt0) REVERT: f 445 ASN cc_start: 0.8365 (m110) cc_final: 0.8126 (m110) REVERT: g 262 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7006 (mt-10) REVERT: g 266 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7149 (mt-10) REVERT: g 304 GLU cc_start: 0.7511 (tt0) cc_final: 0.7224 (tt0) REVERT: g 305 GLN cc_start: 0.8431 (tt0) cc_final: 0.8209 (tt0) REVERT: g 320 GLU cc_start: 0.8221 (tt0) cc_final: 0.7960 (tt0) REVERT: g 384 GLU cc_start: 0.7744 (tt0) cc_final: 0.7538 (tt0) REVERT: g 422 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6500 (pt0) REVERT: h 266 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7194 (mt-10) REVERT: h 298 MET cc_start: 0.8884 (mtp) cc_final: 0.8559 (mtp) REVERT: h 320 GLU cc_start: 0.8182 (tt0) cc_final: 0.7946 (tt0) REVERT: h 385 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7888 (ttm170) REVERT: h 442 ASP cc_start: 0.8588 (m-30) cc_final: 0.8368 (m-30) outliers start: 170 outliers final: 67 residues processed: 1375 average time/residue: 0.8552 time to fit residues: 1390.6262 Evaluate side-chains 1015 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 915 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 387 GLN Chi-restraints excluded: chain G residue 422 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 422 GLU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 387 GLN Chi-restraints excluded: chain I residue 422 GLU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 387 GLN Chi-restraints excluded: chain J residue 422 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 313 ASN Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 387 GLN Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain L residue 387 GLN Chi-restraints excluded: chain L residue 422 GLU Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 422 GLU Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 387 GLN Chi-restraints excluded: chain N residue 422 GLU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 422 GLU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 422 GLU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 422 GLU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 387 GLN Chi-restraints excluded: chain R residue 422 GLU Chi-restraints excluded: chain R residue 423 ILE Chi-restraints excluded: chain S residue 313 ASN Chi-restraints excluded: chain S residue 387 GLN Chi-restraints excluded: chain S residue 422 GLU Chi-restraints excluded: chain T residue 264 GLU Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 422 GLU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 387 GLN Chi-restraints excluded: chain U residue 422 GLU Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 387 GLN Chi-restraints excluded: chain V residue 422 GLU Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 380 THR Chi-restraints excluded: chain X residue 387 GLN Chi-restraints excluded: chain X residue 422 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 422 GLU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 387 GLN Chi-restraints excluded: chain Z residue 422 GLU Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 422 GLU Chi-restraints excluded: chain b residue 280 VAL Chi-restraints excluded: chain b residue 313 ASN Chi-restraints excluded: chain b residue 387 GLN Chi-restraints excluded: chain b residue 422 GLU Chi-restraints excluded: chain c residue 387 GLN Chi-restraints excluded: chain c residue 422 GLU Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 313 ASN Chi-restraints excluded: chain d residue 422 GLU Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 387 GLN Chi-restraints excluded: chain e residue 422 GLU Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain f residue 387 GLN Chi-restraints excluded: chain f residue 422 GLU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 422 GLU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 422 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 387 GLN A 438 GLN B 263 GLN B 293 GLN B 387 GLN B 438 GLN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 305 GLN C 387 GLN C 438 GLN D 387 GLN E 271 GLN E 293 GLN E 305 GLN E 387 GLN F 263 GLN F 293 GLN F 305 GLN F 387 GLN G 263 GLN G 293 GLN G 305 GLN G 387 GLN G 438 GLN H 263 GLN H 293 GLN H 305 GLN H 438 GLN I 263 GLN I 293 GLN I 305 GLN I 387 GLN I 438 GLN J 293 GLN J 305 GLN J 387 GLN K 263 GLN K 293 GLN K 305 GLN K 387 GLN L 293 GLN L 305 GLN L 387 GLN M 293 GLN M 438 GLN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 271 GLN N 293 GLN N 305 GLN N 387 GLN O 305 GLN O 387 GLN O 438 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 GLN P 293 GLN P 387 GLN P 438 GLN Q 263 GLN Q 271 GLN Q 293 GLN Q 305 GLN R 263 GLN R 271 GLN R 305 GLN R 387 GLN R 438 GLN S 263 GLN S 293 GLN S 387 GLN S 438 GLN ** T 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 293 GLN T 305 GLN T 387 GLN T 438 GLN U 387 GLN V 263 GLN V 271 GLN V 293 GLN V 305 GLN V 387 GLN W 263 GLN W 293 GLN W 305 GLN X 263 GLN X 293 GLN X 305 GLN X 387 GLN X 438 GLN Y 263 GLN Y 293 GLN Y 305 GLN Y 387 GLN Z 263 GLN Z 271 GLN Z 293 GLN Z 305 GLN Z 387 GLN Z 438 GLN a 263 GLN a 293 GLN b 263 GLN b 387 GLN c 305 GLN c 387 GLN d 293 GLN d 438 GLN ** e 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 293 GLN e 305 GLN e 387 GLN f 305 GLN f 387 GLN f 438 GLN g 269 GLN g 271 GLN g 293 GLN g 305 GLN g 387 GLN g 438 GLN h 263 GLN h 271 GLN h 293 GLN h 305 GLN Total number of N/Q/H flips: 122 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.156559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134354 restraints weight = 40777.761| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.24 r_work: 0.3388 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40188 Z= 0.142 Angle : 0.494 5.417 53992 Z= 0.265 Chirality : 0.041 0.143 6154 Planarity : 0.003 0.025 7140 Dihedral : 7.174 59.746 5765 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.73 % Allowed : 15.42 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.12), residues: 4828 helix: 3.21 (0.12), residues: 1326 sheet: 0.32 (0.11), residues: 2244 loop : -1.78 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 309 TYR 0.016 0.001 TYR D 326 PHE 0.010 0.001 PHE e 451 HIS 0.002 0.001 HIS P 383 Details of bonding type rmsd covalent geometry : bond 0.00332 (40188) covalent geometry : angle 0.49414 (53992) hydrogen bonds : bond 0.03456 ( 2449) hydrogen bonds : angle 4.87518 ( 6939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1017 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8346 (tt0) cc_final: 0.8120 (tt0) REVERT: A 320 GLU cc_start: 0.8291 (tt0) cc_final: 0.8036 (tt0) REVERT: A 442 ASP cc_start: 0.8554 (m-30) cc_final: 0.8345 (m-30) REVERT: A 445 ASN cc_start: 0.8359 (m110) cc_final: 0.7873 (m110) REVERT: B 386 LYS cc_start: 0.8655 (mmtm) cc_final: 0.7965 (mptt) REVERT: C 264 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7439 (mp0) REVERT: C 386 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8231 (mptt) REVERT: D 264 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7450 (mp0) REVERT: D 278 ASP cc_start: 0.7658 (m-30) cc_final: 0.7445 (t0) REVERT: E 320 GLU cc_start: 0.8198 (tt0) cc_final: 0.7902 (tt0) REVERT: E 377 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8801 (mt) REVERT: F 297 GLN cc_start: 0.8209 (tt0) cc_final: 0.7975 (tt0) REVERT: F 320 GLU cc_start: 0.8226 (tt0) cc_final: 0.7989 (tt0) REVERT: G 320 GLU cc_start: 0.8236 (tt0) cc_final: 0.7925 (tt0) REVERT: G 445 ASN cc_start: 0.8313 (m110) cc_final: 0.8023 (m110) REVERT: H 263 GLN cc_start: 0.7491 (mt0) cc_final: 0.7001 (mt0) REVERT: H 264 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7001 (mp0) REVERT: H 266 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7180 (mt-10) REVERT: H 267 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6712 (mtm180) REVERT: H 298 MET cc_start: 0.8883 (mtp) cc_final: 0.8480 (mtp) REVERT: H 377 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8667 (mt) REVERT: H 385 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7750 (ttm170) REVERT: H 386 LYS cc_start: 0.8787 (mmtm) cc_final: 0.7973 (mptt) REVERT: H 445 ASN cc_start: 0.8437 (m110) cc_final: 0.7913 (m-40) REVERT: I 267 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7405 (mtt180) REVERT: I 298 MET cc_start: 0.8734 (mtp) cc_final: 0.8467 (mtp) REVERT: I 305 GLN cc_start: 0.8412 (tt0) cc_final: 0.8162 (tt0) REVERT: I 320 GLU cc_start: 0.8202 (tt0) cc_final: 0.7917 (tt0) REVERT: I 385 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7718 (ttp80) REVERT: I 386 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8469 (mmmt) REVERT: I 426 ILE cc_start: 0.8335 (mm) cc_final: 0.8123 (mm) REVERT: J 298 MET cc_start: 0.8732 (mtp) cc_final: 0.8517 (mtp) REVERT: J 377 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8665 (mp) REVERT: J 386 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8038 (mptt) REVERT: J 422 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6628 (mt-10) REVERT: J 445 ASN cc_start: 0.8138 (m110) cc_final: 0.7867 (m110) REVERT: J 450 LYS cc_start: 0.7719 (mptt) cc_final: 0.7312 (tptt) REVERT: K 262 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6632 (mt-10) REVERT: K 298 MET cc_start: 0.8720 (mtp) cc_final: 0.8407 (ttm) REVERT: K 320 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: K 370 GLU cc_start: 0.8171 (tt0) cc_final: 0.7885 (tt0) REVERT: K 385 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7679 (ttm170) REVERT: K 386 LYS cc_start: 0.8450 (mptt) cc_final: 0.8211 (mptp) REVERT: L 308 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8040 (ttpt) REVERT: L 320 GLU cc_start: 0.8158 (tt0) cc_final: 0.7921 (tt0) REVERT: L 385 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7786 (ttm170) REVERT: L 386 LYS cc_start: 0.8604 (mptp) cc_final: 0.8399 (mptp) REVERT: M 267 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7492 (mtt180) REVERT: M 326 TYR cc_start: 0.7855 (m-80) cc_final: 0.7623 (m-80) REVERT: M 327 ASN cc_start: 0.7792 (m110) cc_final: 0.7531 (m110) REVERT: M 386 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8287 (mptp) REVERT: M 445 ASN cc_start: 0.8322 (m110) cc_final: 0.8049 (m110) REVERT: N 267 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7092 (mtm180) REVERT: N 305 GLN cc_start: 0.8370 (tt0) cc_final: 0.7988 (tt0) REVERT: N 320 GLU cc_start: 0.8080 (tt0) cc_final: 0.7760 (tt0) REVERT: N 386 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: N 426 ILE cc_start: 0.8338 (mm) cc_final: 0.8123 (mm) REVERT: O 305 GLN cc_start: 0.8381 (tt0) cc_final: 0.8130 (tt0) REVERT: O 324 GLU cc_start: 0.7323 (tt0) cc_final: 0.6909 (tm-30) REVERT: O 377 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8571 (mt) REVERT: P 262 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6773 (mt-10) REVERT: P 264 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: P 271 GLN cc_start: 0.8356 (tt0) cc_final: 0.8021 (tp-100) REVERT: P 290 TYR cc_start: 0.8305 (p90) cc_final: 0.7888 (p90) REVERT: P 320 GLU cc_start: 0.8220 (tt0) cc_final: 0.7931 (tt0) REVERT: P 377 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8389 (mt) REVERT: Q 298 MET cc_start: 0.8828 (mtp) cc_final: 0.8515 (mtp) REVERT: Q 377 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8862 (mt) REVERT: R 278 ASP cc_start: 0.7826 (m-30) cc_final: 0.7573 (t0) REVERT: R 305 GLN cc_start: 0.8336 (tt0) cc_final: 0.8088 (tt0) REVERT: R 320 GLU cc_start: 0.8227 (tt0) cc_final: 0.7950 (tt0) REVERT: R 442 ASP cc_start: 0.8534 (m-30) cc_final: 0.8328 (m-30) REVERT: R 445 ASN cc_start: 0.8220 (m110) cc_final: 0.7561 (m-40) REVERT: S 386 LYS cc_start: 0.8615 (mmtm) cc_final: 0.7956 (mptt) REVERT: T 278 ASP cc_start: 0.7562 (m-30) cc_final: 0.7188 (t0) REVERT: T 320 GLU cc_start: 0.8119 (tt0) cc_final: 0.7903 (tt0) REVERT: T 386 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8209 (mptt) REVERT: T 430 LEU cc_start: 0.8000 (mt) cc_final: 0.7740 (mt) REVERT: U 262 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6580 (mt-10) REVERT: U 264 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7182 (mp0) REVERT: V 278 ASP cc_start: 0.7415 (m-30) cc_final: 0.7188 (t0) REVERT: V 320 GLU cc_start: 0.8182 (tt0) cc_final: 0.7885 (tt0) REVERT: W 263 GLN cc_start: 0.7397 (mt0) cc_final: 0.7160 (mt0) REVERT: W 320 GLU cc_start: 0.8202 (tt0) cc_final: 0.7978 (tt0) REVERT: X 262 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6917 (mt-10) REVERT: X 266 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7251 (mt-10) REVERT: X 269 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7441 (mm-40) REVERT: X 320 GLU cc_start: 0.8267 (tt0) cc_final: 0.7948 (tt0) REVERT: X 377 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8588 (mt) REVERT: X 445 ASN cc_start: 0.8298 (m110) cc_final: 0.7968 (m110) REVERT: Y 263 GLN cc_start: 0.7358 (mt0) cc_final: 0.6970 (mt0) REVERT: Y 264 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7019 (mp0) REVERT: Y 266 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7209 (mt-10) REVERT: Y 267 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: Y 298 MET cc_start: 0.8871 (mtp) cc_final: 0.8464 (mtp) REVERT: Y 377 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8724 (mt) REVERT: Y 385 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7775 (ttm170) REVERT: Y 386 LYS cc_start: 0.8745 (mmtm) cc_final: 0.7949 (mptt) REVERT: Y 445 ASN cc_start: 0.8434 (m110) cc_final: 0.7919 (m-40) REVERT: Z 280 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8047 (t) REVERT: Z 298 MET cc_start: 0.8741 (mtp) cc_final: 0.8474 (mtp) REVERT: Z 305 GLN cc_start: 0.8446 (tt0) cc_final: 0.8203 (tt0) REVERT: Z 320 GLU cc_start: 0.8194 (tt0) cc_final: 0.7930 (tt0) REVERT: Z 385 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7725 (ttp80) REVERT: Z 386 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8460 (mmmt) REVERT: a 298 MET cc_start: 0.8738 (mtp) cc_final: 0.8519 (mtp) REVERT: a 377 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8627 (mt) REVERT: a 386 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8035 (mptt) REVERT: a 445 ASN cc_start: 0.8153 (m110) cc_final: 0.7926 (m110) REVERT: b 262 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6694 (mt-10) REVERT: b 278 ASP cc_start: 0.7312 (m-30) cc_final: 0.7056 (t0) REVERT: b 298 MET cc_start: 0.8696 (mtp) cc_final: 0.8389 (ttm) REVERT: b 320 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: b 370 GLU cc_start: 0.8173 (tt0) cc_final: 0.7890 (tt0) REVERT: b 385 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7777 (ttm170) REVERT: c 308 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8071 (ttpt) REVERT: c 320 GLU cc_start: 0.8145 (tt0) cc_final: 0.7914 (tt0) REVERT: d 327 ASN cc_start: 0.7787 (m110) cc_final: 0.7561 (m110) REVERT: d 386 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8193 (mptp) REVERT: d 445 ASN cc_start: 0.8335 (m110) cc_final: 0.8075 (m110) REVERT: e 267 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7199 (mtm180) REVERT: e 275 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7929 (mt-10) REVERT: e 305 GLN cc_start: 0.8335 (tt0) cc_final: 0.8013 (tt0) REVERT: e 320 GLU cc_start: 0.8063 (tt0) cc_final: 0.7733 (tt0) REVERT: e 386 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8048 (mttp) REVERT: e 426 ILE cc_start: 0.8324 (mm) cc_final: 0.8107 (mm) REVERT: f 305 GLN cc_start: 0.8409 (tt0) cc_final: 0.8206 (tt0) REVERT: f 313 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7717 (p0) REVERT: f 377 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8604 (mt) REVERT: f 386 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8138 (mptt) REVERT: f 442 ASP cc_start: 0.8542 (m-30) cc_final: 0.8318 (m-30) REVERT: g 262 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6792 (mt-10) REVERT: g 264 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: g 266 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7242 (mt-10) REVERT: g 304 GLU cc_start: 0.7425 (tt0) cc_final: 0.7164 (tt0) REVERT: g 305 GLN cc_start: 0.8453 (tt0) cc_final: 0.8252 (tt0) REVERT: g 320 GLU cc_start: 0.8169 (tt0) cc_final: 0.7890 (tt0) REVERT: g 377 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8330 (mp) REVERT: h 298 MET cc_start: 0.8857 (mtp) cc_final: 0.8549 (mtp) REVERT: h 326 TYR cc_start: 0.8110 (m-80) cc_final: 0.7874 (m-80) REVERT: h 377 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8830 (mt) outliers start: 206 outliers final: 106 residues processed: 1173 average time/residue: 0.6970 time to fit residues: 997.6137 Evaluate side-chains 1071 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 937 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 267 ARG Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 397 SER Chi-restraints excluded: chain J residue 422 GLU Chi-restraints excluded: chain K residue 267 ARG Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 397 SER Chi-restraints excluded: chain L residue 422 GLU Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 422 GLU Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 397 SER Chi-restraints excluded: chain O residue 422 GLU Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 268 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain Q residue 422 GLU Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 422 GLU Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 422 GLU Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 377 LEU Chi-restraints excluded: chain X residue 380 THR Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 397 SER Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 280 VAL Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 422 GLU Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 422 GLU Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain e residue 422 GLU Chi-restraints excluded: chain f residue 313 ASN Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain f residue 397 SER Chi-restraints excluded: chain f residue 422 GLU Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 388 THR Chi-restraints excluded: chain h residue 395 THR Chi-restraints excluded: chain h residue 422 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 73 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 452 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 461 optimal weight: 7.9990 chunk 312 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN B 263 GLN B 293 GLN C 305 GLN C 438 GLN D 327 ASN E 271 GLN E 293 GLN E 327 ASN H 293 GLN I 438 GLN K 293 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 GLN M 293 GLN M 438 GLN N 271 GLN O 269 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN ** Q 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 271 GLN Q 327 ASN R 271 GLN R 438 GLN S 263 GLN S 293 GLN T 438 GLN U 327 ASN V 271 GLN V 293 GLN V 327 ASN X 438 GLN Z 271 GLN Z 438 GLN d 293 GLN e 293 GLN f 269 GLN g 269 GLN g 271 GLN ** h 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 271 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129199 restraints weight = 41218.051| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.25 r_work: 0.3326 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 40188 Z= 0.297 Angle : 0.621 6.650 53992 Z= 0.332 Chirality : 0.045 0.166 6154 Planarity : 0.005 0.040 7140 Dihedral : 6.327 56.089 5626 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.97 % Allowed : 19.16 % Favored : 74.86 % 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: 0.26 (0.12), residues: 4828 helix: 2.62 (0.12), residues: 1326 sheet: -0.43 (0.10), residues: 2414 loop : -1.27 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 309 TYR 0.014 0.002 TYR S 326 PHE 0.018 0.002 PHE N 451 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00703 (40188) covalent geometry : angle 0.62071 (53992) hydrogen bonds : bond 0.04786 ( 2449) hydrogen bonds : angle 5.19967 ( 6939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 958 time to evaluate : 1.691 Fit side-chains REVERT: A 305 GLN cc_start: 0.8436 (tt0) cc_final: 0.8139 (tt0) REVERT: A 324 GLU cc_start: 0.7658 (tt0) cc_final: 0.7315 (tt0) REVERT: B 262 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 386 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8128 (mptt) REVERT: C 264 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7547 (mp0) REVERT: C 390 THR cc_start: 0.8204 (m) cc_final: 0.7962 (p) REVERT: D 262 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7048 (mt-10) REVERT: D 264 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7358 (mt-10) REVERT: E 262 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7033 (mt-10) REVERT: E 320 GLU cc_start: 0.8300 (tt0) cc_final: 0.8040 (tt0) REVERT: E 368 ARG cc_start: 0.8018 (ttt90) cc_final: 0.7769 (ttt180) REVERT: E 377 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8784 (mt) REVERT: F 262 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7174 (mt-10) REVERT: F 320 GLU cc_start: 0.8221 (tt0) cc_final: 0.8016 (tt0) REVERT: G 262 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6966 (mt-10) REVERT: G 275 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7516 (mt-10) REVERT: G 305 GLN cc_start: 0.8652 (tt0) cc_final: 0.8393 (tt0) REVERT: G 320 GLU cc_start: 0.8333 (tt0) cc_final: 0.8015 (tt0) REVERT: G 445 ASN cc_start: 0.8484 (m110) cc_final: 0.8073 (m110) REVERT: H 262 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7210 (mt-10) REVERT: H 264 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7190 (mt-10) REVERT: H 266 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7574 (mt-10) REVERT: H 267 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6798 (mtm180) REVERT: H 298 MET cc_start: 0.8874 (mtp) cc_final: 0.8623 (mtp) REVERT: H 305 GLN cc_start: 0.8441 (tt0) cc_final: 0.8182 (tt0) REVERT: H 377 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8729 (mt) REVERT: H 385 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7855 (ttm170) REVERT: H 386 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8158 (mptt) REVERT: I 262 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7078 (mt-10) REVERT: I 264 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7391 (mt-10) REVERT: I 266 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7644 (mt-10) REVERT: I 320 GLU cc_start: 0.8200 (tt0) cc_final: 0.7936 (tt0) REVERT: I 386 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8487 (mmmt) REVERT: J 269 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: J 377 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8688 (mt) REVERT: J 386 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8129 (mptt) REVERT: J 401 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7412 (ttpt) REVERT: J 445 ASN cc_start: 0.8226 (m110) cc_final: 0.7935 (m110) REVERT: K 266 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7682 (mt-10) REVERT: K 320 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: K 370 GLU cc_start: 0.8135 (tt0) cc_final: 0.7905 (tt0) REVERT: K 385 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7860 (ttm170) REVERT: K 386 LYS cc_start: 0.8532 (mptt) cc_final: 0.8250 (mptp) REVERT: K 422 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: L 305 GLN cc_start: 0.8571 (tt0) cc_final: 0.8313 (tt0) REVERT: L 320 GLU cc_start: 0.8241 (tt0) cc_final: 0.7950 (tt0) REVERT: L 386 LYS cc_start: 0.8662 (mptp) cc_final: 0.8441 (mptt) REVERT: M 262 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7113 (mt-10) REVERT: M 386 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8348 (mptp) REVERT: N 262 GLU cc_start: 0.7224 (mt-10) cc_final: 0.7007 (mt-10) REVERT: N 305 GLN cc_start: 0.8599 (tt0) cc_final: 0.8140 (tt0) REVERT: N 308 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8282 (ttpt) REVERT: N 320 GLU cc_start: 0.8051 (tt0) cc_final: 0.7727 (tt0) REVERT: N 386 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8150 (mttp) REVERT: N 426 ILE cc_start: 0.8423 (mm) cc_final: 0.8192 (mm) REVERT: O 377 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8565 (mt) REVERT: P 262 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7139 (mt-10) REVERT: P 264 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: P 320 GLU cc_start: 0.8139 (tt0) cc_final: 0.7936 (tt0) REVERT: P 377 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8325 (mt) REVERT: Q 298 MET cc_start: 0.8857 (mtp) cc_final: 0.8555 (mtp) REVERT: Q 377 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8767 (mt) REVERT: R 282 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7588 (tp) REVERT: R 305 GLN cc_start: 0.8441 (tt0) cc_final: 0.8146 (tt0) REVERT: R 324 GLU cc_start: 0.7695 (tt0) cc_final: 0.7349 (tt0) REVERT: S 262 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7034 (mt-10) REVERT: S 386 LYS cc_start: 0.8702 (mmtm) cc_final: 0.7956 (mptt) REVERT: T 282 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7569 (tp) REVERT: T 320 GLU cc_start: 0.8150 (tt0) cc_final: 0.7928 (tt0) REVERT: T 390 THR cc_start: 0.8202 (m) cc_final: 0.7954 (p) REVERT: U 262 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7118 (mt-10) REVERT: U 264 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7303 (mt-10) REVERT: V 262 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7067 (mt-10) REVERT: V 320 GLU cc_start: 0.8267 (tt0) cc_final: 0.8011 (tt0) REVERT: V 368 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7788 (ttt180) REVERT: W 282 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7386 (tp) REVERT: W 320 GLU cc_start: 0.8256 (tt0) cc_final: 0.8043 (tt0) REVERT: X 262 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7023 (mt-10) REVERT: X 266 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7047 (mt-10) REVERT: X 275 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7463 (mt-10) REVERT: X 305 GLN cc_start: 0.8666 (tt0) cc_final: 0.8411 (tt0) REVERT: X 320 GLU cc_start: 0.8362 (tt0) cc_final: 0.8033 (tt0) REVERT: X 445 ASN cc_start: 0.8456 (m110) cc_final: 0.7977 (m110) REVERT: Y 262 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7248 (mt-10) REVERT: Y 263 GLN cc_start: 0.7274 (mt0) cc_final: 0.6839 (mt0) REVERT: Y 264 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7249 (mt-10) REVERT: Y 267 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.6791 (mtm180) REVERT: Y 298 MET cc_start: 0.8918 (mtp) cc_final: 0.8706 (mtp) REVERT: Y 305 GLN cc_start: 0.8447 (tt0) cc_final: 0.8182 (tt0) REVERT: Y 377 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8715 (mt) REVERT: Y 385 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7868 (ttm170) REVERT: Y 386 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8169 (mptt) REVERT: Z 262 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7097 (mt-10) REVERT: Z 264 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7366 (mt-10) REVERT: Z 266 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7654 (mt-10) REVERT: Z 305 GLN cc_start: 0.8581 (tt0) cc_final: 0.8360 (tt0) REVERT: Z 320 GLU cc_start: 0.8201 (tt0) cc_final: 0.7930 (tt0) REVERT: Z 386 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8496 (mmmt) REVERT: a 377 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8683 (mt) REVERT: a 386 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8103 (mptt) REVERT: a 445 ASN cc_start: 0.8228 (m110) cc_final: 0.7930 (m110) REVERT: b 320 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: b 370 GLU cc_start: 0.8132 (tt0) cc_final: 0.7904 (tt0) REVERT: b 385 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7884 (ttm170) REVERT: b 422 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: c 305 GLN cc_start: 0.8596 (tt0) cc_final: 0.8319 (tt0) REVERT: c 320 GLU cc_start: 0.8204 (tt0) cc_final: 0.7939 (tt0) REVERT: c 386 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (mptp) REVERT: d 262 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7098 (mt-10) REVERT: d 269 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: d 386 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8334 (mptp) REVERT: e 262 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6996 (mt-10) REVERT: e 275 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7839 (mt-10) REVERT: e 305 GLN cc_start: 0.8581 (tt0) cc_final: 0.8131 (tt0) REVERT: e 308 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8289 (ttpt) REVERT: e 320 GLU cc_start: 0.8055 (tt0) cc_final: 0.7728 (tt0) REVERT: e 376 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8733 (mm-30) REVERT: e 426 ILE cc_start: 0.8409 (mm) cc_final: 0.8173 (mm) REVERT: f 299 ASP cc_start: 0.7777 (t70) cc_final: 0.7478 (t0) REVERT: f 313 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7846 (p0) REVERT: f 377 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8618 (mt) REVERT: f 386 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8163 (mptt) REVERT: g 262 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7200 (mt-10) REVERT: g 264 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: g 305 GLN cc_start: 0.8629 (tt0) cc_final: 0.8421 (tt0) REVERT: g 377 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8316 (mt) REVERT: h 298 MET cc_start: 0.8863 (mtp) cc_final: 0.8565 (mtp) REVERT: h 326 TYR cc_start: 0.8240 (m-80) cc_final: 0.8014 (m-80) REVERT: h 377 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8752 (mt) outliers start: 260 outliers final: 153 residues processed: 1138 average time/residue: 0.7848 time to fit residues: 1077.2320 Evaluate side-chains 1030 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 848 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 397 SER Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 422 GLU Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 397 SER Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 268 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 268 SER Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 308 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 418 MET Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain O residue 397 SER Chi-restraints excluded: chain O residue 422 GLU Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 268 SER Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 386 LYS Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 268 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 422 GLU Chi-restraints excluded: chain S residue 382 SER Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 422 GLU Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 268 SER Chi-restraints excluded: chain U residue 278 ASP Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 268 SER Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain W residue 282 LEU Chi-restraints excluded: chain W residue 380 THR Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 380 THR Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 268 SER Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 268 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 397 SER Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 268 SER Chi-restraints excluded: chain b residue 280 VAL Chi-restraints excluded: chain b residue 282 LEU Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 382 SER Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 422 GLU Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 386 LYS Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 422 GLU Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 269 GLN Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 268 SER Chi-restraints excluded: chain e residue 280 VAL Chi-restraints excluded: chain e residue 308 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain e residue 418 MET Chi-restraints excluded: chain f residue 280 VAL Chi-restraints excluded: chain f residue 313 ASN Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain f residue 397 SER Chi-restraints excluded: chain f residue 422 GLU Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 382 SER Chi-restraints excluded: chain g residue 386 LYS Chi-restraints excluded: chain g residue 388 THR Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 111 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 455 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 439 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN C 305 GLN D 293 GLN E 271 GLN E 293 GLN E 327 ASN I 438 GLN J 289 ASN K 293 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 GLN M 293 GLN N 271 GLN ** O 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 305 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN P 271 GLN ** Q 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 271 GLN Q 327 ASN R 293 GLN S 293 GLN T 305 GLN T 327 ASN U 293 GLN V 271 GLN V 293 GLN V 327 ASN Z 438 GLN a 289 ASN b 293 GLN c 293 GLN d 293 GLN e 293 GLN ** f 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 305 GLN f 445 ASN g 269 GLN g 271 GLN h 263 GLN h 271 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136163 restraints weight = 40501.233| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.20 r_work: 0.3409 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40188 Z= 0.104 Angle : 0.472 5.282 53992 Z= 0.252 Chirality : 0.040 0.135 6154 Planarity : 0.003 0.047 7140 Dihedral : 5.362 51.533 5600 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.99 % Allowed : 21.90 % Favored : 73.12 % 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: 0.73 (0.12), residues: 4828 helix: 3.16 (0.12), residues: 1326 sheet: 0.13 (0.10), residues: 2210 loop : -1.73 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 309 TYR 0.015 0.001 TYR U 326 PHE 0.006 0.001 PHE e 375 HIS 0.001 0.000 HIS R 383 Details of bonding type rmsd covalent geometry : bond 0.00245 (40188) covalent geometry : angle 0.47152 (53992) hydrogen bonds : bond 0.02940 ( 2449) hydrogen bonds : angle 4.20055 ( 6939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 993 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 320 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: A 324 GLU cc_start: 0.7528 (tt0) cc_final: 0.7065 (tm-30) REVERT: A 437 ASP cc_start: 0.8412 (t0) cc_final: 0.7830 (t0) REVERT: B 267 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7637 (mtt180) REVERT: B 386 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8147 (mptt) REVERT: C 305 GLN cc_start: 0.8267 (tt0) cc_final: 0.7935 (tt0) REVERT: C 386 LYS cc_start: 0.8487 (mmtp) cc_final: 0.8009 (mptt) REVERT: D 264 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7490 (mp0) REVERT: D 309 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7993 (ttm110) REVERT: E 320 GLU cc_start: 0.8128 (tt0) cc_final: 0.7824 (tt0) REVERT: F 320 GLU cc_start: 0.8153 (tt0) cc_final: 0.7944 (tt0) REVERT: G 320 GLU cc_start: 0.8205 (tt0) cc_final: 0.7972 (tt0) REVERT: G 377 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8570 (mt) REVERT: G 445 ASN cc_start: 0.8440 (m110) cc_final: 0.8162 (m110) REVERT: H 264 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7149 (mt-10) REVERT: H 266 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7295 (mt-10) REVERT: H 267 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6717 (mtm180) REVERT: H 298 MET cc_start: 0.8825 (mtp) cc_final: 0.8423 (mtp) REVERT: H 377 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8601 (mt) REVERT: H 386 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8058 (mptt) REVERT: H 445 ASN cc_start: 0.8479 (m110) cc_final: 0.8010 (m-40) REVERT: I 386 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8358 (mmmt) REVERT: J 377 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8571 (mt) REVERT: J 380 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8053 (m) REVERT: J 386 LYS cc_start: 0.8499 (mmtm) cc_final: 0.7980 (mptt) REVERT: J 401 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7318 (ttpt) REVERT: K 263 GLN cc_start: 0.7356 (mt0) cc_final: 0.7110 (mt0) REVERT: K 277 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (mt) REVERT: K 298 MET cc_start: 0.8694 (mtp) cc_final: 0.8433 (ttm) REVERT: K 320 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: K 370 GLU cc_start: 0.8098 (tt0) cc_final: 0.7850 (tt0) REVERT: K 380 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8099 (m) REVERT: K 385 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7774 (ttm170) REVERT: K 386 LYS cc_start: 0.8465 (mptt) cc_final: 0.8233 (mptp) REVERT: L 386 LYS cc_start: 0.8629 (mptp) cc_final: 0.8404 (mptt) REVERT: M 386 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8251 (mptp) REVERT: M 445 ASN cc_start: 0.8394 (m110) cc_final: 0.8191 (m110) REVERT: N 267 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7283 (mtm180) REVERT: N 305 GLN cc_start: 0.8371 (tt0) cc_final: 0.8095 (tt0) REVERT: N 308 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8106 (ttpt) REVERT: N 320 GLU cc_start: 0.7981 (tt0) cc_final: 0.7635 (tt0) REVERT: N 386 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8042 (mttp) REVERT: N 426 ILE cc_start: 0.8243 (mm) cc_final: 0.8014 (mm) REVERT: O 299 ASP cc_start: 0.7998 (t0) cc_final: 0.7722 (t0) REVERT: O 377 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8546 (mt) REVERT: O 442 ASP cc_start: 0.8654 (m-30) cc_final: 0.8443 (m-30) REVERT: P 264 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: P 320 GLU cc_start: 0.8024 (tt0) cc_final: 0.7734 (tt0) REVERT: P 369 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7778 (mttp) REVERT: P 377 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8250 (mp) REVERT: Q 368 ARG cc_start: 0.8020 (ttt180) cc_final: 0.7720 (ttt180) REVERT: Q 377 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8779 (mt) REVERT: R 320 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: S 266 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7122 (mt-10) REVERT: S 386 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8099 (mptt) REVERT: T 278 ASP cc_start: 0.7494 (m-30) cc_final: 0.7248 (m-30) REVERT: T 305 GLN cc_start: 0.8224 (tt0) cc_final: 0.7872 (tt0) REVERT: T 386 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8003 (mptt) REVERT: U 262 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7003 (mt-10) REVERT: U 309 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.8016 (ttm110) REVERT: V 278 ASP cc_start: 0.7572 (m-30) cc_final: 0.7338 (t0) REVERT: V 320 GLU cc_start: 0.8201 (tt0) cc_final: 0.7915 (tt0) REVERT: V 385 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7821 (ttp80) REVERT: W 320 GLU cc_start: 0.8155 (tt0) cc_final: 0.7936 (tt0) REVERT: W 447 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7711 (mm) REVERT: X 266 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7049 (mt-10) REVERT: X 320 GLU cc_start: 0.8182 (tt0) cc_final: 0.7970 (tt0) REVERT: X 402 ASP cc_start: 0.7012 (m-30) cc_final: 0.6732 (m-30) REVERT: X 445 ASN cc_start: 0.8377 (m110) cc_final: 0.7881 (m110) REVERT: Y 264 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7169 (mt-10) REVERT: Y 267 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6720 (mtm180) REVERT: Y 298 MET cc_start: 0.8817 (mtp) cc_final: 0.8401 (mtp) REVERT: Y 377 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8637 (mt) REVERT: Y 386 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8095 (mptt) REVERT: Y 445 ASN cc_start: 0.8468 (m110) cc_final: 0.8000 (m-40) REVERT: Z 269 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: Z 386 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8375 (mmmt) REVERT: a 377 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8605 (mt) REVERT: a 386 LYS cc_start: 0.8470 (mmtm) cc_final: 0.7991 (mptt) REVERT: b 263 GLN cc_start: 0.7443 (mt0) cc_final: 0.7138 (mt0) REVERT: b 298 MET cc_start: 0.8685 (mtp) cc_final: 0.8410 (ttm) REVERT: b 320 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: b 370 GLU cc_start: 0.8066 (tt0) cc_final: 0.7825 (tt0) REVERT: b 385 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7832 (ttm170) REVERT: d 269 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: d 327 ASN cc_start: 0.7874 (m110) cc_final: 0.7667 (m110) REVERT: d 386 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8132 (mptp) REVERT: e 267 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7264 (mtm180) REVERT: e 271 GLN cc_start: 0.8170 (tt0) cc_final: 0.7919 (tp-100) REVERT: e 305 GLN cc_start: 0.8386 (tt0) cc_final: 0.8107 (tt0) REVERT: e 308 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8120 (ttpt) REVERT: e 320 GLU cc_start: 0.7969 (tt0) cc_final: 0.7627 (tt0) REVERT: e 386 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: e 426 ILE cc_start: 0.8236 (mm) cc_final: 0.8013 (mm) REVERT: f 299 ASP cc_start: 0.7735 (t70) cc_final: 0.7421 (t0) REVERT: f 377 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8593 (mt) REVERT: f 386 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8217 (mptt) REVERT: g 264 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: g 377 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8248 (mp) REVERT: h 326 TYR cc_start: 0.8160 (m-80) cc_final: 0.7931 (m-80) REVERT: h 377 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8771 (mt) outliers start: 217 outliers final: 122 residues processed: 1117 average time/residue: 0.6827 time to fit residues: 939.6132 Evaluate side-chains 1037 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 884 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 380 THR Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 268 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 388 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 268 SER Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 268 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 320 GLU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 388 THR Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 268 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 268 SER Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 268 SER Chi-restraints excluded: chain b residue 280 VAL Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 269 GLN Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 388 THR Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 388 THR Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 68 optimal weight: 3.9990 chunk 430 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 415 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 439 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN D 293 GLN D 327 ASN E 271 GLN E 327 ASN F 438 GLN I 327 ASN I 438 GLN J 289 ASN K 293 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 GLN L 293 GLN M 293 GLN N 271 GLN O 305 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN P 271 GLN Q 271 GLN Q 327 ASN R 271 GLN R 293 GLN S 293 GLN U 293 GLN U 327 ASN V 271 GLN V 327 ASN X 289 ASN Z 271 GLN Z 327 ASN Z 438 GLN a 289 ASN b 293 GLN b 327 ASN c 269 GLN c 293 GLN d 293 GLN f 305 GLN g 269 GLN g 271 GLN ** h 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 271 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.152725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130867 restraints weight = 40602.362| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.23 r_work: 0.3344 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 40188 Z= 0.236 Angle : 0.565 5.808 53992 Z= 0.302 Chirality : 0.043 0.151 6154 Planarity : 0.004 0.043 7140 Dihedral : 5.247 50.993 5566 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.35 % Allowed : 23.37 % Favored : 71.28 % 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: 0.30 (0.12), residues: 4828 helix: 2.78 (0.12), residues: 1326 sheet: -0.46 (0.10), residues: 2414 loop : -1.26 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 309 TYR 0.015 0.002 TYR L 326 PHE 0.012 0.002 PHE N 451 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00556 (40188) covalent geometry : angle 0.56482 (53992) hydrogen bonds : bond 0.04172 ( 2449) hydrogen bonds : angle 4.72311 ( 6939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 883 time to evaluate : 1.706 Fit side-chains REVERT: A 320 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 324 GLU cc_start: 0.7617 (tt0) cc_final: 0.7277 (tt0) REVERT: A 437 ASP cc_start: 0.8469 (t0) cc_final: 0.7917 (t0) REVERT: B 262 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 369 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8088 (mtmt) REVERT: C 264 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7516 (mp0) REVERT: C 305 GLN cc_start: 0.8341 (tt0) cc_final: 0.8071 (tt0) REVERT: C 320 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: C 377 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 386 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8252 (mptt) REVERT: C 390 THR cc_start: 0.8061 (m) cc_final: 0.7801 (p) REVERT: D 262 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7104 (mt-10) REVERT: D 264 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7326 (mt-10) REVERT: E 262 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7138 (mt-10) REVERT: E 320 GLU cc_start: 0.8324 (tt0) cc_final: 0.8037 (tt0) REVERT: F 320 GLU cc_start: 0.8212 (tt0) cc_final: 0.7989 (tt0) REVERT: G 445 ASN cc_start: 0.8435 (m110) cc_final: 0.8070 (m110) REVERT: H 262 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7539 (mt-10) REVERT: H 264 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7129 (mt-10) REVERT: H 267 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6828 (mtm180) REVERT: H 298 MET cc_start: 0.8885 (mtp) cc_final: 0.8616 (mtp) REVERT: H 377 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8721 (mt) REVERT: H 386 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8123 (mptt) REVERT: I 264 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7294 (mt-10) REVERT: I 266 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7594 (mt-10) REVERT: I 386 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8415 (mmmt) REVERT: J 269 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: J 377 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8633 (mt) REVERT: J 380 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8086 (m) REVERT: J 386 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8092 (mptt) REVERT: J 401 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7426 (ttpt) REVERT: K 266 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7672 (mt-10) REVERT: K 267 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7898 (mtt180) REVERT: K 320 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: K 385 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7911 (ttm170) REVERT: K 386 LYS cc_start: 0.8622 (mptt) cc_final: 0.8276 (mptp) REVERT: L 305 GLN cc_start: 0.8598 (tt0) cc_final: 0.8359 (tt0) REVERT: L 386 LYS cc_start: 0.8687 (mptp) cc_final: 0.8478 (mptt) REVERT: M 269 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: M 298 MET cc_start: 0.8822 (mtp) cc_final: 0.8537 (mtp) REVERT: M 386 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8297 (mptp) REVERT: N 267 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7260 (mtm180) REVERT: N 298 MET cc_start: 0.8776 (mtp) cc_final: 0.8518 (mtp) REVERT: N 305 GLN cc_start: 0.8577 (tt0) cc_final: 0.8150 (tt0) REVERT: N 320 GLU cc_start: 0.8058 (tt0) cc_final: 0.7703 (tt0) REVERT: N 386 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: N 426 ILE cc_start: 0.8360 (mm) cc_final: 0.8119 (mm) REVERT: O 299 ASP cc_start: 0.7948 (t0) cc_final: 0.7722 (t0) REVERT: O 305 GLN cc_start: 0.8382 (tt0) cc_final: 0.8121 (tt0) REVERT: O 369 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7862 (mttp) REVERT: O 377 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8550 (mt) REVERT: P 262 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7247 (mt-10) REVERT: P 264 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: P 282 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7490 (tp) REVERT: P 320 GLU cc_start: 0.8083 (tt0) cc_final: 0.7865 (tt0) REVERT: P 369 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7737 (mttp) REVERT: P 377 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8356 (mt) REVERT: Q 377 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8843 (mt) REVERT: R 320 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: S 262 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7131 (mt-10) REVERT: S 282 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7594 (tp) REVERT: S 386 LYS cc_start: 0.8714 (mmtm) cc_final: 0.7973 (mptt) REVERT: T 278 ASP cc_start: 0.7693 (m-30) cc_final: 0.7473 (m-30) REVERT: T 305 GLN cc_start: 0.8301 (tt0) cc_final: 0.7942 (tt0) REVERT: T 386 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8254 (mptt) REVERT: T 390 THR cc_start: 0.8113 (m) cc_final: 0.7852 (p) REVERT: U 262 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7109 (mt-10) REVERT: V 262 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7130 (mt-10) REVERT: V 320 GLU cc_start: 0.8287 (tt0) cc_final: 0.8003 (tt0) REVERT: V 385 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7937 (ttp80) REVERT: W 314 THR cc_start: 0.8762 (p) cc_final: 0.8549 (p) REVERT: W 320 GLU cc_start: 0.8220 (tt0) cc_final: 0.7995 (tt0) REVERT: X 445 ASN cc_start: 0.8432 (m110) cc_final: 0.7970 (m110) REVERT: Y 262 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7610 (mt-10) REVERT: Y 264 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7108 (mt-10) REVERT: Y 267 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6807 (mtm180) REVERT: Y 278 ASP cc_start: 0.7736 (m-30) cc_final: 0.7422 (t0) REVERT: Y 298 MET cc_start: 0.8883 (mtp) cc_final: 0.8606 (mtp) REVERT: Y 377 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8721 (mt) REVERT: Y 385 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7802 (ttm170) REVERT: Z 264 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7309 (mt-10) REVERT: Z 266 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7612 (mt-10) REVERT: Z 386 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8426 (mmmt) REVERT: a 269 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: a 369 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: a 377 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8682 (mt) REVERT: a 386 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8065 (mptt) REVERT: a 401 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7411 (ttpt) REVERT: b 320 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: b 385 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7898 (ttm170) REVERT: c 305 GLN cc_start: 0.8610 (tt0) cc_final: 0.8354 (tt0) REVERT: d 386 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8270 (mptp) REVERT: e 267 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7247 (mtt180) REVERT: e 305 GLN cc_start: 0.8565 (tt0) cc_final: 0.8133 (tt0) REVERT: e 320 GLU cc_start: 0.8061 (tt0) cc_final: 0.7706 (tt0) REVERT: e 386 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8079 (mttp) REVERT: e 426 ILE cc_start: 0.8315 (mm) cc_final: 0.8073 (mm) REVERT: f 299 ASP cc_start: 0.7800 (t70) cc_final: 0.7456 (t0) REVERT: f 305 GLN cc_start: 0.8376 (tt0) cc_final: 0.8127 (tt0) REVERT: f 313 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7817 (p0) REVERT: f 377 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8610 (mt) REVERT: f 386 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8469 (mptm) REVERT: g 262 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7319 (mt-10) REVERT: g 264 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: g 282 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7473 (tp) REVERT: g 369 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7750 (mttp) REVERT: g 377 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8349 (mt) REVERT: h 377 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (mt) outliers start: 233 outliers final: 152 residues processed: 1029 average time/residue: 0.6514 time to fit residues: 824.4255 Evaluate side-chains 1023 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 833 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 267 ARG Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 269 GLN Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 382 SER Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 268 SER Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain O residue 397 SER Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 268 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 386 LYS Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 268 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 382 SER Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 320 GLU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 268 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 268 SER Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain V residue 418 MET Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 380 THR Chi-restraints excluded: chain W residue 382 SER Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 268 SER Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 268 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 268 SER Chi-restraints excluded: chain b residue 282 LEU Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 268 SER Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 382 SER Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 382 SER Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain e residue 418 MET Chi-restraints excluded: chain f residue 313 ASN Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain f residue 397 SER Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 386 LYS Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 89 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 332 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 290 optimal weight: 9.9990 chunk 320 optimal weight: 0.5980 chunk 370 optimal weight: 4.9990 chunk 421 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 271 GLN D 293 GLN E 271 GLN H 289 ASN I 438 GLN J 289 ASN K 293 GLN ** K 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 GLN L 293 GLN M 293 GLN N 271 GLN ** O 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN Q 271 GLN R 293 GLN S 271 GLN S 293 GLN U 293 GLN U 327 ASN V 271 GLN Z 438 GLN a 289 ASN b 293 GLN c 293 GLN d 293 GLN ** f 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 271 GLN h 271 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.157502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135708 restraints weight = 40405.198| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.23 r_work: 0.3404 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40188 Z= 0.108 Angle : 0.476 5.226 53992 Z= 0.254 Chirality : 0.040 0.135 6154 Planarity : 0.004 0.051 7140 Dihedral : 4.862 48.407 5564 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.78 % Allowed : 24.54 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 4828 helix: 3.17 (0.12), residues: 1326 sheet: 0.13 (0.10), residues: 2210 loop : -1.74 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 309 TYR 0.017 0.001 TYR U 326 PHE 0.006 0.001 PHE N 375 HIS 0.001 0.000 HIS P 383 Details of bonding type rmsd covalent geometry : bond 0.00254 (40188) covalent geometry : angle 0.47624 (53992) hydrogen bonds : bond 0.02972 ( 2449) hydrogen bonds : angle 4.08242 ( 6939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 900 time to evaluate : 1.590 Fit side-chains REVERT: A 320 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: A 437 ASP cc_start: 0.8458 (t0) cc_final: 0.7879 (t0) REVERT: B 386 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8134 (mptt) REVERT: C 264 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7537 (mp0) REVERT: C 305 GLN cc_start: 0.8288 (tt0) cc_final: 0.7991 (tt0) REVERT: C 386 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8136 (mptt) REVERT: D 264 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7353 (mt-10) REVERT: D 309 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.8034 (ttm110) REVERT: E 320 GLU cc_start: 0.8165 (tt0) cc_final: 0.7845 (tt0) REVERT: F 320 GLU cc_start: 0.8182 (tt0) cc_final: 0.7953 (tt0) REVERT: G 377 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8569 (mt) REVERT: G 445 ASN cc_start: 0.8490 (m110) cc_final: 0.8201 (m110) REVERT: H 264 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7142 (mt-10) REVERT: H 267 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6739 (mtm180) REVERT: H 298 MET cc_start: 0.8830 (mtp) cc_final: 0.8432 (mtp) REVERT: H 377 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8625 (mt) REVERT: H 386 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8099 (mptt) REVERT: H 445 ASN cc_start: 0.8446 (m110) cc_final: 0.7995 (m110) REVERT: I 267 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7545 (mtt180) REVERT: I 386 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8393 (mmmt) REVERT: J 369 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7908 (mttp) REVERT: J 377 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8618 (mt) REVERT: J 380 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8082 (m) REVERT: J 386 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8235 (mptp) REVERT: J 401 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7282 (ttpt) REVERT: K 298 MET cc_start: 0.8698 (mtp) cc_final: 0.8416 (ttm) REVERT: K 320 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: K 385 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7805 (ttm170) REVERT: K 386 LYS cc_start: 0.8490 (mptt) cc_final: 0.8193 (mptp) REVERT: M 267 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: M 386 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8204 (mptp) REVERT: N 263 GLN cc_start: 0.7243 (mt0) cc_final: 0.6936 (mt0) REVERT: N 267 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7270 (mtt180) REVERT: N 305 GLN cc_start: 0.8410 (tt0) cc_final: 0.8101 (tt0) REVERT: N 308 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8115 (ttpt) REVERT: N 320 GLU cc_start: 0.8012 (tt0) cc_final: 0.7645 (tt0) REVERT: N 369 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7777 (mttp) REVERT: N 386 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: N 426 ILE cc_start: 0.8285 (mm) cc_final: 0.8062 (mm) REVERT: O 299 ASP cc_start: 0.7898 (t0) cc_final: 0.7643 (t0) REVERT: O 305 GLN cc_start: 0.8268 (tt0) cc_final: 0.7960 (tt0) REVERT: O 377 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8559 (mt) REVERT: P 264 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: P 282 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7454 (tp) REVERT: P 309 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.8060 (ttp-110) REVERT: P 320 GLU cc_start: 0.8038 (tt0) cc_final: 0.7768 (tt0) REVERT: P 368 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: P 369 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7792 (mttp) REVERT: P 377 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8239 (mp) REVERT: Q 377 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8842 (mt) REVERT: R 320 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: R 437 ASP cc_start: 0.8457 (t0) cc_final: 0.7833 (t0) REVERT: S 267 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7446 (mtt90) REVERT: S 386 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8021 (mptt) REVERT: T 278 ASP cc_start: 0.7420 (m-30) cc_final: 0.7053 (t0) REVERT: T 305 GLN cc_start: 0.8248 (tt0) cc_final: 0.7927 (tt0) REVERT: T 386 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8111 (mptt) REVERT: U 262 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6992 (mt-10) REVERT: U 309 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8074 (ttm110) REVERT: V 320 GLU cc_start: 0.8140 (tt0) cc_final: 0.7814 (tt0) REVERT: W 320 GLU cc_start: 0.8187 (tt0) cc_final: 0.7954 (tt0) REVERT: W 447 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7759 (mm) REVERT: X 445 ASN cc_start: 0.8373 (m110) cc_final: 0.7779 (m110) REVERT: Y 264 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7193 (mt-10) REVERT: Y 267 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6781 (mtm180) REVERT: Y 298 MET cc_start: 0.8816 (mtp) cc_final: 0.8400 (mtp) REVERT: Y 377 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8629 (mt) REVERT: Y 445 ASN cc_start: 0.8428 (m110) cc_final: 0.7961 (m110) REVERT: Z 386 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8396 (mmmt) REVERT: a 369 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7906 (mttp) REVERT: a 377 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8571 (mt) REVERT: a 380 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8024 (m) REVERT: a 386 LYS cc_start: 0.8437 (mmtm) cc_final: 0.8226 (mptp) REVERT: a 401 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7259 (ttpt) REVERT: b 298 MET cc_start: 0.8676 (mtp) cc_final: 0.8391 (ttm) REVERT: b 305 GLN cc_start: 0.8566 (tt0) cc_final: 0.8354 (tp40) REVERT: b 320 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: b 385 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7869 (ttm170) REVERT: d 386 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8235 (mptp) REVERT: e 263 GLN cc_start: 0.7216 (mt0) cc_final: 0.6924 (mt0) REVERT: e 267 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7271 (mtt180) REVERT: e 271 GLN cc_start: 0.8171 (tt0) cc_final: 0.7939 (tp-100) REVERT: e 305 GLN cc_start: 0.8407 (tt0) cc_final: 0.8099 (tt0) REVERT: e 308 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8121 (ttpt) REVERT: e 320 GLU cc_start: 0.7989 (tt0) cc_final: 0.7624 (tt0) REVERT: e 369 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7783 (mttp) REVERT: e 386 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8073 (mttp) REVERT: e 426 ILE cc_start: 0.8268 (mm) cc_final: 0.8034 (mm) REVERT: f 299 ASP cc_start: 0.7701 (t70) cc_final: 0.7389 (t0) REVERT: f 305 GLN cc_start: 0.8274 (tt0) cc_final: 0.8011 (tt0) REVERT: f 377 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8604 (mt) REVERT: f 386 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8448 (mptm) REVERT: g 264 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: g 309 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.8059 (ttp-110) REVERT: g 369 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (mttp) REVERT: g 377 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8241 (mp) REVERT: g 424 ASN cc_start: 0.7904 (t0) cc_final: 0.7570 (t0) REVERT: h 377 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8865 (mt) outliers start: 208 outliers final: 136 residues processed: 1034 average time/residue: 0.6131 time to fit residues: 783.7880 Evaluate side-chains 1030 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 857 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 267 ARG Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 369 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 268 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 388 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 369 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 368 ARG Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 320 GLU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 267 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 264 GLU Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 278 ASP Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 382 SER Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain V residue 418 MET Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 268 SER Chi-restraints excluded: chain e residue 369 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 386 LYS Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 382 SER Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 391 optimal weight: 4.9990 chunk 434 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 435 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 410 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 237 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 271 GLN I 438 GLN J 289 ASN K 271 GLN K 327 ASN L 269 GLN N 271 GLN O 445 ASN P 271 GLN Q 271 GLN Q 327 ASN U 327 ASN Y 289 ASN Z 271 GLN Z 438 GLN a 289 ASN b 271 GLN b 293 GLN b 327 ASN c 293 GLN ** f 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 271 GLN h 271 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.154513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132711 restraints weight = 40565.736| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.23 r_work: 0.3368 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 40188 Z= 0.173 Angle : 0.520 5.427 53992 Z= 0.278 Chirality : 0.041 0.144 6154 Planarity : 0.004 0.059 7140 Dihedral : 4.973 49.218 5564 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.06 % Allowed : 24.82 % Favored : 70.13 % 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: 0.56 (0.12), residues: 4828 helix: 3.00 (0.12), residues: 1326 sheet: 0.05 (0.10), residues: 2210 loop : -1.82 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG W 309 TYR 0.016 0.002 TYR E 321 PHE 0.008 0.001 PHE e 451 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00409 (40188) covalent geometry : angle 0.51988 (53992) hydrogen bonds : bond 0.03614 ( 2449) hydrogen bonds : angle 4.35700 ( 6939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 843 time to evaluate : 1.769 Fit side-chains REVERT: A 320 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: A 437 ASP cc_start: 0.8475 (t0) cc_final: 0.7919 (t0) REVERT: A 445 ASN cc_start: 0.8260 (m110) cc_final: 0.7988 (m110) REVERT: B 369 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8051 (mtmt) REVERT: B 386 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8151 (mptt) REVERT: C 264 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7523 (mp0) REVERT: C 305 GLN cc_start: 0.8283 (tt0) cc_final: 0.7957 (tt0) REVERT: C 320 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: C 386 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8206 (mptt) REVERT: D 262 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7111 (mt-10) REVERT: D 264 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7322 (mt-10) REVERT: E 320 GLU cc_start: 0.8200 (tt0) cc_final: 0.7873 (tt0) REVERT: F 320 GLU cc_start: 0.8202 (tt0) cc_final: 0.7964 (tt0) REVERT: G 445 ASN cc_start: 0.8470 (m110) cc_final: 0.8128 (m110) REVERT: H 264 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7109 (mt-10) REVERT: H 267 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6748 (mtm180) REVERT: H 298 MET cc_start: 0.8894 (mtp) cc_final: 0.8599 (mtp) REVERT: H 377 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8709 (mt) REVERT: I 264 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7331 (mt-10) REVERT: I 266 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7565 (mt-10) REVERT: I 320 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: I 386 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8439 (mmmt) REVERT: J 369 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7952 (mttp) REVERT: J 377 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8659 (mt) REVERT: J 380 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7990 (m) REVERT: J 386 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8258 (mptp) REVERT: J 401 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7402 (ttpt) REVERT: K 266 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7641 (mt-10) REVERT: K 320 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: K 385 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7855 (ttm170) REVERT: K 386 LYS cc_start: 0.8566 (mptt) cc_final: 0.8240 (mptp) REVERT: L 305 GLN cc_start: 0.8566 (tt0) cc_final: 0.8321 (tt0) REVERT: L 386 LYS cc_start: 0.8613 (mptp) cc_final: 0.8407 (mppt) REVERT: M 267 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7457 (mtt180) REVERT: M 386 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8269 (mptp) REVERT: N 263 GLN cc_start: 0.7325 (mt0) cc_final: 0.7100 (mt0) REVERT: N 267 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7185 (mtm180) REVERT: N 305 GLN cc_start: 0.8551 (tt0) cc_final: 0.8215 (tt0) REVERT: N 308 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8093 (ttpt) REVERT: N 320 GLU cc_start: 0.8026 (tt0) cc_final: 0.7660 (tt0) REVERT: N 369 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7801 (mttp) REVERT: N 386 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8129 (mttp) REVERT: N 426 ILE cc_start: 0.8283 (mm) cc_final: 0.8044 (mm) REVERT: O 299 ASP cc_start: 0.7909 (t0) cc_final: 0.7659 (t0) REVERT: O 305 GLN cc_start: 0.8337 (tt0) cc_final: 0.8029 (tt0) REVERT: O 369 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7815 (mttp) REVERT: O 377 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8559 (mt) REVERT: P 264 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: P 282 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7318 (tp) REVERT: P 320 GLU cc_start: 0.8019 (tt0) cc_final: 0.7754 (tt0) REVERT: P 369 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7790 (mttp) REVERT: P 377 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8315 (mt) REVERT: Q 377 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8858 (mt) REVERT: R 320 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: R 437 ASP cc_start: 0.8452 (t0) cc_final: 0.7905 (t0) REVERT: S 369 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: S 386 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8176 (mptt) REVERT: T 278 ASP cc_start: 0.7543 (m-30) cc_final: 0.7291 (m-30) REVERT: T 305 GLN cc_start: 0.8280 (tt0) cc_final: 0.7971 (tt0) REVERT: T 386 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8150 (mptt) REVERT: U 262 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7105 (mt-10) REVERT: V 320 GLU cc_start: 0.8175 (tt0) cc_final: 0.7848 (tt0) REVERT: W 264 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: W 320 GLU cc_start: 0.8195 (tt0) cc_final: 0.7957 (tt0) REVERT: X 377 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8565 (mt) REVERT: X 445 ASN cc_start: 0.8416 (m110) cc_final: 0.7985 (m110) REVERT: Y 264 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7142 (mt-10) REVERT: Y 267 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6724 (mtm180) REVERT: Y 278 ASP cc_start: 0.7588 (m-30) cc_final: 0.7259 (t0) REVERT: Y 298 MET cc_start: 0.8884 (mtp) cc_final: 0.8582 (mtp) REVERT: Y 377 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8708 (mt) REVERT: Y 385 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7765 (ttm170) REVERT: Z 264 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7286 (mt-10) REVERT: Z 269 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: Z 386 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8447 (mmmt) REVERT: a 269 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: a 369 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7945 (mttp) REVERT: a 377 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8660 (mt) REVERT: a 386 LYS cc_start: 0.8512 (mmtm) cc_final: 0.7997 (mptt) REVERT: a 401 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7396 (ttpt) REVERT: b 305 GLN cc_start: 0.8600 (tt0) cc_final: 0.8372 (tt0) REVERT: b 320 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: b 385 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7864 (ttm170) REVERT: d 386 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8257 (mptp) REVERT: e 267 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7238 (mtm180) REVERT: e 305 GLN cc_start: 0.8540 (tt0) cc_final: 0.8201 (tt0) REVERT: e 308 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8086 (ttpt) REVERT: e 320 GLU cc_start: 0.8018 (tt0) cc_final: 0.7651 (tt0) REVERT: e 369 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: e 386 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8084 (mttp) REVERT: e 426 ILE cc_start: 0.8292 (mm) cc_final: 0.8059 (mm) REVERT: f 305 GLN cc_start: 0.8346 (tt0) cc_final: 0.8121 (tt0) REVERT: f 313 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7800 (p0) REVERT: f 377 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8576 (mt) REVERT: f 386 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8458 (mptm) REVERT: g 264 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: g 282 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7456 (tp) REVERT: g 369 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7716 (mttp) REVERT: g 377 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8308 (mt) REVERT: h 377 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8923 (mt) outliers start: 220 outliers final: 150 residues processed: 978 average time/residue: 0.6712 time to fit residues: 807.8125 Evaluate side-chains 1022 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 830 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 369 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 268 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 382 SER Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 369 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 268 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 386 LYS Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 320 GLU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 264 GLU Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 282 LEU Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 382 SER Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 280 VAL Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain V residue 418 MET Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 380 THR Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 377 LEU Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 397 SER Chi-restraints excluded: chain Z residue 269 GLN Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 268 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 268 SER Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 278 ASP Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 268 SER Chi-restraints excluded: chain e residue 369 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 382 SER Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 313 ASN Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 386 LYS Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 382 SER Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 252 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 chunk 458 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 383 HIS B 293 GLN D 293 GLN D 327 ASN E 271 GLN E 293 GLN H 383 HIS I 327 ASN I 438 GLN J 289 ASN K 293 GLN K 327 ASN M 293 GLN N 271 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN P 271 GLN P 293 GLN Q 271 GLN Q 327 ASN R 293 GLN R 383 HIS S 293 GLN U 293 GLN U 327 ASN V 293 GLN V 383 HIS W 305 GLN Y 293 GLN Z 327 ASN Z 438 GLN a 289 ASN a 305 GLN b 327 ASN c 269 GLN d 293 GLN d 327 ASN ** f 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 271 GLN g 293 GLN h 271 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.151249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129374 restraints weight = 41032.896| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.25 r_work: 0.3344 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 40188 Z= 0.293 Angle : 0.622 6.680 53992 Z= 0.333 Chirality : 0.045 0.160 6154 Planarity : 0.005 0.053 7140 Dihedral : 5.317 49.432 5562 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.47 % Allowed : 24.86 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.12), residues: 4828 helix: 2.60 (0.13), residues: 1326 sheet: -0.65 (0.10), residues: 2414 loop : -1.41 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 309 TYR 0.019 0.002 TYR U 326 PHE 0.016 0.002 PHE e 451 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00693 (40188) covalent geometry : angle 0.62165 (53992) hydrogen bonds : bond 0.04572 ( 2449) hydrogen bonds : angle 4.84031 ( 6939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 848 time to evaluate : 1.680 Fit side-chains REVERT: A 320 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 437 ASP cc_start: 0.8514 (t0) cc_final: 0.8020 (t0) REVERT: B 262 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7168 (mt-10) REVERT: B 369 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8158 (mtmt) REVERT: B 386 LYS cc_start: 0.8647 (mmtm) cc_final: 0.7994 (mptt) REVERT: C 264 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7509 (mp0) REVERT: C 266 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7511 (mt-10) REVERT: C 386 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8172 (mptt) REVERT: C 390 THR cc_start: 0.8139 (m) cc_final: 0.7890 (p) REVERT: D 262 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7186 (mt-10) REVERT: D 264 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7339 (mt-10) REVERT: D 309 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.8082 (ttm110) REVERT: E 262 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 320 GLU cc_start: 0.8347 (tt0) cc_final: 0.8070 (tt0) REVERT: F 320 GLU cc_start: 0.8168 (tt0) cc_final: 0.7964 (tt0) REVERT: G 305 GLN cc_start: 0.8649 (tt0) cc_final: 0.8423 (tt0) REVERT: G 320 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: G 373 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7901 (ttm170) REVERT: G 445 ASN cc_start: 0.8564 (m110) cc_final: 0.8172 (m110) REVERT: H 264 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7086 (mt-10) REVERT: H 267 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6719 (mtm180) REVERT: H 298 MET cc_start: 0.8898 (mtp) cc_final: 0.8631 (mtp) REVERT: H 305 GLN cc_start: 0.8482 (tt0) cc_final: 0.8254 (tt0) REVERT: H 377 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8658 (mt) REVERT: H 385 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7797 (ttm170) REVERT: I 264 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7407 (mt-10) REVERT: I 266 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7591 (mt-10) REVERT: I 386 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8379 (mmmt) REVERT: J 269 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: J 369 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7948 (mttp) REVERT: J 377 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8687 (mt) REVERT: J 380 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8005 (m) REVERT: J 386 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8013 (mptt) REVERT: J 401 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7483 (ttpt) REVERT: K 266 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7665 (mt-10) REVERT: K 320 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: K 385 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7942 (ttm170) REVERT: K 386 LYS cc_start: 0.8678 (mptt) cc_final: 0.8286 (mptp) REVERT: L 262 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7457 (mt-10) REVERT: L 305 GLN cc_start: 0.8638 (tt0) cc_final: 0.8379 (tt0) REVERT: M 262 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7225 (mt-10) REVERT: M 264 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7415 (mp0) REVERT: M 386 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8305 (mptp) REVERT: N 267 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (mtt180) REVERT: N 305 GLN cc_start: 0.8589 (tt0) cc_final: 0.8135 (tt0) REVERT: N 308 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8227 (ttpt) REVERT: N 320 GLU cc_start: 0.8052 (tt0) cc_final: 0.7692 (tt0) REVERT: N 369 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7837 (mttp) REVERT: N 386 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8204 (mttp) REVERT: N 426 ILE cc_start: 0.8426 (mm) cc_final: 0.8189 (mm) REVERT: O 305 GLN cc_start: 0.8413 (tt0) cc_final: 0.8164 (tt0) REVERT: O 369 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: O 377 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8547 (mt) REVERT: P 264 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: P 282 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7539 (tp) REVERT: P 320 GLU cc_start: 0.8083 (tt0) cc_final: 0.7852 (tt0) REVERT: P 369 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7777 (mttp) REVERT: P 377 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8342 (mt) REVERT: Q 377 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8849 (mt) REVERT: R 437 ASP cc_start: 0.8505 (t0) cc_final: 0.8010 (t0) REVERT: S 262 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7214 (mt-10) REVERT: S 369 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: S 386 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8169 (mptt) REVERT: T 305 GLN cc_start: 0.8351 (tt0) cc_final: 0.8027 (tt0) REVERT: T 386 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8161 (mptt) REVERT: T 390 THR cc_start: 0.8120 (m) cc_final: 0.7869 (p) REVERT: U 262 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7158 (mt-10) REVERT: V 262 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7168 (mt-10) REVERT: V 320 GLU cc_start: 0.8325 (tt0) cc_final: 0.8044 (tt0) REVERT: W 264 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: W 447 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7697 (mm) REVERT: X 445 ASN cc_start: 0.8518 (m110) cc_final: 0.8071 (m110) REVERT: Y 264 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7203 (mt-10) REVERT: Y 267 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6698 (mtm180) REVERT: Y 278 ASP cc_start: 0.7787 (m-30) cc_final: 0.7538 (t0) REVERT: Y 298 MET cc_start: 0.8856 (mtp) cc_final: 0.8573 (mtp) REVERT: Y 377 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8703 (mt) REVERT: Y 385 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7835 (ttm170) REVERT: Z 264 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7358 (mt-10) REVERT: Z 386 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8384 (mmmt) REVERT: a 269 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: a 369 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8012 (mttp) REVERT: a 377 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8653 (mt) REVERT: a 386 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8079 (mptt) REVERT: a 401 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7465 (ttpt) REVERT: b 320 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: b 385 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7900 (ttm170) REVERT: c 262 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7276 (mt-10) REVERT: c 305 GLN cc_start: 0.8610 (tt0) cc_final: 0.8349 (tt0) REVERT: c 386 LYS cc_start: 0.8641 (mptp) cc_final: 0.8434 (mptp) REVERT: d 262 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7204 (mt-10) REVERT: d 386 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8368 (mptp) REVERT: e 267 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7310 (mtt180) REVERT: e 305 GLN cc_start: 0.8566 (tt0) cc_final: 0.8101 (tt0) REVERT: e 308 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8227 (ttpt) REVERT: e 320 GLU cc_start: 0.8041 (tt0) cc_final: 0.7693 (tt0) REVERT: e 369 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7835 (mttp) REVERT: e 386 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8146 (mttp) REVERT: e 426 ILE cc_start: 0.8416 (mm) cc_final: 0.8180 (mm) REVERT: f 299 ASP cc_start: 0.7758 (t70) cc_final: 0.7411 (t0) REVERT: f 305 GLN cc_start: 0.8419 (tt0) cc_final: 0.8183 (tt0) REVERT: f 313 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7812 (p0) REVERT: f 369 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7807 (mttp) REVERT: f 377 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8587 (mt) REVERT: f 386 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8475 (mptm) REVERT: g 264 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: g 282 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7529 (tp) REVERT: g 369 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (mttp) REVERT: g 377 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8342 (mt) REVERT: h 377 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8910 (mt) outliers start: 238 outliers final: 162 residues processed: 1003 average time/residue: 0.7183 time to fit residues: 881.5250 Evaluate side-chains 1028 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 824 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 369 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 268 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 382 SER Chi-restraints excluded: chain M residue 388 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 397 SER Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 268 SER Chi-restraints excluded: chain N residue 295 ASP Chi-restraints excluded: chain N residue 308 LYS Chi-restraints excluded: chain N residue 369 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 280 VAL Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 268 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 386 LYS Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 268 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 382 SER Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 382 SER Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 282 LEU Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 382 SER Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 380 THR Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain V residue 418 MET Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 380 THR Chi-restraints excluded: chain W residue 382 SER Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain X residue 268 SER Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 268 SER Chi-restraints excluded: chain a residue 269 GLN Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 268 SER Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 382 SER Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 268 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 382 SER Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 268 SER Chi-restraints excluded: chain e residue 295 ASP Chi-restraints excluded: chain e residue 308 LYS Chi-restraints excluded: chain e residue 369 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 382 SER Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 280 VAL Chi-restraints excluded: chain f residue 313 ASN Chi-restraints excluded: chain f residue 369 LYS Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 268 SER Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 382 SER Chi-restraints excluded: chain g residue 386 LYS Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 382 SER Chi-restraints excluded: chain h residue 395 THR Chi-restraints excluded: chain h residue 421 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 290 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 415 optimal weight: 0.0030 chunk 251 optimal weight: 0.7980 chunk 317 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN C 305 GLN D 293 GLN D 305 GLN E 271 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN J 289 ASN K 293 GLN K 327 ASN M 293 GLN N 271 GLN ** O 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN P 271 GLN P 293 GLN Q 271 GLN R 293 GLN S 293 GLN ** U 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 GLN V 293 GLN W 305 GLN X 445 ASN Y 293 GLN Z 438 GLN a 289 ASN b 327 ASN c 293 GLN d 293 GLN ** f 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 271 GLN g 293 GLN h 271 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.157540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135902 restraints weight = 40501.058| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.23 r_work: 0.3419 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40188 Z= 0.102 Angle : 0.488 5.968 53992 Z= 0.260 Chirality : 0.040 0.135 6154 Planarity : 0.004 0.064 7140 Dihedral : 4.845 43.050 5562 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.09 % Allowed : 26.24 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.12), residues: 4828 helix: 3.10 (0.12), residues: 1326 sheet: -0.03 (0.10), residues: 2210 loop : -1.84 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 309 TYR 0.012 0.001 TYR I 326 PHE 0.007 0.001 PHE X 375 HIS 0.001 0.000 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00240 (40188) covalent geometry : angle 0.48758 (53992) hydrogen bonds : bond 0.02948 ( 2449) hydrogen bonds : angle 4.05625 ( 6939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 887 time to evaluate : 1.392 Fit side-chains REVERT: A 324 GLU cc_start: 0.7578 (tt0) cc_final: 0.7108 (tm-30) REVERT: A 437 ASP cc_start: 0.8479 (t0) cc_final: 0.7912 (t0) REVERT: B 386 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8160 (mptt) REVERT: C 264 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7582 (mp0) REVERT: C 386 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8125 (mptt) REVERT: D 262 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7151 (mt-10) REVERT: D 264 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7396 (mt-10) REVERT: D 309 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.8077 (ttm110) REVERT: E 320 GLU cc_start: 0.8259 (tt0) cc_final: 0.7974 (tt0) REVERT: F 320 GLU cc_start: 0.8130 (tt0) cc_final: 0.7913 (tt0) REVERT: G 373 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7856 (ttm170) REVERT: G 445 ASN cc_start: 0.8484 (m110) cc_final: 0.8183 (m110) REVERT: H 264 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7179 (mt-10) REVERT: H 267 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6778 (mtm180) REVERT: H 298 MET cc_start: 0.8813 (mtp) cc_final: 0.8449 (mtp) REVERT: H 385 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7717 (ttm170) REVERT: H 445 ASN cc_start: 0.8433 (m110) cc_final: 0.8003 (m110) REVERT: I 386 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8415 (mmmt) REVERT: J 369 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7945 (mttp) REVERT: J 377 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 380 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7985 (m) REVERT: J 386 LYS cc_start: 0.8514 (mmtm) cc_final: 0.7945 (mptt) REVERT: J 401 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7430 (ttpt) REVERT: K 298 MET cc_start: 0.8695 (mtp) cc_final: 0.8404 (ttm) REVERT: K 320 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: K 385 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7846 (ttm170) REVERT: K 386 LYS cc_start: 0.8542 (mptt) cc_final: 0.8168 (mppt) REVERT: M 386 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8176 (mptp) REVERT: N 267 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7251 (mtt180) REVERT: N 305 GLN cc_start: 0.8447 (tt0) cc_final: 0.8173 (tt0) REVERT: N 308 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8041 (ttpt) REVERT: N 320 GLU cc_start: 0.7978 (tt0) cc_final: 0.7630 (tt0) REVERT: N 369 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7799 (mttp) REVERT: N 386 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: N 426 ILE cc_start: 0.8298 (mm) cc_final: 0.8068 (mm) REVERT: O 305 GLN cc_start: 0.8267 (tt0) cc_final: 0.7979 (tt0) REVERT: O 369 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7808 (mttp) REVERT: O 377 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8569 (mt) REVERT: O 443 LEU cc_start: 0.8337 (tt) cc_final: 0.8049 (pp) REVERT: P 264 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: P 309 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7940 (ttm110) REVERT: P 320 GLU cc_start: 0.7969 (tt0) cc_final: 0.7716 (tt0) REVERT: P 377 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8250 (mt) REVERT: Q 377 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8765 (mt) REVERT: Q 401 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7419 (ttpt) REVERT: R 437 ASP cc_start: 0.8472 (t0) cc_final: 0.7907 (t0) REVERT: R 445 ASN cc_start: 0.8386 (m110) cc_final: 0.8047 (m110) REVERT: S 386 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8176 (mptt) REVERT: T 278 ASP cc_start: 0.7434 (m-30) cc_final: 0.7126 (t0) REVERT: T 305 GLN cc_start: 0.8215 (tt0) cc_final: 0.7963 (tt0) REVERT: T 386 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8168 (mptt) REVERT: U 262 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7107 (mt-10) REVERT: U 309 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.8016 (ttm110) REVERT: V 289 ASN cc_start: 0.8576 (m-40) cc_final: 0.8374 (m-40) REVERT: V 320 GLU cc_start: 0.8258 (tt0) cc_final: 0.7966 (tt0) REVERT: W 320 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: W 447 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7757 (mm) REVERT: X 369 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7709 (mttp) REVERT: X 445 ASN cc_start: 0.8235 (m-40) cc_final: 0.7743 (m110) REVERT: Y 264 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7203 (mt-10) REVERT: Y 267 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.6813 (mtm180) REVERT: Y 278 ASP cc_start: 0.7562 (m-30) cc_final: 0.7280 (t0) REVERT: Y 298 MET cc_start: 0.8814 (mtp) cc_final: 0.8334 (mtp) REVERT: Y 377 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8556 (mt) REVERT: Y 385 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7712 (ttm170) REVERT: Y 445 ASN cc_start: 0.8414 (m110) cc_final: 0.8001 (m110) REVERT: Z 264 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7329 (mt-10) REVERT: Z 386 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8410 (mmmt) REVERT: a 369 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7932 (mttp) REVERT: a 377 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8519 (mt) REVERT: a 386 LYS cc_start: 0.8480 (mmtm) cc_final: 0.7925 (mptt) REVERT: a 401 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7261 (ttpt) REVERT: b 298 MET cc_start: 0.8668 (mtp) cc_final: 0.8370 (ttm) REVERT: b 320 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: b 385 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7827 (ttm170) REVERT: d 386 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8117 (mptp) REVERT: d 445 ASN cc_start: 0.8295 (m110) cc_final: 0.8092 (m110) REVERT: e 267 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7244 (mtt180) REVERT: e 271 GLN cc_start: 0.8136 (tt0) cc_final: 0.7932 (tp-100) REVERT: e 305 GLN cc_start: 0.8440 (tt0) cc_final: 0.8173 (tt0) REVERT: e 308 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8037 (ttpt) REVERT: e 320 GLU cc_start: 0.7943 (tt0) cc_final: 0.7588 (tt0) REVERT: e 369 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7797 (mttp) REVERT: e 386 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: e 426 ILE cc_start: 0.8317 (mm) cc_final: 0.8090 (mm) REVERT: f 305 GLN cc_start: 0.8255 (tt0) cc_final: 0.8035 (tt0) REVERT: f 377 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8599 (mt) REVERT: f 386 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8463 (mptm) REVERT: g 264 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: g 282 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7475 (tp) REVERT: g 309 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7918 (ttm110) REVERT: g 369 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7783 (mttp) REVERT: g 377 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8226 (mp) REVERT: h 377 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8888 (mt) REVERT: h 401 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7420 (ttpt) outliers start: 178 outliers final: 125 residues processed: 1002 average time/residue: 0.6986 time to fit residues: 861.4466 Evaluate side-chains 1008 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 853 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 369 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 397 SER Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 388 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 369 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 382 SER Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 264 GLU Chi-restraints excluded: chain T residue 280 VAL Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 320 GLU Chi-restraints excluded: chain W residue 380 THR Chi-restraints excluded: chain W residue 382 SER Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 369 LYS Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 397 SER Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 382 SER Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 369 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 382 SER Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 382 SER Chi-restraints excluded: chain h residue 395 THR Chi-restraints excluded: chain h residue 421 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 334 optimal weight: 1.9990 chunk 235 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 349 optimal weight: 0.9980 chunk 436 optimal weight: 3.9990 chunk 361 optimal weight: 0.5980 chunk 239 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN J 289 ASN K 327 ASN N 271 GLN ** O 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN Q 271 GLN ** U 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 305 GLN Z 271 GLN Z 438 GLN a 289 ASN b 271 GLN b 305 GLN b 327 ASN ** f 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 445 ASN g 269 GLN g 271 GLN h 271 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.157002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135461 restraints weight = 40200.378| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.21 r_work: 0.3414 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40188 Z= 0.117 Angle : 0.493 6.108 53992 Z= 0.263 Chirality : 0.040 0.135 6154 Planarity : 0.004 0.064 7140 Dihedral : 4.709 40.718 5561 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.79 % Allowed : 26.63 % Favored : 69.58 % 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: 0.68 (0.12), residues: 4828 helix: 3.16 (0.13), residues: 1326 sheet: 0.11 (0.10), residues: 2210 loop : -1.82 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 309 TYR 0.015 0.001 TYR f 326 PHE 0.007 0.001 PHE X 375 HIS 0.001 0.000 HIS W 383 Details of bonding type rmsd covalent geometry : bond 0.00278 (40188) covalent geometry : angle 0.49336 (53992) hydrogen bonds : bond 0.03048 ( 2449) hydrogen bonds : angle 4.00431 ( 6939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9656 Ramachandran restraints generated. 4828 Oldfield, 0 Emsley, 4828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 846 time to evaluate : 1.398 Fit side-chains REVERT: A 324 GLU cc_start: 0.7550 (tt0) cc_final: 0.7093 (tt0) REVERT: A 437 ASP cc_start: 0.8469 (t0) cc_final: 0.7892 (t0) REVERT: B 369 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8053 (mtmt) REVERT: B 386 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8150 (mptt) REVERT: C 264 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7596 (mp0) REVERT: C 305 GLN cc_start: 0.8183 (tt0) cc_final: 0.7927 (tt0) REVERT: C 386 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8144 (mptt) REVERT: D 262 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 264 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7401 (mt-10) REVERT: D 309 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.8080 (ttm110) REVERT: E 320 GLU cc_start: 0.8139 (tt0) cc_final: 0.7818 (tt0) REVERT: F 314 THR cc_start: 0.8567 (p) cc_final: 0.8356 (p) REVERT: F 320 GLU cc_start: 0.8114 (tt0) cc_final: 0.7894 (tt0) REVERT: G 445 ASN cc_start: 0.8539 (m110) cc_final: 0.8211 (m110) REVERT: H 264 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7207 (mt-10) REVERT: H 267 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6719 (mtm180) REVERT: H 298 MET cc_start: 0.8833 (mtp) cc_final: 0.8443 (mtp) REVERT: H 377 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8552 (mt) REVERT: H 385 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7694 (ttm170) REVERT: H 445 ASN cc_start: 0.8416 (m110) cc_final: 0.7992 (m110) REVERT: I 386 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8466 (mmmt) REVERT: J 369 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: J 377 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8520 (mt) REVERT: J 380 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7933 (m) REVERT: J 386 LYS cc_start: 0.8490 (mmtm) cc_final: 0.7927 (mptt) REVERT: J 401 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7496 (ttpt) REVERT: K 320 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: K 385 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7849 (ttm170) REVERT: K 386 LYS cc_start: 0.8560 (mptt) cc_final: 0.8255 (mptp) REVERT: M 386 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8211 (mptp) REVERT: M 401 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7365 (ttpt) REVERT: N 267 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7245 (mtt180) REVERT: N 305 GLN cc_start: 0.8451 (tt0) cc_final: 0.8210 (tt0) REVERT: N 308 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8059 (ttpt) REVERT: N 320 GLU cc_start: 0.7985 (tt0) cc_final: 0.7624 (tt0) REVERT: N 369 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7708 (mttp) REVERT: N 386 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8159 (mttp) REVERT: N 426 ILE cc_start: 0.8313 (mm) cc_final: 0.8094 (mm) REVERT: O 305 GLN cc_start: 0.8256 (tt0) cc_final: 0.7971 (tt0) REVERT: O 369 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7806 (mttp) REVERT: O 377 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8562 (mt) REVERT: O 443 LEU cc_start: 0.8354 (tt) cc_final: 0.8057 (pp) REVERT: P 264 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: P 309 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.8030 (ttm110) REVERT: P 320 GLU cc_start: 0.7957 (tt0) cc_final: 0.7715 (tt0) REVERT: P 377 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8248 (mp) REVERT: P 424 ASN cc_start: 0.7907 (t0) cc_final: 0.7558 (t0) REVERT: Q 401 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7420 (ttpt) REVERT: R 437 ASP cc_start: 0.8476 (t0) cc_final: 0.7920 (t0) REVERT: R 445 ASN cc_start: 0.8388 (m110) cc_final: 0.8032 (m110) REVERT: S 267 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7518 (mtt90) REVERT: S 369 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8049 (mtmt) REVERT: S 386 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8169 (mptt) REVERT: T 278 ASP cc_start: 0.7406 (m-30) cc_final: 0.7200 (m-30) REVERT: T 305 GLN cc_start: 0.8237 (tt0) cc_final: 0.7994 (tt0) REVERT: T 386 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8161 (mptt) REVERT: U 262 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7123 (mt-10) REVERT: U 309 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.8041 (ttm110) REVERT: V 320 GLU cc_start: 0.8144 (tt0) cc_final: 0.7822 (tt0) REVERT: W 314 THR cc_start: 0.8512 (p) cc_final: 0.8311 (p) REVERT: W 320 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: X 445 ASN cc_start: 0.8312 (m-40) cc_final: 0.8061 (m110) REVERT: Y 264 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7221 (mt-10) REVERT: Y 267 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6732 (mtm180) REVERT: Y 278 ASP cc_start: 0.7559 (m-30) cc_final: 0.7236 (t0) REVERT: Y 298 MET cc_start: 0.8824 (mtp) cc_final: 0.8429 (mtp) REVERT: Y 377 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8556 (mt) REVERT: Y 385 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7728 (ttm170) REVERT: Y 445 ASN cc_start: 0.8402 (m110) cc_final: 0.7962 (m110) REVERT: Z 386 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8466 (mmmt) REVERT: a 369 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: a 377 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (mt) REVERT: a 386 LYS cc_start: 0.8485 (mmtm) cc_final: 0.7946 (mptt) REVERT: a 401 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7251 (ttpt) REVERT: b 320 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: b 385 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7805 (ttm170) REVERT: d 386 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8153 (mptp) REVERT: e 267 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7390 (mtt180) REVERT: e 305 GLN cc_start: 0.8414 (tt0) cc_final: 0.8165 (tt0) REVERT: e 320 GLU cc_start: 0.7947 (tt0) cc_final: 0.7592 (tt0) REVERT: e 369 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7712 (mttp) REVERT: e 386 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8098 (mttp) REVERT: e 426 ILE cc_start: 0.8313 (mm) cc_final: 0.8085 (mm) REVERT: f 377 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8608 (mt) REVERT: f 386 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8158 (mptt) REVERT: g 264 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: g 282 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7477 (tp) REVERT: g 309 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.8014 (ttm110) REVERT: g 369 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7809 (mttp) REVERT: g 377 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8245 (mp) REVERT: g 424 ASN cc_start: 0.7894 (t0) cc_final: 0.7570 (t0) REVERT: h 377 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9013 (mt) REVERT: h 401 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7408 (ttpt) outliers start: 165 outliers final: 120 residues processed: 957 average time/residue: 0.6743 time to fit residues: 794.5652 Evaluate side-chains 981 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 830 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 386 LYS Chi-restraints excluded: chain G residue 395 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain H residue 267 ARG Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain I residue 382 SER Chi-restraints excluded: chain I residue 395 THR Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 448 SER Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 369 LYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 382 SER Chi-restraints excluded: chain J residue 395 THR Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain K residue 320 GLU Chi-restraints excluded: chain K residue 382 SER Chi-restraints excluded: chain K residue 395 THR Chi-restraints excluded: chain K residue 448 SER Chi-restraints excluded: chain L residue 380 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 397 SER Chi-restraints excluded: chain L residue 448 SER Chi-restraints excluded: chain M residue 280 VAL Chi-restraints excluded: chain M residue 388 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 418 MET Chi-restraints excluded: chain N residue 267 ARG Chi-restraints excluded: chain N residue 369 LYS Chi-restraints excluded: chain N residue 380 THR Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain N residue 386 LYS Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 380 THR Chi-restraints excluded: chain O residue 395 THR Chi-restraints excluded: chain P residue 264 GLU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 380 THR Chi-restraints excluded: chain P residue 382 SER Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 388 THR Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain S residue 267 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 382 SER Chi-restraints excluded: chain S residue 395 THR Chi-restraints excluded: chain S residue 397 SER Chi-restraints excluded: chain S residue 448 SER Chi-restraints excluded: chain T residue 264 GLU Chi-restraints excluded: chain T residue 382 SER Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 395 THR Chi-restraints excluded: chain U residue 448 SER Chi-restraints excluded: chain V residue 382 SER Chi-restraints excluded: chain V residue 390 THR Chi-restraints excluded: chain V residue 395 THR Chi-restraints excluded: chain V residue 397 SER Chi-restraints excluded: chain W residue 268 SER Chi-restraints excluded: chain W residue 313 ASN Chi-restraints excluded: chain W residue 320 GLU Chi-restraints excluded: chain W residue 382 SER Chi-restraints excluded: chain W residue 395 THR Chi-restraints excluded: chain W residue 422 GLU Chi-restraints excluded: chain W residue 426 ILE Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 386 LYS Chi-restraints excluded: chain X residue 395 THR Chi-restraints excluded: chain X residue 421 SER Chi-restraints excluded: chain X residue 448 SER Chi-restraints excluded: chain Y residue 267 ARG Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 395 THR Chi-restraints excluded: chain Z residue 448 SER Chi-restraints excluded: chain a residue 280 VAL Chi-restraints excluded: chain a residue 369 LYS Chi-restraints excluded: chain a residue 377 LEU Chi-restraints excluded: chain a residue 382 SER Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 448 SER Chi-restraints excluded: chain b residue 320 GLU Chi-restraints excluded: chain b residue 395 THR Chi-restraints excluded: chain b residue 448 SER Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 382 SER Chi-restraints excluded: chain c residue 395 THR Chi-restraints excluded: chain c residue 397 SER Chi-restraints excluded: chain c residue 448 SER Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain d residue 382 SER Chi-restraints excluded: chain d residue 388 THR Chi-restraints excluded: chain d residue 395 THR Chi-restraints excluded: chain d residue 397 SER Chi-restraints excluded: chain d residue 418 MET Chi-restraints excluded: chain e residue 267 ARG Chi-restraints excluded: chain e residue 369 LYS Chi-restraints excluded: chain e residue 380 THR Chi-restraints excluded: chain e residue 382 SER Chi-restraints excluded: chain e residue 386 LYS Chi-restraints excluded: chain e residue 395 THR Chi-restraints excluded: chain f residue 377 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain g residue 264 GLU Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 369 LYS Chi-restraints excluded: chain g residue 377 LEU Chi-restraints excluded: chain g residue 380 THR Chi-restraints excluded: chain g residue 382 SER Chi-restraints excluded: chain g residue 395 THR Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 377 LEU Chi-restraints excluded: chain h residue 380 THR Chi-restraints excluded: chain h residue 382 SER Chi-restraints excluded: chain h residue 395 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 217 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 363 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 466 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 GLN D 327 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN J 289 ASN K 271 GLN K 293 GLN K 327 ASN N 271 GLN ** O 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN Q 271 GLN U 305 GLN U 327 ASN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 305 GLN Z 438 GLN a 289 ASN b 305 GLN b 327 ASN c 293 GLN ** f 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 305 GLN ** f 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 271 GLN h 271 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132172 restraints weight = 40716.014| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.23 r_work: 0.3374 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 40188 Z= 0.199 Angle : 0.554 6.273 53992 Z= 0.296 Chirality : 0.042 0.149 6154 Planarity : 0.005 0.064 7140 Dihedral : 4.906 45.434 5557 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.25 % Allowed : 26.82 % Favored : 68.93 % 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: 0.41 (0.12), residues: 4828 helix: 2.93 (0.13), residues: 1326 sheet: -0.07 (0.10), residues: 2210 loop : -1.92 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 309 TYR 0.016 0.002 TYR L 326 PHE 0.010 0.002 PHE N 451 HIS 0.002 0.001 HIS P 383 Details of bonding type rmsd covalent geometry : bond 0.00471 (40188) covalent geometry : angle 0.55408 (53992) hydrogen bonds : bond 0.03798 ( 2449) hydrogen bonds : angle 4.40002 ( 6939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18328.80 seconds wall clock time: 311 minutes 29.62 seconds (18689.62 seconds total)