Starting phenix.real_space_refine on Tue Aug 26 23:22:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjr_37590/08_2025/8wjr_37590.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 26384 2.51 5 N 8058 2.21 5 O 8806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 408 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43350 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 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: 0.07 Number of scatterers: 43350 At special positions: 0 Unit cell: (265.2, 265.2, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 8806 8.00 N 8058 7.00 C 26384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10540 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 70 sheets defined 28.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 229 through 258 removed outlier: 3.608A pdb=" N ILE A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'D' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 Processing helix chain 'E' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE E 252 " --> pdb=" O ARG E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 Processing helix chain 'F' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 Processing helix chain 'G' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 Processing helix chain 'H' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE H 252 " --> pdb=" O ARG H 248 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 Processing helix chain 'I' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE I 252 " --> pdb=" O ARG I 248 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'J' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE J 252 " --> pdb=" O ARG J 248 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 Processing helix chain 'K' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE K 252 " --> pdb=" O ARG K 248 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 Processing helix chain 'L' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE L 252 " --> pdb=" O ARG L 248 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 Processing helix chain 'M' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE M 252 " --> pdb=" O ARG M 248 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 Processing helix chain 'N' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE N 252 " --> pdb=" O ARG N 248 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 Processing helix chain 'O' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE O 252 " --> pdb=" O ARG O 248 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 Processing helix chain 'P' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE P 252 " --> pdb=" O ARG P 248 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 Processing helix chain 'Q' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Q 252 " --> pdb=" O ARG Q 248 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 Processing helix chain 'R' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 Processing helix chain 'S' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE S 252 " --> pdb=" O ARG S 248 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 Processing helix chain 'T' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE T 252 " --> pdb=" O ARG T 248 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE U 252 " --> pdb=" O ARG U 248 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 Processing helix chain 'V' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE V 252 " --> pdb=" O ARG V 248 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 Processing helix chain 'W' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 Processing helix chain 'X' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE X 252 " --> pdb=" O ARG X 248 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 Processing helix chain 'Y' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE Y 252 " --> pdb=" O ARG Y 248 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 Processing helix chain 'Z' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Z 252 " --> pdb=" O ARG Z 248 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 Processing helix chain 'a' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE a 252 " --> pdb=" O ARG a 248 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 Processing helix chain 'b' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE b 252 " --> pdb=" O ARG b 248 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 Processing helix chain 'c' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE c 252 " --> pdb=" O ARG c 248 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 Processing helix chain 'd' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE d 252 " --> pdb=" O ARG d 248 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 Processing helix chain 'e' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE e 252 " --> pdb=" O ARG e 248 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 Processing helix chain 'f' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE f 252 " --> pdb=" O ARG f 248 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 Processing helix chain 'g' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE g 252 " --> pdb=" O ARG g 248 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 Processing helix chain 'h' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE h 252 " --> pdb=" O ARG h 248 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 303 removed outlier: 5.370A pdb=" N LEU A 293 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU A 367 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 293 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU B 367 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 293 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU C 367 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU D 293 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU D 367 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU E 293 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU E 367 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU F 293 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU F 367 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU G 293 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU G 367 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 293 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU H 367 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU I 293 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU I 367 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU J 293 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU J 367 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU K 293 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU K 367 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU L 293 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU L 367 " --> pdb=" O LEU L 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU M 293 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU M 367 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU N 293 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU N 367 " --> pdb=" O LEU N 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU O 293 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU O 367 " --> pdb=" O LEU O 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU P 293 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU P 367 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Q 293 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Q 367 " --> pdb=" O LEU Q 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU R 293 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU R 367 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 293 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU S 367 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU T 293 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU T 367 " --> pdb=" O LEU T 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU U 293 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU U 367 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU V 293 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU V 367 " --> pdb=" O LEU V 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU W 293 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU W 367 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU X 293 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU X 367 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Y 293 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Y 367 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Z 293 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU Z 367 " --> pdb=" O LEU Z 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU a 293 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU a 367 " --> pdb=" O LEU a 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU b 293 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU b 367 " --> pdb=" O LEU b 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU c 293 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU c 367 " --> pdb=" O LEU c 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU d 293 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU d 367 " --> pdb=" O LEU d 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU e 293 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU e 367 " --> pdb=" O LEU e 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU f 293 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU f 367 " --> pdb=" O LEU f 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU g 293 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU g 367 " --> pdb=" O LEU g 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU h 293 " --> pdb=" O GLU h 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU h 367 " --> pdb=" O LEU h 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 394 through 395 Processing sheet with id=AB4, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 394 through 395 Processing sheet with id=AB6, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 394 through 395 Processing sheet with id=AB8, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 394 through 395 Processing sheet with id=AC1, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 394 through 395 Processing sheet with id=AC3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 394 through 395 Processing sheet with id=AC5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 394 through 395 Processing sheet with id=AC7, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 394 through 395 Processing sheet with id=AC9, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 394 through 395 Processing sheet with id=AD2, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 394 through 395 Processing sheet with id=AD4, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 394 through 395 Processing sheet with id=AD6, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 394 through 395 Processing sheet with id=AD8, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 394 through 395 Processing sheet with id=AE1, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 394 through 395 Processing sheet with id=AE3, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 394 through 395 Processing sheet with id=AE5, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 394 through 395 Processing sheet with id=AE7, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 394 through 395 Processing sheet with id=AE9, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 394 through 395 Processing sheet with id=AF2, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 394 through 395 Processing sheet with id=AF4, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 394 through 395 Processing sheet with id=AF6, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 394 through 395 Processing sheet with id=AF8, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 394 through 395 Processing sheet with id=AG1, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AG3, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AG5, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 394 through 395 Processing sheet with id=AG7, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 394 through 395 Processing sheet with id=AG9, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 394 through 395 Processing sheet with id=AH2, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 394 through 395 Processing sheet with id=AH4, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 394 through 395 Processing sheet with id=AH6, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 394 through 395 2619 hydrogen bonds defined for protein. 7245 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: 9.99 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12392 1.33 - 1.45: 6070 1.45 - 1.57: 25160 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 43826 Sorted by residual: bond pdb=" N VAL a 257 " pdb=" CA VAL a 257 " ideal model delta sigma weight residual 1.459 1.505 -0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" N VAL J 257 " pdb=" CA VAL J 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.19e+01 bond pdb=" N VAL V 257 " pdb=" CA VAL V 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" N VAL E 257 " pdb=" CA VAL E 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" N VAL R 257 " pdb=" CA VAL R 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.17e+01 ... (remaining 43821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 57110 1.53 - 3.06: 1447 3.06 - 4.59: 467 4.59 - 6.12: 102 6.12 - 7.65: 68 Bond angle restraints: 59194 Sorted by residual: angle pdb=" N ASN Q 261 " pdb=" CA ASN Q 261 " pdb=" C ASN Q 261 " ideal model delta sigma weight residual 113.02 106.55 6.47 1.20e+00 6.94e-01 2.91e+01 angle pdb=" N ASN h 261 " pdb=" CA ASN h 261 " pdb=" C ASN h 261 " ideal model delta sigma weight residual 113.02 106.55 6.47 1.20e+00 6.94e-01 2.91e+01 angle pdb=" N ASN g 261 " pdb=" CA ASN g 261 " pdb=" C ASN g 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.90e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" C ASN E 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN V 261 " pdb=" CA ASN V 261 " pdb=" C ASN V 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.89e+01 ... (remaining 59189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 22981 16.79 - 33.59: 2859 33.59 - 50.38: 1122 50.38 - 67.18: 238 67.18 - 83.97: 102 Dihedral angle restraints: 27302 sinusoidal: 11152 harmonic: 16150 Sorted by residual: dihedral pdb=" CA ARG c 294 " pdb=" CB ARG c 294 " pdb=" CG ARG c 294 " pdb=" CD ARG c 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.99 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG L 294 " pdb=" CB ARG L 294 " pdb=" CG ARG L 294 " pdb=" CD ARG L 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.99 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG H 294 " pdb=" CB ARG H 294 " pdb=" CG ARG H 294 " pdb=" CD ARG H 294 " ideal model delta sinusoidal sigma weight residual 180.00 121.00 59.00 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 27299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3981 0.027 - 0.053: 1853 0.053 - 0.080: 488 0.080 - 0.107: 222 0.107 - 0.134: 222 Chirality restraints: 6766 Sorted by residual: chirality pdb=" CA VAL a 257 " pdb=" N VAL a 257 " pdb=" C VAL a 257 " pdb=" CB VAL a 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL K 257 " pdb=" N VAL K 257 " pdb=" C VAL K 257 " pdb=" CB VAL K 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL b 257 " pdb=" N VAL b 257 " pdb=" C VAL b 257 " pdb=" CB VAL b 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 6763 not shown) Planarity restraints: 8024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE Q 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE Q 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL Q 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE h 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE h 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE h 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL h 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE E 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE E 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL E 257 " -0.019 2.00e-02 2.50e+03 ... (remaining 8021 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 15168 2.87 - 3.38: 36374 3.38 - 3.88: 72097 3.88 - 4.39: 81332 4.39 - 4.90: 142880 Nonbonded interactions: 347851 Sorted by model distance: nonbonded pdb=" OG1 THR d 429 " pdb=" OE1 GLU e 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR M 429 " pdb=" OE1 GLU N 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR a 429 " pdb=" OE1 GLU b 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR G 429 " pdb=" OE1 GLU H 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR X 429 " pdb=" OE1 GLU Y 418 " model vdw 2.362 3.040 ... (remaining 347846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.040 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.004 0.047 43826 Z= 0.220 Angle : 0.707 7.653 59194 Z= 0.443 Chirality : 0.040 0.134 6766 Planarity : 0.004 0.032 8024 Dihedral : 18.035 83.972 16762 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.71 % Allowed : 32.62 % Favored : 66.67 % 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 aren not related in a simple way. whole: 1.83 (0.12), residues: 5440 helix: 4.05 (0.12), residues: 1428 sheet: 0.82 (0.11), residues: 2482 loop : -0.97 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 296 TYR 0.004 0.001 TYR a 366 PHE 0.007 0.001 PHE J 237 HIS 0.005 0.001 HIS e 263 Details of bonding type rmsd covalent geometry : bond 0.00351 (43826) covalent geometry : angle 0.70678 (59194) hydrogen bonds : bond 0.18113 ( 2619) hydrogen bonds : angle 5.91215 ( 7245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 978 time to evaluate : 1.307 Fit side-chains REVERT: A 244 ARG cc_start: 0.7049 (mtt90) cc_final: 0.6787 (ptm160) REVERT: A 290 LYS cc_start: 0.8246 (mtmt) cc_final: 0.8034 (mtmm) REVERT: A 376 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8301 (mtpp) REVERT: A 383 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 394 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6348 (mtpp) REVERT: B 296 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7553 (ttm-80) REVERT: B 376 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8388 (mtpp) REVERT: B 394 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6158 (mtmm) REVERT: C 275 LYS cc_start: 0.8268 (mtmp) cc_final: 0.7968 (mttm) REVERT: C 290 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8089 (mtmm) REVERT: C 356 ARG cc_start: 0.6095 (mtp180) cc_final: 0.5792 (ttp-170) REVERT: C 383 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 394 LYS cc_start: 0.7254 (mmmt) cc_final: 0.6404 (mtpp) REVERT: D 246 GLN cc_start: 0.7779 (tt0) cc_final: 0.7300 (tt0) REVERT: D 373 ARG cc_start: 0.8322 (ttt90) cc_final: 0.8026 (tpp-160) REVERT: D 394 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6598 (mtpp) REVERT: D 409 MET cc_start: 0.7068 (mmp) cc_final: 0.6843 (mmm) REVERT: E 244 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6853 (ptm160) REVERT: E 269 GLN cc_start: 0.7541 (mp10) cc_final: 0.7258 (mp-120) REVERT: E 279 GLU cc_start: 0.7687 (tt0) cc_final: 0.7487 (mt-10) REVERT: E 302 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7197 (mt-10) REVERT: E 356 ARG cc_start: 0.6430 (mtp180) cc_final: 0.6192 (ttp-170) REVERT: E 394 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6378 (mtpp) REVERT: E 420 MET cc_start: 0.8382 (ptm) cc_final: 0.8150 (ptp) REVERT: F 244 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6821 (ptm160) REVERT: F 247 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7116 (mtp180) REVERT: F 275 LYS cc_start: 0.8488 (mtmp) cc_final: 0.8220 (mttt) REVERT: F 356 ARG cc_start: 0.6751 (mtp180) cc_final: 0.6550 (ttp-170) REVERT: F 373 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7750 (tpp80) REVERT: G 244 ARG cc_start: 0.6842 (mtt90) cc_final: 0.6612 (ptm160) REVERT: G 290 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7943 (mtmm) REVERT: G 356 ARG cc_start: 0.6670 (mtp180) cc_final: 0.6416 (ttp-170) REVERT: G 373 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7887 (tpp80) REVERT: G 376 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8173 (mtpp) REVERT: G 394 LYS cc_start: 0.7377 (mmmt) cc_final: 0.6358 (mtpm) REVERT: H 244 ARG cc_start: 0.7261 (mtt90) cc_final: 0.7010 (ptm160) REVERT: H 356 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6419 (mtp85) REVERT: H 376 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8346 (mtpp) REVERT: H 383 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7324 (mt-10) REVERT: H 386 SER cc_start: 0.8995 (p) cc_final: 0.8630 (p) REVERT: H 394 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6318 (mtpp) REVERT: I 244 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6666 (ptm160) REVERT: I 290 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8069 (mtmm) REVERT: I 356 ARG cc_start: 0.6499 (mtp180) cc_final: 0.6184 (ttp-170) REVERT: I 376 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8201 (mtpp) REVERT: I 394 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6472 (mmmm) REVERT: I 420 MET cc_start: 0.8167 (ptm) cc_final: 0.7815 (ptp) REVERT: J 244 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6794 (ptm160) REVERT: J 356 ARG cc_start: 0.6444 (mtp180) cc_final: 0.6158 (ttp-170) REVERT: J 376 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8346 (mtpp) REVERT: J 394 LYS cc_start: 0.6981 (mmmt) cc_final: 0.5992 (mtpp) REVERT: K 244 ARG cc_start: 0.6885 (mtt90) cc_final: 0.6673 (ptm160) REVERT: K 271 ASP cc_start: 0.7784 (t0) cc_final: 0.7562 (t0) REVERT: K 275 LYS cc_start: 0.8268 (mtmp) cc_final: 0.8049 (mttm) REVERT: K 361 ASN cc_start: 0.8778 (m-40) cc_final: 0.8562 (m-40) REVERT: K 376 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8294 (mtpp) REVERT: K 394 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6242 (mtpp) REVERT: L 244 ARG cc_start: 0.7228 (mtt90) cc_final: 0.6966 (ptm160) REVERT: L 376 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8416 (mtpp) REVERT: L 394 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6089 (ttmm) REVERT: M 373 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7897 (ttm-80) REVERT: M 383 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7558 (mt-10) REVERT: M 394 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6441 (mmmm) REVERT: N 271 ASP cc_start: 0.7651 (t0) cc_final: 0.7422 (t0) REVERT: N 275 LYS cc_start: 0.8270 (mtmp) cc_final: 0.8044 (mttm) REVERT: N 295 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8904 (p) REVERT: N 376 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8245 (mtpp) REVERT: N 383 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7058 (mm-30) REVERT: N 394 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6166 (mtpp) REVERT: N 416 THR cc_start: 0.7861 (m) cc_final: 0.7475 (p) REVERT: N 420 MET cc_start: 0.8200 (ptm) cc_final: 0.7806 (ptm) REVERT: O 244 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6819 (ptm160) REVERT: O 294 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8110 (ttm170) REVERT: O 303 GLN cc_start: 0.7466 (mt0) cc_final: 0.7265 (mt0) REVERT: O 370 ARG cc_start: 0.8297 (tmm-80) cc_final: 0.7978 (ttm170) REVERT: O 376 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8178 (OUTLIER) REVERT: O 417 ARG cc_start: 0.7250 (mtt90) cc_final: 0.6840 (mtp85) REVERT: O 420 MET cc_start: 0.8259 (ptm) cc_final: 0.7916 (ptp) REVERT: P 244 ARG cc_start: 0.6976 (mtt90) cc_final: 0.6748 (ptm160) REVERT: P 394 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6338 (mtpp) REVERT: P 416 THR cc_start: 0.8457 (m) cc_final: 0.8011 (p) REVERT: Q 271 ASP cc_start: 0.7656 (t0) cc_final: 0.7387 (t0) REVERT: Q 275 LYS cc_start: 0.8259 (mtmp) cc_final: 0.8054 (mttm) REVERT: Q 290 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8186 (mtmm) REVERT: Q 303 GLN cc_start: 0.7809 (mt0) cc_final: 0.7469 (mt0) REVERT: Q 383 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7640 (mt-10) REVERT: Q 420 MET cc_start: 0.8223 (ptm) cc_final: 0.7974 (ptp) REVERT: R 244 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6784 (ptm160) REVERT: R 290 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8034 (mtmm) REVERT: R 376 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8306 (mtpp) REVERT: R 383 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7227 (mt-10) REVERT: R 394 LYS cc_start: 0.7366 (mmmt) cc_final: 0.6348 (mtpp) REVERT: S 296 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7554 (ttm-80) REVERT: S 376 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8389 (mtpp) REVERT: S 394 LYS cc_start: 0.7241 (mmmt) cc_final: 0.6152 (mtmm) REVERT: T 275 LYS cc_start: 0.8269 (mtmp) cc_final: 0.7970 (mttm) REVERT: T 290 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8085 (mtmm) REVERT: T 356 ARG cc_start: 0.6094 (mtp180) cc_final: 0.5791 (ttp-170) REVERT: T 383 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7504 (mt-10) REVERT: T 394 LYS cc_start: 0.7253 (mmmt) cc_final: 0.6402 (mtpp) REVERT: U 246 GLN cc_start: 0.7782 (tt0) cc_final: 0.7304 (tt0) REVERT: U 373 ARG cc_start: 0.8326 (ttt90) cc_final: 0.8032 (tpp-160) REVERT: U 394 LYS cc_start: 0.7447 (mmmt) cc_final: 0.6597 (mtpp) REVERT: U 409 MET cc_start: 0.7071 (mmp) cc_final: 0.6845 (mmm) REVERT: V 244 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6855 (ptm160) REVERT: V 269 GLN cc_start: 0.7540 (mp10) cc_final: 0.7256 (mp-120) REVERT: V 279 GLU cc_start: 0.7687 (tt0) cc_final: 0.7485 (mt-10) REVERT: V 302 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7190 (mt-10) REVERT: V 356 ARG cc_start: 0.6427 (mtp180) cc_final: 0.6023 (ttp-170) REVERT: V 394 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6375 (mtpp) REVERT: V 420 MET cc_start: 0.8383 (ptm) cc_final: 0.8150 (ptp) REVERT: W 244 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6818 (ptm160) REVERT: W 247 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7114 (mtp180) REVERT: W 275 LYS cc_start: 0.8489 (mtmp) cc_final: 0.8222 (mttt) REVERT: W 373 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7756 (tpp80) REVERT: X 244 ARG cc_start: 0.6843 (mtt90) cc_final: 0.6612 (ptm160) REVERT: X 290 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7945 (mtmm) REVERT: X 356 ARG cc_start: 0.6671 (mtp180) cc_final: 0.6417 (ttp-170) REVERT: X 373 ARG cc_start: 0.8229 (ttt90) cc_final: 0.7896 (tpp80) REVERT: X 376 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8171 (mtpp) REVERT: X 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6356 (mtpm) REVERT: Y 244 ARG cc_start: 0.7257 (mtt90) cc_final: 0.7008 (ptm160) REVERT: Y 356 ARG cc_start: 0.6734 (mtp180) cc_final: 0.6418 (mtp85) REVERT: Y 376 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8347 (mtpp) REVERT: Y 383 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7327 (mt-10) REVERT: Y 386 SER cc_start: 0.8991 (p) cc_final: 0.8626 (p) REVERT: Y 394 LYS cc_start: 0.7305 (mmmt) cc_final: 0.6322 (mtpp) REVERT: Z 244 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6666 (ptm160) REVERT: Z 290 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8069 (mtmm) REVERT: Z 356 ARG cc_start: 0.6505 (mtp180) cc_final: 0.6188 (ttp-170) REVERT: Z 376 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8203 (mtpp) REVERT: Z 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6468 (mmmm) REVERT: Z 420 MET cc_start: 0.8172 (ptm) cc_final: 0.7821 (ptp) REVERT: a 244 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6794 (ptm160) REVERT: a 356 ARG cc_start: 0.6443 (mtp180) cc_final: 0.6157 (ttp-170) REVERT: a 376 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8351 (mtpp) REVERT: a 394 LYS cc_start: 0.6980 (mmmt) cc_final: 0.5993 (mtpp) REVERT: b 244 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6674 (ptm160) REVERT: b 271 ASP cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: b 275 LYS cc_start: 0.8267 (mtmp) cc_final: 0.8049 (mttm) REVERT: b 361 ASN cc_start: 0.8783 (m-40) cc_final: 0.8564 (m-40) REVERT: b 376 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8297 (mtpp) REVERT: b 394 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6243 (mtpp) REVERT: c 244 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6967 (ptm160) REVERT: c 376 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8418 (mtpp) REVERT: c 394 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6091 (ttmm) REVERT: d 373 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7896 (ttm-80) REVERT: d 383 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7560 (mt-10) REVERT: d 394 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6444 (mmmm) REVERT: e 271 ASP cc_start: 0.7652 (t0) cc_final: 0.7422 (t0) REVERT: e 275 LYS cc_start: 0.8270 (mtmp) cc_final: 0.8044 (mttm) REVERT: e 295 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8903 (p) REVERT: e 376 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8244 (mtpp) REVERT: e 383 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7054 (mm-30) REVERT: e 394 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6174 (mtpp) REVERT: e 416 THR cc_start: 0.7859 (m) cc_final: 0.7476 (p) REVERT: e 420 MET cc_start: 0.8202 (ptm) cc_final: 0.7807 (ptm) REVERT: f 244 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6818 (ptm160) REVERT: f 294 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8113 (ttm170) REVERT: f 370 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.7980 (ttm170) REVERT: f 376 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8178 (OUTLIER) REVERT: f 417 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6846 (mtp85) REVERT: f 420 MET cc_start: 0.8262 (ptm) cc_final: 0.7916 (ptp) REVERT: g 244 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6748 (ptm160) REVERT: g 394 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6340 (mtpp) REVERT: g 416 THR cc_start: 0.8459 (m) cc_final: 0.8011 (p) REVERT: h 244 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6792 (ptm160) REVERT: h 271 ASP cc_start: 0.7657 (t0) cc_final: 0.7388 (t0) REVERT: h 275 LYS cc_start: 0.8258 (mtmp) cc_final: 0.8052 (mttm) REVERT: h 290 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8186 (mtmm) REVERT: h 303 GLN cc_start: 0.7807 (mt0) cc_final: 0.7467 (mt0) REVERT: h 383 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7642 (mt-10) REVERT: h 420 MET cc_start: 0.8222 (ptm) cc_final: 0.7973 (ptp) outliers start: 34 outliers final: 30 residues processed: 984 average time/residue: 0.8229 time to fit residues: 945.3651 Evaluate side-chains 854 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 824 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 295 SER Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain U residue 295 SER Chi-restraints excluded: chain V residue 295 SER Chi-restraints excluded: chain W residue 295 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain a residue 295 SER Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain h residue 295 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 303 GLN A 374 HIS A 431 ASN A 434 ASN B 231 ASN B 269 GLN B 303 GLN B 374 HIS B 431 ASN B 434 ASN C 231 ASN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN C 374 HIS C 434 ASN D 231 ASN D 303 GLN D 374 HIS D 434 ASN E 231 ASN E 303 GLN E 374 HIS E 431 ASN E 434 ASN F 231 ASN F 303 GLN F 374 HIS F 431 ASN F 434 ASN G 303 GLN G 374 HIS G 434 ASN H 231 ASN H 303 GLN H 374 HIS H 431 ASN H 434 ASN I 303 GLN I 361 ASN I 374 HIS I 431 ASN I 434 ASN J 303 GLN J 374 HIS J 431 ASN J 434 ASN K 231 ASN K 303 GLN K 374 HIS K 434 ASN L 231 ASN L 269 GLN L 303 GLN L 374 HIS L 434 ASN M 231 ASN M 303 GLN M 374 HIS M 431 ASN M 434 ASN N 231 ASN N 269 GLN N 303 GLN N 374 HIS N 434 ASN O 231 ASN O 269 GLN O 303 GLN O 374 HIS O 431 ASN O 434 ASN P 231 ASN P 269 GLN P 303 GLN P 361 ASN P 374 HIS P 434 ASN Q 303 GLN Q 374 HIS Q 431 ASN Q 434 ASN R 231 ASN R 303 GLN R 374 HIS R 431 ASN R 434 ASN S 231 ASN S 269 GLN S 303 GLN S 374 HIS S 434 ASN T 231 ASN T 285 ASN T 303 GLN T 374 HIS T 434 ASN U 231 ASN U 303 GLN U 374 HIS U 434 ASN V 231 ASN V 303 GLN V 374 HIS V 431 ASN V 434 ASN W 231 ASN W 303 GLN W 374 HIS W 431 ASN W 434 ASN X 303 GLN X 374 HIS X 434 ASN Y 231 ASN Y 303 GLN Y 374 HIS Y 431 ASN Y 434 ASN Z 231 ASN Z 303 GLN Z 361 ASN Z 374 HIS Z 431 ASN Z 434 ASN a 303 GLN a 374 HIS a 431 ASN a 434 ASN b 231 ASN b 303 GLN b 374 HIS b 434 ASN c 231 ASN c 269 GLN c 303 GLN c 374 HIS c 431 ASN c 434 ASN d 231 ASN d 303 GLN d 374 HIS d 431 ASN d 434 ASN e 231 ASN e 269 GLN e 303 GLN e 374 HIS e 434 ASN f 231 ASN f 269 GLN f 374 HIS f 431 ASN f 434 ASN g 231 ASN g 269 GLN g 303 GLN g 361 ASN g 374 HIS g 434 ASN h 303 GLN h 374 HIS h 431 ASN h 434 ASN Total number of N/Q/H flips: 163 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120779 restraints weight = 49264.800| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.51 r_work: 0.3268 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 43826 Z= 0.237 Angle : 0.626 6.261 59194 Z= 0.334 Chirality : 0.045 0.193 6766 Planarity : 0.004 0.062 8024 Dihedral : 4.305 17.736 6048 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.36 % Allowed : 29.43 % Favored : 67.21 % 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 aren not related in a simple way. whole: 1.96 (0.12), residues: 5440 helix: 3.97 (0.12), residues: 1428 sheet: 0.75 (0.11), residues: 2618 loop : -0.48 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 296 TYR 0.013 0.003 TYR e 282 PHE 0.015 0.002 PHE D 422 HIS 0.005 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00555 (43826) covalent geometry : angle 0.62631 (59194) hydrogen bonds : bond 0.05250 ( 2619) hydrogen bonds : angle 4.67148 ( 7245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 849 time to evaluate : 1.688 Fit side-chains REVERT: A 244 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7374 (mtm110) REVERT: A 394 LYS cc_start: 0.7367 (mmmt) cc_final: 0.6548 (mtpp) REVERT: B 244 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7269 (mtm110) REVERT: B 275 LYS cc_start: 0.8712 (mttp) cc_final: 0.8457 (mtmp) REVERT: B 377 MET cc_start: 0.8372 (mpt) cc_final: 0.7897 (mpt) REVERT: B 394 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6594 (ttpp) REVERT: C 244 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7265 (mtp85) REVERT: C 394 LYS cc_start: 0.7577 (mmmt) cc_final: 0.6724 (ttpp) REVERT: D 377 MET cc_start: 0.8486 (mpt) cc_final: 0.8285 (mpt) REVERT: D 394 LYS cc_start: 0.7481 (mmmt) cc_final: 0.6777 (ttpp) REVERT: E 244 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7299 (ptm160) REVERT: E 269 GLN cc_start: 0.7930 (mp10) cc_final: 0.7721 (mp-120) REVERT: E 356 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6782 (ttp-170) REVERT: F 246 GLN cc_start: 0.8195 (tt0) cc_final: 0.7886 (tt0) REVERT: F 247 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7511 (mtp180) REVERT: F 275 LYS cc_start: 0.8609 (mtmp) cc_final: 0.8123 (mttt) REVERT: F 287 ASP cc_start: 0.7463 (t0) cc_final: 0.7003 (p0) REVERT: F 290 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8167 (mtpt) REVERT: F 376 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8288 (mtpp) REVERT: F 431 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8155 (t0) REVERT: G 244 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7139 (ptm160) REVERT: G 356 ARG cc_start: 0.7042 (mtp180) cc_final: 0.6805 (ttp-170) REVERT: G 394 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6694 (ttpp) REVERT: H 244 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7395 (mtm110) REVERT: H 294 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8726 (ttm170) REVERT: H 376 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8264 (mtpp) REVERT: H 383 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7669 (mt-10) REVERT: H 394 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6700 (mtpp) REVERT: I 244 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7174 (ptm160) REVERT: I 356 ARG cc_start: 0.6935 (mtp180) cc_final: 0.6717 (ttp-170) REVERT: I 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6426 (mtpp) REVERT: J 244 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7262 (ptm160) REVERT: J 246 GLN cc_start: 0.8161 (tt0) cc_final: 0.7817 (tt0) REVERT: K 244 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7231 (ptm160) REVERT: K 246 GLN cc_start: 0.8262 (tt0) cc_final: 0.7842 (tt0) REVERT: K 247 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7434 (mtm110) REVERT: K 361 ASN cc_start: 0.8730 (m-40) cc_final: 0.8404 (m-40) REVERT: K 394 LYS cc_start: 0.7414 (mmmt) cc_final: 0.6582 (mtpp) REVERT: L 244 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7469 (ptm160) REVERT: L 394 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6399 (ttpp) REVERT: M 244 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7179 (mtm110) REVERT: M 294 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8769 (tpp-160) REVERT: M 376 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8100 (mtpp) REVERT: M 394 LYS cc_start: 0.7346 (mmmt) cc_final: 0.6677 (mtpt) REVERT: N 244 ARG cc_start: 0.7527 (ptm160) cc_final: 0.7171 (mtt-85) REVERT: N 294 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (tpp-160) REVERT: N 367 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8720 (mm-30) REVERT: N 394 LYS cc_start: 0.7390 (mmmt) cc_final: 0.6524 (tttp) REVERT: O 244 ARG cc_start: 0.7743 (mtt90) cc_final: 0.7513 (mtm110) REVERT: O 294 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8728 (tpp-160) REVERT: O 376 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8375 (mtpp) REVERT: P 244 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7271 (mtp85) REVERT: P 246 GLN cc_start: 0.8245 (tt0) cc_final: 0.7939 (tt0) REVERT: P 247 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7603 (mtm110) REVERT: P 394 LYS cc_start: 0.7099 (mmmt) cc_final: 0.6413 (mtpp) REVERT: Q 246 GLN cc_start: 0.8103 (tt0) cc_final: 0.7841 (tt0) REVERT: Q 275 LYS cc_start: 0.8413 (mtmp) cc_final: 0.8195 (mttm) REVERT: Q 303 GLN cc_start: 0.7602 (mt0) cc_final: 0.7324 (mt0) REVERT: Q 383 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7791 (mt-10) REVERT: R 244 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7378 (mtm110) REVERT: R 394 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6555 (mtpp) REVERT: S 244 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7270 (mtm110) REVERT: S 275 LYS cc_start: 0.8711 (mttp) cc_final: 0.8468 (mtmp) REVERT: S 377 MET cc_start: 0.8398 (mpt) cc_final: 0.7978 (mpt) REVERT: S 394 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6597 (ttpp) REVERT: T 244 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7259 (mtp85) REVERT: T 394 LYS cc_start: 0.7574 (mmmt) cc_final: 0.6725 (ttpp) REVERT: U 377 MET cc_start: 0.8496 (mpt) cc_final: 0.8292 (mpt) REVERT: U 394 LYS cc_start: 0.7482 (mmmt) cc_final: 0.6781 (ttpp) REVERT: V 244 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7299 (ptm160) REVERT: V 269 GLN cc_start: 0.7935 (mp10) cc_final: 0.7724 (mp-120) REVERT: V 356 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6779 (ttp-170) REVERT: W 246 GLN cc_start: 0.8199 (tt0) cc_final: 0.7886 (tt0) REVERT: W 247 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7526 (mtp180) REVERT: W 275 LYS cc_start: 0.8614 (mtmp) cc_final: 0.8129 (mttt) REVERT: W 287 ASP cc_start: 0.7466 (t0) cc_final: 0.6996 (p0) REVERT: W 290 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8168 (mtpt) REVERT: W 376 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8288 (mtpp) REVERT: W 431 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (t0) REVERT: X 244 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7152 (ptm160) REVERT: X 356 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6796 (ttp-170) REVERT: X 394 LYS cc_start: 0.7277 (mmmt) cc_final: 0.6696 (ttpp) REVERT: Y 244 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7397 (mtm110) REVERT: Y 294 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (ttm170) REVERT: Y 376 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8258 (mtpp) REVERT: Y 383 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7664 (mt-10) REVERT: Y 394 LYS cc_start: 0.7499 (mmmt) cc_final: 0.6708 (mtpp) REVERT: Z 244 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7175 (ptm160) REVERT: Z 356 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6724 (ttp-170) REVERT: Z 394 LYS cc_start: 0.7264 (mmmt) cc_final: 0.6427 (mtpp) REVERT: a 244 ARG cc_start: 0.7691 (mtt90) cc_final: 0.7277 (ptm160) REVERT: a 246 GLN cc_start: 0.8162 (tt0) cc_final: 0.7822 (tt0) REVERT: b 244 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7241 (ptm160) REVERT: b 246 GLN cc_start: 0.8259 (tt0) cc_final: 0.7840 (tt0) REVERT: b 247 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7452 (mtm110) REVERT: b 361 ASN cc_start: 0.8731 (m-40) cc_final: 0.8402 (m-40) REVERT: b 394 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6590 (mtpp) REVERT: c 244 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7476 (ptm160) REVERT: c 394 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6400 (ttpp) REVERT: d 244 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7187 (mtm110) REVERT: d 294 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8765 (tpp-160) REVERT: d 376 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8104 (mtpp) REVERT: d 394 LYS cc_start: 0.7351 (mmmt) cc_final: 0.6679 (mtpt) REVERT: e 244 ARG cc_start: 0.7521 (ptm160) cc_final: 0.7170 (mtt-85) REVERT: e 294 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8692 (tpp-160) REVERT: e 367 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8724 (mm-30) REVERT: e 394 LYS cc_start: 0.7400 (mmmt) cc_final: 0.6534 (tttp) REVERT: f 244 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7509 (mtm110) REVERT: f 294 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8721 (tpp-160) REVERT: f 376 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8365 (mtpp) REVERT: g 244 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7274 (mtp85) REVERT: g 246 GLN cc_start: 0.8251 (tt0) cc_final: 0.7941 (tt0) REVERT: g 247 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7587 (mtm110) REVERT: g 394 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6412 (mtpp) REVERT: h 244 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7252 (ptm160) REVERT: h 275 LYS cc_start: 0.8406 (mtmp) cc_final: 0.8189 (mttm) REVERT: h 303 GLN cc_start: 0.7613 (mt0) cc_final: 0.7337 (mt0) REVERT: h 383 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7805 (mt-10) REVERT: h 420 MET cc_start: 0.8676 (ptm) cc_final: 0.8468 (ptp) outliers start: 161 outliers final: 54 residues processed: 941 average time/residue: 0.9508 time to fit residues: 1038.4714 Evaluate side-chains 865 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 797 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain H residue 294 ARG Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 294 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 294 ARG Chi-restraints excluded: chain O residue 423 SER Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain R residue 356 ARG Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 431 ASN Chi-restraints excluded: chain Y residue 294 ARG Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 294 ARG Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 294 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 294 ARG Chi-restraints excluded: chain f residue 423 SER Chi-restraints excluded: chain g residue 289 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 92 optimal weight: 0.0470 chunk 271 optimal weight: 3.9990 chunk 346 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 419 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 351 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN C 277 GLN F 303 GLN G 231 ASN G 269 GLN H 303 GLN I 274 ASN J 231 ASN K 277 GLN K 303 GLN M 431 ASN N 269 GLN O 269 GLN O 431 ASN P 269 GLN R 274 ASN S 274 ASN T 277 GLN W 303 GLN X 231 ASN X 269 GLN X 303 GLN Y 303 GLN a 231 ASN b 277 GLN b 303 GLN d 431 ASN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125912 restraints weight = 47386.073| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.54 r_work: 0.3320 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 43826 Z= 0.114 Angle : 0.496 5.510 59194 Z= 0.263 Chirality : 0.040 0.122 6766 Planarity : 0.003 0.045 8024 Dihedral : 3.875 14.437 6018 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 1.79 % Allowed : 27.39 % Favored : 70.82 % 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 aren not related in a simple way. whole: 2.27 (0.12), residues: 5440 helix: 4.30 (0.12), residues: 1428 sheet: 0.89 (0.11), residues: 2618 loop : -0.31 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 296 TYR 0.006 0.001 TYR e 282 PHE 0.008 0.001 PHE U 422 HIS 0.003 0.001 HIS M 263 Details of bonding type rmsd covalent geometry : bond 0.00261 (43826) covalent geometry : angle 0.49636 (59194) hydrogen bonds : bond 0.03697 ( 2619) hydrogen bonds : angle 4.13920 ( 7245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 830 time to evaluate : 1.362 Fit side-chains REVERT: A 244 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7356 (mtm110) REVERT: A 290 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7975 (mtmt) REVERT: A 373 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7677 (ttp-170) REVERT: A 394 LYS cc_start: 0.7374 (mmmt) cc_final: 0.6635 (mtpp) REVERT: B 244 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7682 (mtt-85) REVERT: B 287 ASP cc_start: 0.7455 (t0) cc_final: 0.6842 (p0) REVERT: B 394 LYS cc_start: 0.7187 (mmmt) cc_final: 0.6594 (ttpp) REVERT: C 244 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: C 394 LYS cc_start: 0.7524 (mmmt) cc_final: 0.6770 (ttpp) REVERT: D 246 GLN cc_start: 0.8191 (tt0) cc_final: 0.7898 (tt0) REVERT: D 394 LYS cc_start: 0.7502 (mmmt) cc_final: 0.6910 (ttpp) REVERT: E 244 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7267 (ptm160) REVERT: E 269 GLN cc_start: 0.8015 (mp10) cc_final: 0.7757 (mp-120) REVERT: E 356 ARG cc_start: 0.6846 (mtp180) cc_final: 0.6545 (ttp-170) REVERT: E 394 LYS cc_start: 0.7499 (mmmt) cc_final: 0.6731 (ttpp) REVERT: F 246 GLN cc_start: 0.8423 (tt0) cc_final: 0.8063 (tt0) REVERT: F 247 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7303 (mpp-170) REVERT: F 275 LYS cc_start: 0.8633 (mtmp) cc_final: 0.8227 (mttt) REVERT: F 287 ASP cc_start: 0.7551 (t0) cc_final: 0.7002 (p0) REVERT: F 290 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8255 (mtpt) REVERT: F 370 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7327 (ttm-80) REVERT: F 431 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7795 (t0) REVERT: G 244 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7236 (mtp85) REVERT: G 247 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7886 (mtm110) REVERT: G 394 LYS cc_start: 0.7361 (mmmt) cc_final: 0.6757 (ttpp) REVERT: H 244 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7381 (mtp85) REVERT: H 367 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8602 (mm-30) REVERT: H 376 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8247 (mtpp) REVERT: H 386 SER cc_start: 0.8930 (p) cc_final: 0.8524 (p) REVERT: H 394 LYS cc_start: 0.7539 (mmmt) cc_final: 0.6783 (mtpp) REVERT: I 244 ARG cc_start: 0.7674 (mtt90) cc_final: 0.7346 (ptm160) REVERT: I 356 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6570 (ttp-170) REVERT: I 394 LYS cc_start: 0.7211 (mmmt) cc_final: 0.6465 (mtpp) REVERT: J 244 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7243 (ptm160) REVERT: J 246 GLN cc_start: 0.8322 (tt0) cc_final: 0.8005 (tt0) REVERT: K 244 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7295 (ptm160) REVERT: K 246 GLN cc_start: 0.8291 (tt0) cc_final: 0.7930 (tt0) REVERT: K 247 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7425 (mtm110) REVERT: K 295 SER cc_start: 0.8776 (p) cc_final: 0.8478 (t) REVERT: K 361 ASN cc_start: 0.8637 (m-40) cc_final: 0.8368 (m-40) REVERT: K 394 LYS cc_start: 0.7273 (mmmt) cc_final: 0.6357 (mtpp) REVERT: L 287 ASP cc_start: 0.7478 (t0) cc_final: 0.6938 (p0) REVERT: L 394 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6617 (ttpp) REVERT: M 244 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7190 (mtm110) REVERT: M 376 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8081 (mtpp) REVERT: M 394 LYS cc_start: 0.7294 (mmmt) cc_final: 0.6618 (mtpt) REVERT: M 431 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8140 (t0) REVERT: N 244 ARG cc_start: 0.7552 (ptm160) cc_final: 0.7207 (mtt-85) REVERT: N 246 GLN cc_start: 0.8372 (tt0) cc_final: 0.8103 (tt0) REVERT: N 275 LYS cc_start: 0.8480 (mtmp) cc_final: 0.8163 (mttm) REVERT: N 367 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8641 (mm-30) REVERT: N 394 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6509 (tttp) REVERT: O 244 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7507 (mtm110) REVERT: O 253 LEU cc_start: 0.7923 (mt) cc_final: 0.7637 (mp) REVERT: O 376 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8355 (mtpp) REVERT: O 394 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6513 (ttpp) REVERT: P 244 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7324 (mtm110) REVERT: P 246 GLN cc_start: 0.8313 (tt0) cc_final: 0.7990 (tt0) REVERT: P 295 SER cc_start: 0.8865 (p) cc_final: 0.8603 (t) REVERT: P 394 LYS cc_start: 0.7141 (mmmt) cc_final: 0.6524 (mtpp) REVERT: Q 246 GLN cc_start: 0.8053 (tt0) cc_final: 0.7715 (tt0) REVERT: Q 275 LYS cc_start: 0.8529 (mtmp) cc_final: 0.8296 (mttm) REVERT: Q 303 GLN cc_start: 0.7769 (mt0) cc_final: 0.7528 (mt0) REVERT: Q 394 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6601 (ttpp) REVERT: R 244 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7325 (mtm110) REVERT: R 290 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: R 373 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: R 394 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6640 (mtpp) REVERT: S 244 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7682 (mtt-85) REVERT: S 287 ASP cc_start: 0.7458 (t0) cc_final: 0.6839 (p0) REVERT: S 394 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6527 (ttpp) REVERT: T 244 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7297 (mtp85) REVERT: T 394 LYS cc_start: 0.7524 (mmmt) cc_final: 0.6782 (ttpp) REVERT: U 246 GLN cc_start: 0.8197 (tt0) cc_final: 0.7903 (tt0) REVERT: U 377 MET cc_start: 0.8546 (mpt) cc_final: 0.8272 (mpt) REVERT: U 394 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6917 (ttpp) REVERT: V 244 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7247 (ptm160) REVERT: V 269 GLN cc_start: 0.8010 (mp10) cc_final: 0.7753 (mp-120) REVERT: V 356 ARG cc_start: 0.6853 (mtp180) cc_final: 0.6550 (ttp-170) REVERT: V 394 LYS cc_start: 0.7497 (mmmt) cc_final: 0.6731 (ttpp) REVERT: W 246 GLN cc_start: 0.8427 (tt0) cc_final: 0.8063 (tt0) REVERT: W 247 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7313 (mpp-170) REVERT: W 275 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8235 (mttt) REVERT: W 287 ASP cc_start: 0.7545 (t0) cc_final: 0.6990 (p0) REVERT: W 290 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8259 (mtpt) REVERT: W 370 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7323 (ttm-80) REVERT: W 431 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7803 (t0) REVERT: X 244 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7225 (mtp85) REVERT: X 247 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7877 (mtm110) REVERT: X 394 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6769 (ttpp) REVERT: Y 244 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7384 (mtp85) REVERT: Y 367 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8612 (mm-30) REVERT: Y 376 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8246 (mtpp) REVERT: Y 386 SER cc_start: 0.8880 (p) cc_final: 0.8471 (p) REVERT: Y 394 LYS cc_start: 0.7535 (mmmt) cc_final: 0.6783 (mtpp) REVERT: Z 244 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7343 (ptm160) REVERT: Z 356 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6583 (ttp-170) REVERT: Z 394 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6472 (mtpp) REVERT: a 244 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7247 (ptm160) REVERT: a 246 GLN cc_start: 0.8316 (tt0) cc_final: 0.7999 (tt0) REVERT: b 244 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7293 (ptm160) REVERT: b 246 GLN cc_start: 0.8294 (tt0) cc_final: 0.7937 (tt0) REVERT: b 247 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7425 (mtm110) REVERT: b 295 SER cc_start: 0.8768 (p) cc_final: 0.8480 (t) REVERT: b 361 ASN cc_start: 0.8633 (m-40) cc_final: 0.8361 (m-40) REVERT: b 394 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6362 (mtpp) REVERT: c 287 ASP cc_start: 0.7466 (t0) cc_final: 0.6939 (p0) REVERT: c 394 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6616 (ttpp) REVERT: d 244 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7187 (mtm110) REVERT: d 376 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8081 (mtpp) REVERT: d 377 MET cc_start: 0.8665 (mpt) cc_final: 0.8455 (mpt) REVERT: d 394 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6621 (mtpt) REVERT: d 431 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8132 (t0) REVERT: e 244 ARG cc_start: 0.7551 (ptm160) cc_final: 0.7212 (mtt-85) REVERT: e 246 GLN cc_start: 0.8369 (tt0) cc_final: 0.8101 (tt0) REVERT: e 275 LYS cc_start: 0.8478 (mtmp) cc_final: 0.8160 (mttm) REVERT: e 367 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8643 (mm-30) REVERT: e 394 LYS cc_start: 0.7172 (mmmt) cc_final: 0.6504 (tttp) REVERT: f 244 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7488 (mtm110) REVERT: f 253 LEU cc_start: 0.7920 (mt) cc_final: 0.7637 (mp) REVERT: f 376 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8352 (mtpp) REVERT: f 394 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6518 (ttpp) REVERT: g 244 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7325 (mtm110) REVERT: g 246 GLN cc_start: 0.8323 (tt0) cc_final: 0.7999 (tt0) REVERT: g 295 SER cc_start: 0.8857 (p) cc_final: 0.8597 (t) REVERT: g 394 LYS cc_start: 0.7140 (mmmt) cc_final: 0.6524 (mtpp) REVERT: h 244 ARG cc_start: 0.7433 (mtt90) cc_final: 0.7227 (ptm160) REVERT: h 247 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7760 (ttp-170) REVERT: h 275 LYS cc_start: 0.8527 (mtmp) cc_final: 0.8294 (mttm) REVERT: h 296 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7724 (ttm-80) REVERT: h 303 GLN cc_start: 0.7763 (mt0) cc_final: 0.7520 (mt0) REVERT: h 394 LYS cc_start: 0.7303 (mmmt) cc_final: 0.6602 (ttpp) REVERT: h 420 MET cc_start: 0.8615 (ptm) cc_final: 0.8407 (ptp) outliers start: 86 outliers final: 36 residues processed: 880 average time/residue: 1.0214 time to fit residues: 1040.7279 Evaluate side-chains 817 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 767 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain K residue 356 ARG Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain R residue 290 LYS Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 431 ASN Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain b residue 356 ARG Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 381 ASP Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 520 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 222 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 447 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN E 303 GLN F 303 GLN F 431 ASN G 269 GLN G 303 GLN H 303 GLN I 231 ASN J 303 GLN K 277 GLN K 303 GLN L 303 GLN M 431 ASN O 269 GLN O 431 ASN P 269 GLN P 303 GLN T 246 GLN V 303 GLN W 303 GLN W 431 ASN X 269 GLN Y 303 GLN Z 274 ASN a 303 GLN b 277 GLN b 303 GLN d 431 ASN f 269 GLN f 431 ASN g 269 GLN g 303 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122399 restraints weight = 48972.662| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.51 r_work: 0.3298 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 43826 Z= 0.156 Angle : 0.518 5.681 59194 Z= 0.276 Chirality : 0.042 0.165 6766 Planarity : 0.004 0.042 8024 Dihedral : 3.954 14.630 6018 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.21 % Allowed : 25.07 % Favored : 71.71 % 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 aren not related in a simple way. whole: 2.28 (0.12), residues: 5440 helix: 4.21 (0.12), residues: 1428 sheet: 0.91 (0.11), residues: 2618 loop : -0.23 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 356 TYR 0.006 0.001 TYR e 366 PHE 0.011 0.002 PHE U 422 HIS 0.003 0.001 HIS Z 263 Details of bonding type rmsd covalent geometry : bond 0.00364 (43826) covalent geometry : angle 0.51818 (59194) hydrogen bonds : bond 0.04083 ( 2619) hydrogen bonds : angle 4.24738 ( 7245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 794 time to evaluate : 1.766 Fit side-chains REVERT: A 244 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7524 (mtm110) REVERT: A 290 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8063 (mtmt) REVERT: A 373 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: A 394 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6636 (mtpp) REVERT: B 244 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7774 (mtt-85) REVERT: B 275 LYS cc_start: 0.8731 (mtmp) cc_final: 0.8492 (mtmp) REVERT: B 394 LYS cc_start: 0.7205 (mmmt) cc_final: 0.6777 (ttpp) REVERT: C 244 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: C 394 LYS cc_start: 0.7470 (mmmt) cc_final: 0.6788 (ttpp) REVERT: D 373 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8232 (ttt90) REVERT: D 394 LYS cc_start: 0.7589 (mmmt) cc_final: 0.6908 (ttpp) REVERT: E 244 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7459 (ptm160) REVERT: E 269 GLN cc_start: 0.8131 (mp10) cc_final: 0.7923 (mp-120) REVERT: E 356 ARG cc_start: 0.6977 (mtp180) cc_final: 0.6709 (ttp-170) REVERT: E 394 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6589 (ttpp) REVERT: F 246 GLN cc_start: 0.8304 (tt0) cc_final: 0.8022 (tt0) REVERT: F 275 LYS cc_start: 0.8652 (mtmp) cc_final: 0.8152 (mttt) REVERT: F 370 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7352 (ttm-80) REVERT: F 373 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7939 (tpp80) REVERT: F 394 LYS cc_start: 0.7541 (mmmt) cc_final: 0.6768 (ttpp) REVERT: G 244 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7235 (mtp85) REVERT: G 247 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7960 (mtm110) REVERT: G 394 LYS cc_start: 0.7357 (mmmt) cc_final: 0.6828 (ttpp) REVERT: H 244 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7604 (mtp85) REVERT: H 294 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8682 (ttm170) REVERT: H 376 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: H 394 LYS cc_start: 0.7504 (mmmt) cc_final: 0.6774 (mtpp) REVERT: I 244 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7386 (mtp85) REVERT: I 356 ARG cc_start: 0.6913 (mtp180) cc_final: 0.6689 (ttp-170) REVERT: I 376 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8335 (mtpp) REVERT: I 394 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6490 (mtpp) REVERT: J 244 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7396 (ptm160) REVERT: J 246 GLN cc_start: 0.8286 (tt0) cc_final: 0.7968 (tt0) REVERT: J 373 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7780 (ttp-170) REVERT: J 394 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6675 (ttpp) REVERT: K 244 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7591 (mtp85) REVERT: K 246 GLN cc_start: 0.8365 (tt0) cc_final: 0.8034 (tt0) REVERT: K 361 ASN cc_start: 0.8631 (m-40) cc_final: 0.8313 (m-40) REVERT: K 394 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6220 (mtpp) REVERT: L 244 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7622 (mtp85) REVERT: L 394 LYS cc_start: 0.7167 (mmmt) cc_final: 0.6592 (ttpp) REVERT: M 244 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7317 (mtm110) REVERT: M 246 GLN cc_start: 0.8237 (tt0) cc_final: 0.7967 (tt0) REVERT: M 376 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: M 394 LYS cc_start: 0.7329 (mmmt) cc_final: 0.6776 (mtpt) REVERT: M 431 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: N 244 ARG cc_start: 0.7597 (ptm160) cc_final: 0.7362 (mtt-85) REVERT: N 246 GLN cc_start: 0.8459 (tt0) cc_final: 0.8193 (tt0) REVERT: N 275 LYS cc_start: 0.8538 (mtmp) cc_final: 0.8249 (mttm) REVERT: N 367 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8684 (mm-30) REVERT: N 394 LYS cc_start: 0.7114 (mmmt) cc_final: 0.6550 (tttp) REVERT: O 244 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7653 (mtm110) REVERT: O 376 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8389 (mtpp) REVERT: O 394 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6546 (ttpp) REVERT: P 244 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7429 (mtm110) REVERT: P 246 GLN cc_start: 0.8368 (tt0) cc_final: 0.8061 (tt0) REVERT: P 394 LYS cc_start: 0.7111 (mmmt) cc_final: 0.6665 (ttpp) REVERT: Q 275 LYS cc_start: 0.8590 (mtmp) cc_final: 0.8333 (mttm) REVERT: Q 394 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6659 (ttpp) REVERT: R 244 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7518 (mtm110) REVERT: R 290 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: R 373 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7540 (ttp-170) REVERT: R 394 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6635 (mtpp) REVERT: S 244 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7768 (mtt-85) REVERT: S 275 LYS cc_start: 0.8732 (mtmp) cc_final: 0.8421 (mtmp) REVERT: S 377 MET cc_start: 0.8452 (mpt) cc_final: 0.7984 (mpt) REVERT: S 394 LYS cc_start: 0.7216 (mmmt) cc_final: 0.6784 (ttpp) REVERT: T 244 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7405 (mtp85) REVERT: T 394 LYS cc_start: 0.7471 (mmmt) cc_final: 0.6793 (ttpp) REVERT: U 373 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8246 (ttt90) REVERT: U 377 MET cc_start: 0.8579 (mpt) cc_final: 0.8241 (mpt) REVERT: U 394 LYS cc_start: 0.7587 (mmmt) cc_final: 0.6911 (ttpp) REVERT: V 244 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7448 (ptm160) REVERT: V 269 GLN cc_start: 0.8130 (mp10) cc_final: 0.7919 (mp-120) REVERT: V 356 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6707 (ttp-170) REVERT: V 373 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: V 394 LYS cc_start: 0.7337 (mmmt) cc_final: 0.6592 (ttpp) REVERT: W 246 GLN cc_start: 0.8309 (tt0) cc_final: 0.8022 (tt0) REVERT: W 275 LYS cc_start: 0.8659 (mtmp) cc_final: 0.8160 (mttt) REVERT: W 370 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7364 (ttm-80) REVERT: W 373 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7947 (tpp80) REVERT: W 394 LYS cc_start: 0.7530 (mmmt) cc_final: 0.6766 (ttpp) REVERT: X 244 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7240 (mtp85) REVERT: X 247 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7955 (mtm110) REVERT: X 394 LYS cc_start: 0.7361 (mmmt) cc_final: 0.6831 (ttpp) REVERT: Y 244 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7605 (mtp85) REVERT: Y 294 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8674 (ttm170) REVERT: Y 376 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: Y 394 LYS cc_start: 0.7506 (mmmt) cc_final: 0.6778 (mtpp) REVERT: Z 244 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7388 (mtp85) REVERT: Z 356 ARG cc_start: 0.6916 (mtp180) cc_final: 0.6700 (ttp-170) REVERT: Z 376 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8342 (mtpp) REVERT: Z 394 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6489 (mtpp) REVERT: a 244 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7402 (ptm160) REVERT: a 246 GLN cc_start: 0.8289 (tt0) cc_final: 0.7963 (tt0) REVERT: a 373 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7774 (ttp-170) REVERT: a 394 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6676 (ttpp) REVERT: b 244 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7598 (mtp85) REVERT: b 246 GLN cc_start: 0.8376 (tt0) cc_final: 0.8046 (tt0) REVERT: b 361 ASN cc_start: 0.8638 (m-40) cc_final: 0.8319 (m-40) REVERT: b 394 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6232 (mtpp) REVERT: c 244 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7649 (mtp85) REVERT: c 394 LYS cc_start: 0.7172 (mmmt) cc_final: 0.6598 (ttpp) REVERT: d 244 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7316 (mtm110) REVERT: d 246 GLN cc_start: 0.8234 (tt0) cc_final: 0.7965 (tt0) REVERT: d 376 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: d 394 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6778 (mtpt) REVERT: d 431 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8128 (m-40) REVERT: e 244 ARG cc_start: 0.7594 (ptm160) cc_final: 0.7362 (mtt-85) REVERT: e 246 GLN cc_start: 0.8455 (tt0) cc_final: 0.8193 (tt0) REVERT: e 275 LYS cc_start: 0.8540 (mtmp) cc_final: 0.8253 (mttm) REVERT: e 367 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8698 (mm-30) REVERT: e 394 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6552 (tttp) REVERT: f 244 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7654 (mtm110) REVERT: f 376 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8406 (mtpp) REVERT: f 394 LYS cc_start: 0.7243 (mmmt) cc_final: 0.6541 (ttpp) REVERT: g 244 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7424 (mtm110) REVERT: g 246 GLN cc_start: 0.8367 (tt0) cc_final: 0.8055 (tt0) REVERT: g 394 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6672 (ttpp) REVERT: h 244 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7413 (ptm160) REVERT: h 275 LYS cc_start: 0.8582 (mtmp) cc_final: 0.8325 (mttm) REVERT: h 394 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6664 (ttpp) outliers start: 154 outliers final: 78 residues processed: 896 average time/residue: 1.0697 time to fit residues: 1110.5329 Evaluate side-chains 884 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 781 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain H residue 294 ARG Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 290 LYS Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 247 ARG Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain Y residue 294 ARG Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 356 ARG Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 373 ARG Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 381 ASP Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 200 optimal weight: 5.9990 chunk 488 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 533 optimal weight: 3.9990 chunk 220 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 539 optimal weight: 2.9990 chunk 450 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN C 303 GLN E 303 GLN G 269 GLN H 303 GLN J 303 GLN K 297 GLN K 303 GLN M 431 ASN N 269 GLN O 431 ASN P 269 GLN P 303 GLN R 277 GLN T 303 GLN V 303 GLN X 269 GLN Y 303 GLN a 303 GLN b 297 GLN b 303 GLN d 431 ASN e 269 GLN f 431 ASN g 269 GLN g 303 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119859 restraints weight = 49244.557| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.56 r_work: 0.3257 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 43826 Z= 0.198 Angle : 0.544 5.702 59194 Z= 0.290 Chirality : 0.043 0.176 6766 Planarity : 0.004 0.041 8024 Dihedral : 4.127 16.188 6018 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 4.21 % Allowed : 23.70 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.12), residues: 5440 helix: 4.01 (0.13), residues: 1428 sheet: 0.79 (0.11), residues: 2618 loop : -0.24 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 356 TYR 0.007 0.002 TYR e 366 PHE 0.014 0.002 PHE D 422 HIS 0.003 0.001 HIS W 263 Details of bonding type rmsd covalent geometry : bond 0.00467 (43826) covalent geometry : angle 0.54355 (59194) hydrogen bonds : bond 0.04335 ( 2619) hydrogen bonds : angle 4.41565 ( 7245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 814 time to evaluate : 1.742 Fit side-chains REVERT: A 244 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7647 (mtm110) REVERT: A 290 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: A 373 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7680 (ttp-170) REVERT: A 394 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6657 (ttpp) REVERT: B 244 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7809 (mtt-85) REVERT: B 246 GLN cc_start: 0.8359 (tt0) cc_final: 0.8066 (tt0) REVERT: B 275 LYS cc_start: 0.8839 (mtmp) cc_final: 0.8547 (mtmp) REVERT: B 359 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: B 377 MET cc_start: 0.8457 (mpt) cc_final: 0.8108 (mpt) REVERT: B 394 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6824 (ttpp) REVERT: C 244 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: C 394 LYS cc_start: 0.7552 (mmmt) cc_final: 0.6926 (ttpp) REVERT: C 416 THR cc_start: 0.8223 (m) cc_final: 0.7919 (p) REVERT: C 424 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: D 244 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7324 (mtt-85) REVERT: D 370 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8326 (ttm170) REVERT: D 373 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8221 (ttt90) REVERT: D 394 LYS cc_start: 0.7601 (mmmt) cc_final: 0.6863 (ttpp) REVERT: E 244 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7443 (mtp85) REVERT: E 356 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6747 (ttp-170) REVERT: E 394 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6540 (ttpp) REVERT: F 246 GLN cc_start: 0.8360 (tt0) cc_final: 0.8031 (tt0) REVERT: F 247 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7354 (mpp-170) REVERT: F 275 LYS cc_start: 0.8757 (mtmp) cc_final: 0.8414 (mttm) REVERT: F 370 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7308 (ttm-80) REVERT: F 373 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (tpp80) REVERT: F 394 LYS cc_start: 0.7502 (mmmt) cc_final: 0.6899 (ttpp) REVERT: G 244 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7371 (mtp85) REVERT: G 247 ARG cc_start: 0.8214 (mtm180) cc_final: 0.8010 (mtm110) REVERT: G 394 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6849 (ttpp) REVERT: H 244 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7657 (mtp85) REVERT: H 376 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8494 (mtpp) REVERT: H 394 LYS cc_start: 0.7541 (mmmt) cc_final: 0.6790 (mtpp) REVERT: I 244 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7443 (mtp85) REVERT: I 290 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8003 (ptmt) REVERT: I 356 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6686 (ttp-170) REVERT: I 394 LYS cc_start: 0.7211 (mmmt) cc_final: 0.6493 (mtpp) REVERT: J 244 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7635 (mtp85) REVERT: J 246 GLN cc_start: 0.8323 (tt0) cc_final: 0.7999 (tt0) REVERT: J 281 HIS cc_start: 0.7862 (m90) cc_final: 0.7617 (m90) REVERT: J 376 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8244 (mtpp) REVERT: J 394 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6685 (ttpp) REVERT: K 244 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7609 (mtm110) REVERT: K 246 GLN cc_start: 0.8300 (tt0) cc_final: 0.7879 (tt0) REVERT: K 361 ASN cc_start: 0.8657 (m-40) cc_final: 0.8313 (m-40) REVERT: K 394 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6302 (ttpp) REVERT: L 244 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7659 (mtp85) REVERT: L 373 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8133 (ttt180) REVERT: L 394 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6631 (ttpp) REVERT: L 416 THR cc_start: 0.8083 (m) cc_final: 0.7876 (p) REVERT: M 244 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7368 (mtm110) REVERT: M 246 GLN cc_start: 0.8390 (tt0) cc_final: 0.8166 (tt0) REVERT: M 394 LYS cc_start: 0.7425 (mmmt) cc_final: 0.6833 (ttpt) REVERT: M 416 THR cc_start: 0.8275 (m) cc_final: 0.7984 (p) REVERT: M 431 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: N 244 ARG cc_start: 0.7632 (ptm160) cc_final: 0.7396 (mtt-85) REVERT: N 275 LYS cc_start: 0.8656 (mtmp) cc_final: 0.8381 (mttm) REVERT: N 370 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7717 (ttm-80) REVERT: N 394 LYS cc_start: 0.7182 (mmmt) cc_final: 0.6667 (ttpp) REVERT: O 244 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7623 (mtm110) REVERT: O 376 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: P 244 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7540 (mtm110) REVERT: P 246 GLN cc_start: 0.8390 (tt0) cc_final: 0.8110 (tt0) REVERT: P 247 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (mtm110) REVERT: P 394 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6628 (ttpp) REVERT: Q 246 GLN cc_start: 0.8266 (tt0) cc_final: 0.8053 (tt0) REVERT: Q 275 LYS cc_start: 0.8656 (mtmp) cc_final: 0.8396 (mttm) REVERT: Q 394 LYS cc_start: 0.7297 (mmmt) cc_final: 0.6723 (ttpp) REVERT: R 244 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7656 (mtm110) REVERT: R 290 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (mtmt) REVERT: R 373 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: R 376 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8293 (mtpp) REVERT: R 394 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6650 (ttpp) REVERT: S 244 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7813 (mtt-85) REVERT: S 246 GLN cc_start: 0.8354 (tt0) cc_final: 0.8065 (tt0) REVERT: S 275 LYS cc_start: 0.8843 (mtmp) cc_final: 0.8535 (mtmp) REVERT: S 359 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: S 376 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8473 (mtpp) REVERT: S 377 MET cc_start: 0.8480 (mpt) cc_final: 0.8150 (mpt) REVERT: S 394 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6839 (ttpp) REVERT: T 244 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7442 (mtp85) REVERT: T 394 LYS cc_start: 0.7555 (mmmt) cc_final: 0.6917 (ttpp) REVERT: U 244 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7323 (mtt-85) REVERT: U 370 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8331 (ttm170) REVERT: U 373 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: U 377 MET cc_start: 0.8624 (mpt) cc_final: 0.8304 (mpt) REVERT: U 394 LYS cc_start: 0.7604 (mmmt) cc_final: 0.6871 (ttpp) REVERT: V 244 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7438 (mtp85) REVERT: V 356 ARG cc_start: 0.6965 (mtp180) cc_final: 0.6683 (ttp-170) REVERT: V 373 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (tpp-160) REVERT: V 394 LYS cc_start: 0.7439 (mmmt) cc_final: 0.6547 (ttpp) REVERT: W 246 GLN cc_start: 0.8364 (tt0) cc_final: 0.8032 (tt0) REVERT: W 247 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7361 (mpp-170) REVERT: W 275 LYS cc_start: 0.8763 (mtmp) cc_final: 0.8421 (mttm) REVERT: W 373 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8003 (tpp80) REVERT: W 394 LYS cc_start: 0.7503 (mmmt) cc_final: 0.6903 (ttpp) REVERT: X 244 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7378 (mtp85) REVERT: X 247 ARG cc_start: 0.8213 (mtm180) cc_final: 0.8006 (mtm110) REVERT: X 394 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6856 (ttpp) REVERT: Y 244 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7661 (mtp85) REVERT: Y 376 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (mtpp) REVERT: Y 394 LYS cc_start: 0.7542 (mmmt) cc_final: 0.6792 (mtpp) REVERT: Z 244 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7453 (mtp85) REVERT: Z 290 LYS cc_start: 0.8521 (mtmm) cc_final: 0.7986 (ptmt) REVERT: Z 356 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6718 (ttp-170) REVERT: Z 394 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6498 (mtpp) REVERT: a 244 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7634 (mtp85) REVERT: a 246 GLN cc_start: 0.8323 (tt0) cc_final: 0.8001 (tt0) REVERT: a 281 HIS cc_start: 0.7857 (m90) cc_final: 0.7623 (m90) REVERT: a 376 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8242 (mtpp) REVERT: a 394 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6687 (ttpp) REVERT: b 244 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7625 (mtm110) REVERT: b 246 GLN cc_start: 0.8310 (tt0) cc_final: 0.7888 (tt0) REVERT: b 361 ASN cc_start: 0.8670 (m-40) cc_final: 0.8319 (m-40) REVERT: b 394 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6301 (ttpp) REVERT: c 244 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7665 (mtp85) REVERT: c 373 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: c 394 LYS cc_start: 0.7178 (mmmt) cc_final: 0.6630 (ttpp) REVERT: c 416 THR cc_start: 0.8087 (m) cc_final: 0.7881 (p) REVERT: d 244 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7375 (mtm110) REVERT: d 246 GLN cc_start: 0.8392 (tt0) cc_final: 0.8172 (tt0) REVERT: d 394 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6832 (ttpt) REVERT: d 416 THR cc_start: 0.8265 (m) cc_final: 0.7979 (p) REVERT: d 431 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: e 244 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7406 (mtt-85) REVERT: e 275 LYS cc_start: 0.8656 (mtmp) cc_final: 0.8380 (mttm) REVERT: e 370 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7686 (ttm-80) REVERT: e 394 LYS cc_start: 0.7185 (mmmt) cc_final: 0.6667 (ttpp) REVERT: f 244 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7615 (mtm110) REVERT: f 376 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8393 (mtpp) REVERT: g 244 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7556 (mtm110) REVERT: g 246 GLN cc_start: 0.8394 (tt0) cc_final: 0.8122 (tt0) REVERT: g 394 LYS cc_start: 0.7025 (mmmt) cc_final: 0.6619 (ttpp) REVERT: h 244 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7486 (mtm110) REVERT: h 275 LYS cc_start: 0.8659 (mtmp) cc_final: 0.8356 (mttm) REVERT: h 296 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7835 (ttm-80) REVERT: h 367 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8724 (mm-30) REVERT: h 394 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6720 (ttpp) outliers start: 202 outliers final: 87 residues processed: 943 average time/residue: 1.0600 time to fit residues: 1159.6170 Evaluate side-chains 912 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 791 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 373 ARG Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 247 ARG Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 290 LYS Chi-restraints excluded: chain R residue 356 ARG Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 247 ARG Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 247 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 356 ARG Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 373 ARG Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 251 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 470 optimal weight: 0.4980 chunk 398 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN E 303 GLN G 269 GLN J 303 GLN K 297 GLN K 303 GLN N 269 GLN O 431 ASN P 269 GLN S 269 GLN V 303 GLN X 269 GLN a 303 GLN b 297 GLN b 303 GLN e 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121621 restraints weight = 49146.220| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.57 r_work: 0.3276 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43826 Z= 0.135 Angle : 0.488 5.404 59194 Z= 0.259 Chirality : 0.040 0.135 6766 Planarity : 0.003 0.040 8024 Dihedral : 3.929 15.639 6018 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.98 % Allowed : 25.01 % Favored : 72.01 % 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 aren not related in a simple way. whole: 2.21 (0.12), residues: 5440 helix: 4.13 (0.13), residues: 1428 sheet: 0.85 (0.10), residues: 2618 loop : -0.19 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 356 TYR 0.004 0.001 TYR O 282 PHE 0.009 0.002 PHE U 422 HIS 0.003 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00317 (43826) covalent geometry : angle 0.48796 (59194) hydrogen bonds : bond 0.03566 ( 2619) hydrogen bonds : angle 4.18999 ( 7245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 793 time to evaluate : 1.530 Fit side-chains REVERT: A 244 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7557 (mtm110) REVERT: A 290 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: A 373 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7730 (ttp-170) REVERT: A 376 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: A 394 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6713 (ttpp) REVERT: B 244 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7785 (mtt-85) REVERT: B 246 GLN cc_start: 0.8347 (tt0) cc_final: 0.8068 (tt0) REVERT: B 275 LYS cc_start: 0.8822 (mtmp) cc_final: 0.8485 (mtmp) REVERT: B 359 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: B 376 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: B 377 MET cc_start: 0.8528 (mpt) cc_final: 0.8109 (mpt) REVERT: B 394 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6921 (ttpp) REVERT: C 244 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: C 246 GLN cc_start: 0.8091 (tt0) cc_final: 0.7548 (tt0) REVERT: C 394 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6814 (ttpp) REVERT: D 244 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7324 (mtt-85) REVERT: D 246 GLN cc_start: 0.8201 (tt0) cc_final: 0.7944 (tt0) REVERT: D 394 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6870 (ttpp) REVERT: E 244 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7608 (mtp85) REVERT: E 356 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6671 (ttp-170) REVERT: E 394 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6534 (ttpp) REVERT: F 246 GLN cc_start: 0.8344 (tt0) cc_final: 0.8075 (tt0) REVERT: F 247 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7290 (mpp-170) REVERT: F 275 LYS cc_start: 0.8749 (mtmp) cc_final: 0.8380 (mttm) REVERT: F 370 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7331 (ttm-80) REVERT: F 373 ARG cc_start: 0.8298 (ttt90) cc_final: 0.7983 (tpp80) REVERT: F 376 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8244 (mtpt) REVERT: F 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6721 (ttpp) REVERT: G 244 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7311 (mtp85) REVERT: G 246 GLN cc_start: 0.8230 (tt0) cc_final: 0.7778 (tt0) REVERT: G 394 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6754 (ttpp) REVERT: H 244 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7633 (mtp85) REVERT: H 373 ARG cc_start: 0.8484 (ttt180) cc_final: 0.8249 (ttt180) REVERT: H 376 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8425 (mtpp) REVERT: H 394 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6721 (mtpp) REVERT: I 244 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7497 (mtp85) REVERT: I 290 LYS cc_start: 0.8500 (mtmm) cc_final: 0.7980 (ptmt) REVERT: I 394 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6538 (mtpp) REVERT: J 246 GLN cc_start: 0.8318 (tt0) cc_final: 0.7995 (tt0) REVERT: J 281 HIS cc_start: 0.7899 (m90) cc_final: 0.7645 (m90) REVERT: J 376 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8228 (mtpp) REVERT: J 394 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6725 (ttpp) REVERT: K 244 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7617 (mtp85) REVERT: K 246 GLN cc_start: 0.8270 (tt0) cc_final: 0.7835 (tt0) REVERT: K 361 ASN cc_start: 0.8685 (m-40) cc_final: 0.8377 (m-40) REVERT: K 383 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: K 394 LYS cc_start: 0.7210 (mmmt) cc_final: 0.6495 (ttpp) REVERT: K 415 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7593 (mt) REVERT: L 244 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7608 (mtp85) REVERT: L 394 LYS cc_start: 0.7268 (mmmt) cc_final: 0.6784 (ttpp) REVERT: L 415 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7830 (mt) REVERT: M 244 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7340 (mtm110) REVERT: M 394 LYS cc_start: 0.7376 (mmmt) cc_final: 0.6825 (ttpt) REVERT: N 244 ARG cc_start: 0.7588 (ptm160) cc_final: 0.7364 (mtt-85) REVERT: N 246 GLN cc_start: 0.8484 (tt0) cc_final: 0.8114 (tt0) REVERT: N 275 LYS cc_start: 0.8629 (mtmp) cc_final: 0.8334 (mttm) REVERT: N 370 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7690 (ttm-80) REVERT: N 394 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6598 (ttpp) REVERT: O 244 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7685 (mtm110) REVERT: O 376 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: P 244 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7494 (mtp85) REVERT: P 246 GLN cc_start: 0.8398 (tt0) cc_final: 0.8104 (tt0) REVERT: P 359 GLN cc_start: 0.7599 (tt0) cc_final: 0.7391 (tm-30) REVERT: P 394 LYS cc_start: 0.6999 (mmmt) cc_final: 0.6600 (ttpp) REVERT: Q 246 GLN cc_start: 0.8253 (tt0) cc_final: 0.7989 (tt0) REVERT: Q 275 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8372 (mttm) REVERT: Q 394 LYS cc_start: 0.7291 (mmmt) cc_final: 0.6740 (ttpp) REVERT: Q 418 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8184 (mm-30) REVERT: R 244 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7577 (mtm110) REVERT: R 290 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8091 (mtmt) REVERT: R 373 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7723 (ttp-170) REVERT: R 376 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: R 394 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6717 (ttpp) REVERT: S 244 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7785 (mtt-85) REVERT: S 246 GLN cc_start: 0.8349 (tt0) cc_final: 0.8071 (tt0) REVERT: S 275 LYS cc_start: 0.8825 (mtmp) cc_final: 0.8503 (mtmp) REVERT: S 359 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: S 377 MET cc_start: 0.8542 (mpt) cc_final: 0.8129 (mpt) REVERT: S 394 LYS cc_start: 0.7405 (mmmt) cc_final: 0.6936 (ttpp) REVERT: T 244 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7382 (mtp85) REVERT: T 246 GLN cc_start: 0.8159 (tt0) cc_final: 0.7653 (tt0) REVERT: T 394 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6817 (ttpp) REVERT: U 244 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7339 (mtt-85) REVERT: U 246 GLN cc_start: 0.8208 (tt0) cc_final: 0.7945 (tt0) REVERT: U 377 MET cc_start: 0.8611 (mpt) cc_final: 0.8256 (mpt) REVERT: U 394 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6878 (ttpp) REVERT: V 244 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7608 (mtp85) REVERT: V 356 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6666 (ttp-170) REVERT: V 394 LYS cc_start: 0.7342 (mmmt) cc_final: 0.6542 (ttpp) REVERT: W 246 GLN cc_start: 0.8351 (tt0) cc_final: 0.8051 (tt0) REVERT: W 247 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7300 (mpp-170) REVERT: W 275 LYS cc_start: 0.8750 (mtmp) cc_final: 0.8379 (mttm) REVERT: W 370 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7391 (ttm-80) REVERT: W 373 ARG cc_start: 0.8315 (ttt90) cc_final: 0.8005 (tpp80) REVERT: W 376 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8243 (mtpt) REVERT: W 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6726 (ttpp) REVERT: X 244 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7314 (mtp85) REVERT: X 246 GLN cc_start: 0.8242 (tt0) cc_final: 0.7789 (tt0) REVERT: X 394 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6754 (ttpp) REVERT: Y 244 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7640 (mtp85) REVERT: Y 373 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8240 (ttt180) REVERT: Y 376 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8437 (mtpp) REVERT: Y 394 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6718 (mtpp) REVERT: Z 244 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7498 (mtp85) REVERT: Z 290 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7970 (ptmt) REVERT: Z 394 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6580 (mtpp) REVERT: a 244 ARG cc_start: 0.7649 (mtt90) cc_final: 0.7390 (mtp85) REVERT: a 246 GLN cc_start: 0.8312 (tt0) cc_final: 0.7989 (tt0) REVERT: a 281 HIS cc_start: 0.7895 (m90) cc_final: 0.7647 (m90) REVERT: a 394 LYS cc_start: 0.7263 (mmmt) cc_final: 0.6725 (ttpp) REVERT: b 244 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7625 (mtp85) REVERT: b 246 GLN cc_start: 0.8277 (tt0) cc_final: 0.7839 (tt0) REVERT: b 361 ASN cc_start: 0.8688 (m-40) cc_final: 0.8378 (m-40) REVERT: b 383 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: b 394 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6504 (ttpp) REVERT: b 415 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7547 (mt) REVERT: c 244 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7607 (mtp85) REVERT: c 394 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6786 (ttpp) REVERT: c 415 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7846 (mt) REVERT: d 244 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7350 (mtm110) REVERT: d 377 MET cc_start: 0.8628 (mpt) cc_final: 0.8423 (mpt) REVERT: d 394 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6825 (ttpt) REVERT: e 244 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7361 (mtt-85) REVERT: e 246 GLN cc_start: 0.8475 (tt0) cc_final: 0.8105 (tt0) REVERT: e 275 LYS cc_start: 0.8626 (mtmp) cc_final: 0.8328 (mttm) REVERT: e 370 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7703 (ttm-80) REVERT: e 394 LYS cc_start: 0.7128 (mmmt) cc_final: 0.6601 (ttpp) REVERT: f 244 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7670 (mtm110) REVERT: f 376 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: g 244 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7486 (mtp85) REVERT: g 246 GLN cc_start: 0.8400 (tt0) cc_final: 0.8105 (tt0) REVERT: g 394 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6608 (ttpp) REVERT: h 244 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7492 (mtm110) REVERT: h 246 GLN cc_start: 0.8236 (tt0) cc_final: 0.7949 (tt0) REVERT: h 275 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8383 (mttm) REVERT: h 296 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7813 (ttm-80) REVERT: h 394 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6753 (ttpp) REVERT: h 418 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8196 (mm-30) outliers start: 143 outliers final: 84 residues processed: 886 average time/residue: 0.9621 time to fit residues: 992.8922 Evaluate side-chains 893 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 781 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 290 LYS Chi-restraints excluded: chain R residue 356 ARG Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 247 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 253 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 267 optimal weight: 1.9990 chunk 445 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 423 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 72 optimal weight: 6.9990 chunk 290 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN G 269 GLN J 303 GLN K 303 GLN N 269 GLN O 431 ASN P 269 GLN V 303 GLN X 269 GLN a 303 GLN b 303 GLN e 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123000 restraints weight = 48648.645| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.56 r_work: 0.3293 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43826 Z= 0.103 Angle : 0.456 5.660 59194 Z= 0.241 Chirality : 0.039 0.122 6766 Planarity : 0.003 0.048 8024 Dihedral : 3.768 16.278 6018 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.42 % Allowed : 25.89 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.12), residues: 5440 helix: 4.28 (0.13), residues: 1428 sheet: 0.95 (0.10), residues: 2618 loop : -0.17 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 356 TYR 0.004 0.001 TYR X 366 PHE 0.007 0.001 PHE g 237 HIS 0.002 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00239 (43826) covalent geometry : angle 0.45560 (59194) hydrogen bonds : bond 0.03071 ( 2619) hydrogen bonds : angle 3.96061 ( 7245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 795 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 244 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7597 (mtm110) REVERT: A 373 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7690 (ttp-170) REVERT: A 376 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: A 394 LYS cc_start: 0.7421 (mmmt) cc_final: 0.7017 (ttpp) REVERT: B 244 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7743 (mtt-85) REVERT: B 246 GLN cc_start: 0.8341 (tt0) cc_final: 0.7965 (tt0) REVERT: B 275 LYS cc_start: 0.8835 (mtmp) cc_final: 0.8495 (mtmp) REVERT: B 377 MET cc_start: 0.8545 (mpt) cc_final: 0.8087 (mpt) REVERT: B 394 LYS cc_start: 0.7314 (mmmt) cc_final: 0.6871 (ttpp) REVERT: C 244 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7365 (mtp85) REVERT: C 246 GLN cc_start: 0.8052 (tt0) cc_final: 0.7513 (tt0) REVERT: C 394 LYS cc_start: 0.7403 (mmmt) cc_final: 0.6748 (ttpp) REVERT: D 244 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7320 (mtt-85) REVERT: D 246 GLN cc_start: 0.8171 (tt0) cc_final: 0.7893 (tt0) REVERT: D 373 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (ttt180) REVERT: D 377 MET cc_start: 0.8460 (mpt) cc_final: 0.8146 (mpt) REVERT: D 394 LYS cc_start: 0.7434 (mmmt) cc_final: 0.6911 (ttpp) REVERT: E 244 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7659 (mtp85) REVERT: E 356 ARG cc_start: 0.6812 (mtp180) cc_final: 0.6521 (ttp-170) REVERT: E 394 LYS cc_start: 0.7348 (mmmt) cc_final: 0.6569 (ttpp) REVERT: F 246 GLN cc_start: 0.8291 (tt0) cc_final: 0.8014 (tt0) REVERT: F 247 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7190 (mpp-170) REVERT: F 275 LYS cc_start: 0.8726 (mtmp) cc_final: 0.8277 (mttt) REVERT: F 370 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7259 (ttm-80) REVERT: F 373 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8023 (tpp80) REVERT: F 394 LYS cc_start: 0.7239 (mmmt) cc_final: 0.6666 (ttpp) REVERT: G 244 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7246 (mtp85) REVERT: G 246 GLN cc_start: 0.8193 (tt0) cc_final: 0.7662 (tt0) REVERT: G 247 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7680 (mtm180) REVERT: G 394 LYS cc_start: 0.7160 (mmmt) cc_final: 0.6594 (ttpp) REVERT: H 244 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7654 (mtp85) REVERT: H 373 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8268 (ttt180) REVERT: H 376 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8430 (mtpp) REVERT: H 394 LYS cc_start: 0.7362 (mmmt) cc_final: 0.6891 (ttpp) REVERT: H 414 ASP cc_start: 0.7517 (m-30) cc_final: 0.7314 (m-30) REVERT: I 244 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7463 (mtp85) REVERT: I 290 LYS cc_start: 0.8482 (mtmm) cc_final: 0.7977 (ptmt) REVERT: I 394 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6581 (mtpp) REVERT: J 246 GLN cc_start: 0.8314 (tt0) cc_final: 0.7973 (tt0) REVERT: J 281 HIS cc_start: 0.7897 (m90) cc_final: 0.7636 (m90) REVERT: J 373 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7756 (ttp-170) REVERT: J 394 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6724 (ttpp) REVERT: K 244 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7613 (mtp85) REVERT: K 246 GLN cc_start: 0.8392 (tt0) cc_final: 0.7879 (tt0) REVERT: K 361 ASN cc_start: 0.8694 (m-40) cc_final: 0.8442 (m-40) REVERT: K 383 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: K 394 LYS cc_start: 0.7230 (mmmt) cc_final: 0.6520 (ttpp) REVERT: K 415 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7525 (mt) REVERT: L 244 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7610 (mtp85) REVERT: L 373 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8163 (ttt180) REVERT: L 394 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6839 (ttpp) REVERT: M 246 GLN cc_start: 0.8137 (tt0) cc_final: 0.7605 (tt0) REVERT: M 394 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6825 (ttpt) REVERT: N 244 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7337 (mtt-85) REVERT: N 246 GLN cc_start: 0.8454 (tt0) cc_final: 0.8170 (tt0) REVERT: N 275 LYS cc_start: 0.8648 (mtmp) cc_final: 0.8361 (mttm) REVERT: N 370 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: N 394 LYS cc_start: 0.7143 (mmmt) cc_final: 0.6588 (ttpp) REVERT: O 244 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7655 (mtm110) REVERT: O 246 GLN cc_start: 0.8204 (tt0) cc_final: 0.7801 (tt0) REVERT: O 295 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8583 (t) REVERT: O 376 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: P 244 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7471 (mtp85) REVERT: P 246 GLN cc_start: 0.8424 (tt0) cc_final: 0.8142 (tt0) REVERT: P 394 LYS cc_start: 0.6975 (mmmt) cc_final: 0.6578 (ttpp) REVERT: Q 246 GLN cc_start: 0.8156 (tt0) cc_final: 0.7900 (tt0) REVERT: Q 275 LYS cc_start: 0.8636 (mtmp) cc_final: 0.8336 (mttm) REVERT: Q 276 GLU cc_start: 0.8058 (tt0) cc_final: 0.7762 (mt-10) REVERT: Q 394 LYS cc_start: 0.7278 (mmmt) cc_final: 0.6844 (ttpp) REVERT: Q 418 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8159 (mm-30) REVERT: R 244 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7583 (mtm110) REVERT: R 373 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: R 376 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: R 394 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7018 (ttpp) REVERT: S 244 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7732 (mtt-85) REVERT: S 246 GLN cc_start: 0.8329 (tt0) cc_final: 0.7946 (tt0) REVERT: S 275 LYS cc_start: 0.8887 (mtmp) cc_final: 0.8556 (mtmp) REVERT: S 377 MET cc_start: 0.8546 (mpt) cc_final: 0.8076 (mpt) REVERT: S 394 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6881 (ttpp) REVERT: T 244 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7348 (mtp85) REVERT: T 246 GLN cc_start: 0.8050 (tt0) cc_final: 0.7517 (tt0) REVERT: T 394 LYS cc_start: 0.7398 (mmmt) cc_final: 0.6748 (ttpp) REVERT: U 244 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7326 (mtt-85) REVERT: U 246 GLN cc_start: 0.8197 (tt0) cc_final: 0.7922 (tt0) REVERT: U 377 MET cc_start: 0.8590 (mpt) cc_final: 0.8196 (mpt) REVERT: U 394 LYS cc_start: 0.7425 (mmmt) cc_final: 0.6917 (ttpp) REVERT: V 244 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7630 (mtp85) REVERT: V 356 ARG cc_start: 0.6808 (mtp180) cc_final: 0.6514 (ttp-170) REVERT: V 373 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8128 (tpp-160) REVERT: V 394 LYS cc_start: 0.7349 (mmmt) cc_final: 0.6570 (ttpp) REVERT: W 246 GLN cc_start: 0.8288 (tt0) cc_final: 0.8010 (tt0) REVERT: W 247 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7197 (mpp-170) REVERT: W 275 LYS cc_start: 0.8737 (mtmp) cc_final: 0.8288 (mttt) REVERT: W 370 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7358 (ttm-80) REVERT: W 373 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8016 (tpp80) REVERT: W 394 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6674 (ttpp) REVERT: X 244 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7249 (mtp85) REVERT: X 246 GLN cc_start: 0.8188 (tt0) cc_final: 0.7657 (tt0) REVERT: X 247 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7684 (mtm180) REVERT: X 394 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6604 (ttpp) REVERT: Y 244 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7665 (mtp85) REVERT: Y 373 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8260 (ttt180) REVERT: Y 376 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (mtpp) REVERT: Y 394 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6897 (ttpp) REVERT: Y 414 ASP cc_start: 0.7521 (m-30) cc_final: 0.7318 (m-30) REVERT: Z 244 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7412 (mtp85) REVERT: Z 290 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7980 (ptmt) REVERT: Z 394 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6583 (mtpp) REVERT: a 244 ARG cc_start: 0.7598 (mtt90) cc_final: 0.7353 (mtp85) REVERT: a 246 GLN cc_start: 0.8302 (tt0) cc_final: 0.7968 (tt0) REVERT: a 281 HIS cc_start: 0.7898 (m90) cc_final: 0.7640 (m90) REVERT: a 373 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7741 (ttp-170) REVERT: a 376 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: a 394 LYS cc_start: 0.7241 (mmmt) cc_final: 0.6722 (ttpp) REVERT: b 244 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7616 (mtp85) REVERT: b 246 GLN cc_start: 0.8400 (tt0) cc_final: 0.7888 (tt0) REVERT: b 361 ASN cc_start: 0.8693 (m-40) cc_final: 0.8436 (m-40) REVERT: b 383 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: b 394 LYS cc_start: 0.7230 (mmmt) cc_final: 0.6528 (ttpp) REVERT: b 415 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7522 (mt) REVERT: c 244 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7608 (mtp85) REVERT: c 394 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6844 (ttpp) REVERT: d 246 GLN cc_start: 0.8026 (tt0) cc_final: 0.7717 (tt0) REVERT: d 377 MET cc_start: 0.8719 (mpt) cc_final: 0.8512 (mpt) REVERT: d 394 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6830 (ttpt) REVERT: e 244 ARG cc_start: 0.7587 (ptm160) cc_final: 0.7337 (mtt-85) REVERT: e 246 GLN cc_start: 0.8452 (tt0) cc_final: 0.8175 (tt0) REVERT: e 275 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8352 (mttm) REVERT: e 370 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7679 (ttm-80) REVERT: e 394 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6586 (ttpp) REVERT: f 244 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7653 (mtm110) REVERT: f 246 GLN cc_start: 0.8195 (tt0) cc_final: 0.7790 (tt0) REVERT: f 295 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8581 (t) REVERT: f 376 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: g 244 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7465 (mtp85) REVERT: g 246 GLN cc_start: 0.8397 (tt0) cc_final: 0.8036 (tt0) REVERT: g 394 LYS cc_start: 0.6986 (mmmt) cc_final: 0.6585 (ttpp) REVERT: h 244 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7413 (mtm110) REVERT: h 246 GLN cc_start: 0.8164 (tt0) cc_final: 0.7860 (tt0) REVERT: h 275 LYS cc_start: 0.8643 (mtmp) cc_final: 0.8336 (mttm) REVERT: h 394 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6843 (ttpp) REVERT: h 418 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8202 (mm-30) outliers start: 116 outliers final: 54 residues processed: 865 average time/residue: 0.9398 time to fit residues: 942.2457 Evaluate side-chains 854 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 771 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 373 ARG Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 253 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 373 ARG Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 381 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 275 optimal weight: 7.9990 chunk 441 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 404 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 518 optimal weight: 1.9990 chunk 367 optimal weight: 8.9990 chunk 539 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 GLN E 303 GLN F 303 GLN G 269 GLN J 303 GLN K 277 GLN K 303 GLN M 431 ASN N 269 GLN O 269 GLN O 431 ASN P 269 GLN V 303 GLN W 303 GLN X 269 GLN a 303 GLN b 277 GLN b 303 GLN d 431 ASN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119888 restraints weight = 49340.645| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.57 r_work: 0.3251 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43826 Z= 0.175 Angle : 0.513 6.819 59194 Z= 0.272 Chirality : 0.041 0.142 6766 Planarity : 0.004 0.050 8024 Dihedral : 4.019 17.165 6018 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 3.36 % Allowed : 25.16 % Favored : 71.49 % 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 aren not related in a simple way. whole: 2.22 (0.12), residues: 5440 helix: 4.06 (0.13), residues: 1428 sheet: 0.89 (0.10), residues: 2618 loop : -0.16 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 356 TYR 0.007 0.001 TYR C 282 PHE 0.012 0.002 PHE D 422 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00414 (43826) covalent geometry : angle 0.51302 (59194) hydrogen bonds : bond 0.03879 ( 2619) hydrogen bonds : angle 4.25741 ( 7245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 809 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7571 (mtm110) REVERT: A 373 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7712 (ttp-170) REVERT: A 394 LYS cc_start: 0.7291 (mmmt) cc_final: 0.6872 (ttpp) REVERT: B 244 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7832 (mtt-85) REVERT: B 246 GLN cc_start: 0.8408 (tt0) cc_final: 0.8061 (tt0) REVERT: B 275 LYS cc_start: 0.8828 (mtmp) cc_final: 0.8530 (mtmp) REVERT: B 359 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 376 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8408 (mtpp) REVERT: B 394 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6914 (ttpp) REVERT: C 244 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7383 (mtp85) REVERT: C 394 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6723 (ttpp) REVERT: C 416 THR cc_start: 0.8183 (m) cc_final: 0.7884 (p) REVERT: D 244 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7316 (mtt-85) REVERT: D 394 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6844 (ttpp) REVERT: E 244 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7481 (mtp85) REVERT: E 394 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6664 (ttpp) REVERT: F 246 GLN cc_start: 0.8369 (tt0) cc_final: 0.8105 (tt0) REVERT: F 247 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7338 (mpp-170) REVERT: F 275 LYS cc_start: 0.8773 (mtmp) cc_final: 0.8412 (mttm) REVERT: F 373 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7970 (tpp80) REVERT: F 376 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8316 (mtpt) REVERT: F 394 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6721 (ttpp) REVERT: G 244 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7301 (mtp85) REVERT: G 247 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7746 (mtm180) REVERT: G 394 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6850 (ttpp) REVERT: H 244 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7687 (mtp85) REVERT: H 373 ARG cc_start: 0.8512 (ttt180) cc_final: 0.8251 (ttt180) REVERT: H 376 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8489 (mtpp) REVERT: H 394 LYS cc_start: 0.7341 (mmmt) cc_final: 0.6842 (ttpp) REVERT: I 244 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7469 (mtp85) REVERT: I 290 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8054 (ptmt) REVERT: I 356 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6100 (ttp80) REVERT: I 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6552 (mtpp) REVERT: J 242 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8324 (mt-10) REVERT: J 246 GLN cc_start: 0.8301 (tt0) cc_final: 0.7987 (tt0) REVERT: J 281 HIS cc_start: 0.7903 (m90) cc_final: 0.7656 (m90) REVERT: J 290 LYS cc_start: 0.8413 (pttm) cc_final: 0.8150 (pmtt) REVERT: J 373 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7790 (ttp-170) REVERT: J 376 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8281 (mtpp) REVERT: J 394 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6851 (ttpp) REVERT: K 244 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7661 (mtp85) REVERT: K 246 GLN cc_start: 0.8297 (tt0) cc_final: 0.8001 (tt0) REVERT: K 361 ASN cc_start: 0.8725 (m-40) cc_final: 0.8376 (m-40) REVERT: K 383 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: K 394 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6535 (ttpp) REVERT: K 415 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7673 (mt) REVERT: L 244 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7618 (mtp85) REVERT: L 373 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8209 (ttt180) REVERT: L 394 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6837 (ttpp) REVERT: L 416 THR cc_start: 0.8058 (m) cc_final: 0.7855 (p) REVERT: M 244 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7414 (mtm110) REVERT: M 394 LYS cc_start: 0.7442 (mmmt) cc_final: 0.6866 (ttpt) REVERT: M 416 THR cc_start: 0.8321 (m) cc_final: 0.8029 (p) REVERT: M 431 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8123 (t0) REVERT: N 244 ARG cc_start: 0.7622 (ptm160) cc_final: 0.7369 (mtt-85) REVERT: N 275 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8389 (mttm) REVERT: N 370 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7790 (ttm-80) REVERT: N 394 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6583 (ttpp) REVERT: O 244 ARG cc_start: 0.8048 (mtt90) cc_final: 0.7709 (mtm110) REVERT: O 246 GLN cc_start: 0.8198 (tt0) cc_final: 0.7902 (tt0) REVERT: O 376 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8379 (mtpp) REVERT: P 244 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7538 (mtp85) REVERT: P 246 GLN cc_start: 0.8431 (tt0) cc_final: 0.8121 (tt0) REVERT: P 394 LYS cc_start: 0.6942 (mmmt) cc_final: 0.6555 (ttpp) REVERT: Q 246 GLN cc_start: 0.8255 (tt0) cc_final: 0.7919 (tt0) REVERT: Q 275 LYS cc_start: 0.8654 (mtmp) cc_final: 0.8362 (mttm) REVERT: Q 394 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6760 (ttpp) REVERT: Q 418 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8226 (mm-30) REVERT: R 244 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7595 (mtm110) REVERT: R 373 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7725 (ttp-170) REVERT: R 394 LYS cc_start: 0.7292 (mmmt) cc_final: 0.6878 (ttpp) REVERT: S 244 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7852 (mtt-85) REVERT: S 246 GLN cc_start: 0.8403 (tt0) cc_final: 0.8062 (tt0) REVERT: S 275 LYS cc_start: 0.8836 (mtmp) cc_final: 0.8548 (mtmp) REVERT: S 359 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: S 394 LYS cc_start: 0.7330 (mmmt) cc_final: 0.6920 (ttpp) REVERT: T 244 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7398 (mtp85) REVERT: T 394 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6732 (ttpp) REVERT: T 416 THR cc_start: 0.8212 (m) cc_final: 0.7882 (p) REVERT: U 377 MET cc_start: 0.8599 (mpt) cc_final: 0.8217 (mpt) REVERT: U 394 LYS cc_start: 0.7465 (mmmt) cc_final: 0.6853 (ttpp) REVERT: V 244 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7480 (mtp85) REVERT: V 373 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8158 (tpp-160) REVERT: V 394 LYS cc_start: 0.7462 (mmmt) cc_final: 0.6664 (ttpp) REVERT: W 246 GLN cc_start: 0.8368 (tt0) cc_final: 0.8100 (tt0) REVERT: W 247 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7332 (mpp-170) REVERT: W 275 LYS cc_start: 0.8781 (mtmp) cc_final: 0.8416 (mttm) REVERT: W 373 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8000 (tpp80) REVERT: W 376 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8302 (mtpt) REVERT: W 394 LYS cc_start: 0.7263 (mmmt) cc_final: 0.6719 (ttpp) REVERT: X 244 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7309 (mtp85) REVERT: X 247 ARG cc_start: 0.8012 (mtm110) cc_final: 0.7742 (mtm180) REVERT: X 394 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6854 (ttpp) REVERT: Y 244 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7694 (mtp85) REVERT: Y 373 ARG cc_start: 0.8496 (ttt180) cc_final: 0.8241 (ttt180) REVERT: Y 376 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8486 (mtpp) REVERT: Y 394 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6845 (ttpp) REVERT: Z 244 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7477 (mtp85) REVERT: Z 290 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8050 (ptmt) REVERT: Z 356 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6124 (ttp80) REVERT: Z 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6550 (mtpp) REVERT: a 242 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8328 (mt-10) REVERT: a 244 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7438 (mtp85) REVERT: a 246 GLN cc_start: 0.8330 (tt0) cc_final: 0.8051 (tt0) REVERT: a 281 HIS cc_start: 0.7907 (m90) cc_final: 0.7667 (m90) REVERT: a 290 LYS cc_start: 0.8417 (pttm) cc_final: 0.8148 (pmtt) REVERT: a 376 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8264 (mtpp) REVERT: a 394 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6848 (ttpp) REVERT: b 244 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7669 (mtp85) REVERT: b 246 GLN cc_start: 0.8305 (tt0) cc_final: 0.8007 (tt0) REVERT: b 361 ASN cc_start: 0.8732 (m-40) cc_final: 0.8382 (m-40) REVERT: b 376 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: b 383 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: b 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6538 (ttpp) REVERT: b 415 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7671 (mt) REVERT: c 244 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7625 (mtp85) REVERT: c 373 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8222 (ttt180) REVERT: c 394 LYS cc_start: 0.7329 (mmmt) cc_final: 0.6829 (ttpp) REVERT: d 244 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7406 (mtm110) REVERT: d 246 GLN cc_start: 0.8112 (tt0) cc_final: 0.7910 (tt0) REVERT: d 394 LYS cc_start: 0.7441 (mmmt) cc_final: 0.6853 (ttpt) REVERT: d 416 THR cc_start: 0.8314 (m) cc_final: 0.8021 (p) REVERT: d 431 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8125 (t0) REVERT: e 244 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7376 (mtt-85) REVERT: e 275 LYS cc_start: 0.8708 (mtmp) cc_final: 0.8389 (mttm) REVERT: e 370 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7779 (ttm-80) REVERT: e 394 LYS cc_start: 0.7120 (mmmt) cc_final: 0.6587 (ttpp) REVERT: f 244 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7705 (mtm110) REVERT: f 246 GLN cc_start: 0.8226 (tt0) cc_final: 0.7922 (tt0) REVERT: f 376 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: g 244 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7530 (mtp85) REVERT: g 246 GLN cc_start: 0.8410 (tt0) cc_final: 0.8098 (tt0) REVERT: g 394 LYS cc_start: 0.6948 (mmmt) cc_final: 0.6554 (ttpp) REVERT: h 244 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7501 (mtm110) REVERT: h 246 GLN cc_start: 0.8304 (tt0) cc_final: 0.7933 (tt0) REVERT: h 275 LYS cc_start: 0.8657 (mtmp) cc_final: 0.8376 (mttm) REVERT: h 276 GLU cc_start: 0.8059 (tt0) cc_final: 0.7782 (mt-10) REVERT: h 367 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8716 (mm-30) REVERT: h 394 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6747 (ttpp) REVERT: h 418 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8230 (mm-30) outliers start: 161 outliers final: 80 residues processed: 911 average time/residue: 0.8210 time to fit residues: 871.6335 Evaluate side-chains 900 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 786 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 356 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 373 ARG Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 275 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 356 ARG Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 356 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 373 ARG Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 356 ARG Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 275 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 103 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 477 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 417 optimal weight: 0.9980 chunk 523 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 GLN E 303 GLN G 269 GLN J 303 GLN K 303 GLN N 269 GLN O 431 ASN P 269 GLN V 303 GLN W 303 GLN X 269 GLN a 303 GLN b 303 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121703 restraints weight = 48800.926| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.57 r_work: 0.3276 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43826 Z= 0.126 Angle : 0.479 7.376 59194 Z= 0.253 Chirality : 0.039 0.123 6766 Planarity : 0.003 0.056 8024 Dihedral : 3.875 18.133 6018 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 2.54 % Allowed : 26.20 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.12), residues: 5440 helix: 4.09 (0.13), residues: 1428 sheet: 0.94 (0.10), residues: 2618 loop : -0.12 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG T 356 TYR 0.004 0.001 TYR G 366 PHE 0.008 0.001 PHE U 422 HIS 0.002 0.001 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00296 (43826) covalent geometry : angle 0.47937 (59194) hydrogen bonds : bond 0.03310 ( 2619) hydrogen bonds : angle 4.08801 ( 7245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 788 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7592 (mtm110) REVERT: A 373 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7724 (ttp-170) REVERT: A 394 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6964 (ttpp) REVERT: B 244 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7785 (mtt-85) REVERT: B 246 GLN cc_start: 0.8391 (tt0) cc_final: 0.8045 (tt0) REVERT: B 275 LYS cc_start: 0.8820 (mtmp) cc_final: 0.8546 (mtmp) REVERT: B 359 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: B 376 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8347 (mtpp) REVERT: B 394 LYS cc_start: 0.7349 (mmmt) cc_final: 0.6907 (ttpp) REVERT: C 244 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: C 246 GLN cc_start: 0.8028 (tt0) cc_final: 0.7421 (tt0) REVERT: C 394 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6741 (ttpp) REVERT: C 416 THR cc_start: 0.8077 (m) cc_final: 0.7787 (p) REVERT: D 244 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7310 (mtt-85) REVERT: D 377 MET cc_start: 0.8519 (mpt) cc_final: 0.8261 (mpt) REVERT: D 394 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6861 (ttpp) REVERT: E 244 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7619 (mtp85) REVERT: E 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6610 (ttpp) REVERT: F 246 GLN cc_start: 0.8358 (tt0) cc_final: 0.8055 (tt0) REVERT: F 247 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7320 (mpp-170) REVERT: F 275 LYS cc_start: 0.8753 (mtmp) cc_final: 0.8321 (mttt) REVERT: F 373 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7938 (tpp80) REVERT: F 376 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8236 (mtpt) REVERT: F 394 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6697 (ttpp) REVERT: G 244 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7208 (mtp85) REVERT: G 246 GLN cc_start: 0.8200 (tt0) cc_final: 0.7793 (tt0) REVERT: G 247 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7793 (mtm180) REVERT: G 394 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6825 (ttpp) REVERT: H 244 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7724 (mtp85) REVERT: H 373 ARG cc_start: 0.8496 (ttt180) cc_final: 0.8274 (ttt180) REVERT: H 376 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8458 (mtpp) REVERT: H 394 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6849 (ttpp) REVERT: I 244 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7465 (mtp85) REVERT: I 290 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8004 (ptmt) REVERT: I 394 LYS cc_start: 0.7205 (mmmt) cc_final: 0.6535 (mtpp) REVERT: J 246 GLN cc_start: 0.8280 (tt0) cc_final: 0.7966 (tt0) REVERT: J 281 HIS cc_start: 0.7913 (m90) cc_final: 0.7662 (m90) REVERT: J 290 LYS cc_start: 0.8526 (pttm) cc_final: 0.8173 (pmtt) REVERT: J 373 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: J 394 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6880 (ttpp) REVERT: K 244 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7668 (mtp85) REVERT: K 246 GLN cc_start: 0.8299 (tt0) cc_final: 0.7856 (tt0) REVERT: K 361 ASN cc_start: 0.8681 (m-40) cc_final: 0.8419 (m-40) REVERT: K 376 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: K 383 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: K 394 LYS cc_start: 0.7163 (mmmt) cc_final: 0.6440 (ttpp) REVERT: K 415 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7590 (mt) REVERT: L 244 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7586 (mtp85) REVERT: L 383 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: L 394 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6834 (ttpp) REVERT: M 244 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7330 (mtm110) REVERT: M 246 GLN cc_start: 0.8058 (tt0) cc_final: 0.7682 (tt0) REVERT: M 394 LYS cc_start: 0.7374 (mmmt) cc_final: 0.6828 (ttpt) REVERT: N 244 ARG cc_start: 0.7598 (ptm160) cc_final: 0.7371 (mtt-85) REVERT: N 246 GLN cc_start: 0.8471 (tt0) cc_final: 0.8184 (tt0) REVERT: N 275 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8366 (mttm) REVERT: N 370 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7785 (ttm-80) REVERT: N 394 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6594 (ttpp) REVERT: O 244 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7650 (mtm110) REVERT: O 246 GLN cc_start: 0.8206 (tt0) cc_final: 0.7836 (tt0) REVERT: O 376 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: P 244 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7508 (mtp85) REVERT: P 246 GLN cc_start: 0.8423 (tt0) cc_final: 0.8122 (tt0) REVERT: P 394 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6571 (ttpp) REVERT: Q 246 GLN cc_start: 0.8223 (tt0) cc_final: 0.7989 (tt0) REVERT: Q 275 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8350 (mttm) REVERT: Q 276 GLU cc_start: 0.7966 (tt0) cc_final: 0.7749 (mt-10) REVERT: Q 373 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8122 (tpt-90) REVERT: Q 394 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6781 (ttpp) REVERT: R 244 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7591 (mtm110) REVERT: R 373 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7687 (ttp-170) REVERT: R 394 LYS cc_start: 0.7376 (mmmt) cc_final: 0.6976 (ttpp) REVERT: S 244 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7801 (mtt-85) REVERT: S 246 GLN cc_start: 0.8361 (tt0) cc_final: 0.8051 (tt0) REVERT: S 275 LYS cc_start: 0.8862 (mtmp) cc_final: 0.8581 (mtmp) REVERT: S 359 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: S 376 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (mtpp) REVERT: S 394 LYS cc_start: 0.7348 (mmmt) cc_final: 0.6916 (ttpp) REVERT: T 244 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7384 (mtp85) REVERT: T 246 GLN cc_start: 0.8034 (tt0) cc_final: 0.7427 (tt0) REVERT: T 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6752 (ttpp) REVERT: T 416 THR cc_start: 0.8091 (m) cc_final: 0.7803 (p) REVERT: U 244 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7316 (mtt-85) REVERT: U 370 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8362 (ttm170) REVERT: U 377 MET cc_start: 0.8581 (mpt) cc_final: 0.8192 (mpt) REVERT: U 394 LYS cc_start: 0.7434 (mmmt) cc_final: 0.6859 (ttpp) REVERT: V 244 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7612 (mtp85) REVERT: V 373 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (tpp-160) REVERT: V 394 LYS cc_start: 0.7381 (mmmt) cc_final: 0.6612 (ttpp) REVERT: W 246 GLN cc_start: 0.8358 (tt0) cc_final: 0.8058 (tt0) REVERT: W 247 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7310 (mpp-170) REVERT: W 275 LYS cc_start: 0.8756 (mtmp) cc_final: 0.8326 (mttt) REVERT: W 373 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7964 (tpp80) REVERT: W 376 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8227 (mtpt) REVERT: W 394 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6689 (ttpp) REVERT: X 244 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7214 (mtp85) REVERT: X 246 GLN cc_start: 0.8198 (tt0) cc_final: 0.7793 (tt0) REVERT: X 247 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7798 (mtm180) REVERT: X 394 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6824 (ttpp) REVERT: Y 244 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7709 (mtp85) REVERT: Y 290 LYS cc_start: 0.8613 (pttm) cc_final: 0.8164 (pmmt) REVERT: Y 373 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8261 (ttt180) REVERT: Y 376 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8451 (mtpp) REVERT: Y 394 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6855 (ttpp) REVERT: Z 244 ARG cc_start: 0.7715 (mtt90) cc_final: 0.7416 (mtp85) REVERT: Z 290 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7998 (ptmt) REVERT: Z 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6531 (mtpp) REVERT: a 244 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7463 (mtp85) REVERT: a 246 GLN cc_start: 0.8283 (tt0) cc_final: 0.7984 (tt0) REVERT: a 281 HIS cc_start: 0.7907 (m90) cc_final: 0.7658 (m90) REVERT: a 290 LYS cc_start: 0.8529 (pttm) cc_final: 0.8171 (pmtt) REVERT: a 376 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: a 394 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6872 (ttpp) REVERT: b 244 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7682 (mtp85) REVERT: b 246 GLN cc_start: 0.8302 (tt0) cc_final: 0.7862 (tt0) REVERT: b 361 ASN cc_start: 0.8691 (m-40) cc_final: 0.8424 (m-40) REVERT: b 383 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: b 394 LYS cc_start: 0.7165 (mmmt) cc_final: 0.6439 (ttpp) REVERT: b 415 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7602 (mt) REVERT: c 244 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7593 (mtp85) REVERT: c 383 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: c 394 LYS cc_start: 0.7314 (mmmt) cc_final: 0.6828 (ttpp) REVERT: d 394 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6814 (ttpt) REVERT: e 244 ARG cc_start: 0.7611 (ptm160) cc_final: 0.7382 (mtt-85) REVERT: e 246 GLN cc_start: 0.8475 (tt0) cc_final: 0.8187 (tt0) REVERT: e 275 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8364 (mttm) REVERT: e 356 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6570 (ttp-170) REVERT: e 370 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7801 (ttm-80) REVERT: e 394 LYS cc_start: 0.7114 (mmmt) cc_final: 0.6589 (ttpp) REVERT: f 244 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7636 (mtm110) REVERT: f 246 GLN cc_start: 0.8197 (tt0) cc_final: 0.7824 (tt0) REVERT: f 376 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: g 244 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7513 (mtp85) REVERT: g 246 GLN cc_start: 0.8402 (tt0) cc_final: 0.8105 (tt0) REVERT: g 394 LYS cc_start: 0.6965 (mmmt) cc_final: 0.6577 (ttpp) REVERT: h 244 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7463 (mtm110) REVERT: h 246 GLN cc_start: 0.8241 (tt0) cc_final: 0.7921 (tt0) REVERT: h 275 LYS cc_start: 0.8643 (mtmp) cc_final: 0.8340 (mttm) REVERT: h 276 GLU cc_start: 0.8039 (tt0) cc_final: 0.7751 (mt-10) REVERT: h 394 LYS cc_start: 0.7230 (mmmt) cc_final: 0.6775 (ttpp) REVERT: h 418 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8220 (mm-30) outliers start: 122 outliers final: 69 residues processed: 860 average time/residue: 0.9769 time to fit residues: 970.2030 Evaluate side-chains 886 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 786 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 275 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 356 ARG Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 275 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 28 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 540 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 309 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 GLN E 303 GLN G 269 GLN J 303 GLN K 277 GLN K 303 GLN N 269 GLN O 431 ASN P 269 GLN V 303 GLN W 303 GLN X 269 GLN a 303 GLN b 303 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123463 restraints weight = 48706.928| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.57 r_work: 0.3305 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43826 Z= 0.096 Angle : 0.456 7.615 59194 Z= 0.239 Chirality : 0.039 0.123 6766 Planarity : 0.003 0.062 8024 Dihedral : 3.725 18.770 6018 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.90 % Allowed : 26.99 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.12), residues: 5440 helix: 4.24 (0.13), residues: 1428 sheet: 1.01 (0.10), residues: 2618 loop : -0.13 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG T 356 TYR 0.006 0.001 TYR G 366 PHE 0.006 0.001 PHE U 422 HIS 0.002 0.000 HIS R 263 Details of bonding type rmsd covalent geometry : bond 0.00223 (43826) covalent geometry : angle 0.45598 (59194) hydrogen bonds : bond 0.02899 ( 2619) hydrogen bonds : angle 3.87439 ( 7245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 781 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7607 (mtm110) REVERT: A 290 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7945 (ptpp) REVERT: A 373 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7694 (ttp-170) REVERT: A 376 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8223 (mtpp) REVERT: A 394 LYS cc_start: 0.7337 (mmmt) cc_final: 0.6973 (ttpp) REVERT: B 244 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7767 (mtt-85) REVERT: B 246 GLN cc_start: 0.8342 (tt0) cc_final: 0.7952 (tt0) REVERT: B 275 LYS cc_start: 0.8881 (mtmp) cc_final: 0.8612 (mtmp) REVERT: B 276 GLU cc_start: 0.7968 (tt0) cc_final: 0.7752 (mt-10) REVERT: B 376 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: B 394 LYS cc_start: 0.7330 (mmmt) cc_final: 0.6884 (ttpp) REVERT: C 244 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7335 (mtp85) REVERT: C 246 GLN cc_start: 0.7989 (tt0) cc_final: 0.7450 (tt0) REVERT: C 394 LYS cc_start: 0.7364 (mmmt) cc_final: 0.6716 (ttpp) REVERT: D 244 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7281 (mtt-85) REVERT: D 370 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8364 (ttm170) REVERT: D 377 MET cc_start: 0.8415 (mpt) cc_final: 0.8126 (mpt) REVERT: D 394 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6859 (ttpp) REVERT: E 244 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7667 (mtp85) REVERT: E 394 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6518 (ttpp) REVERT: F 246 GLN cc_start: 0.8280 (tt0) cc_final: 0.7981 (tt0) REVERT: F 247 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7184 (mpp-170) REVERT: F 275 LYS cc_start: 0.8751 (mtmp) cc_final: 0.8317 (mttt) REVERT: F 373 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8004 (tpp80) REVERT: F 376 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8285 (mtpt) REVERT: F 394 LYS cc_start: 0.7168 (mmmt) cc_final: 0.6645 (ttpp) REVERT: G 244 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7215 (mtp85) REVERT: G 246 GLN cc_start: 0.8060 (tt0) cc_final: 0.7588 (tt0) REVERT: G 247 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7724 (mtm180) REVERT: G 394 LYS cc_start: 0.7167 (mmmt) cc_final: 0.6694 (ttpp) REVERT: H 244 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7692 (mtp85) REVERT: H 290 LYS cc_start: 0.8418 (pttm) cc_final: 0.8159 (pmmt) REVERT: H 376 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8402 (mtpp) REVERT: H 394 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6930 (ttpp) REVERT: I 244 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7389 (mtp85) REVERT: I 290 LYS cc_start: 0.8415 (mtmm) cc_final: 0.7981 (ptmt) REVERT: I 394 LYS cc_start: 0.7078 (mmmt) cc_final: 0.6472 (mtpp) REVERT: J 246 GLN cc_start: 0.8256 (tt0) cc_final: 0.7897 (tt0) REVERT: J 281 HIS cc_start: 0.7922 (m90) cc_final: 0.7664 (m90) REVERT: J 290 LYS cc_start: 0.8502 (pttm) cc_final: 0.8146 (pmtt) REVERT: J 394 LYS cc_start: 0.7362 (mmmt) cc_final: 0.6866 (ttpp) REVERT: K 244 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7613 (mtp85) REVERT: K 246 GLN cc_start: 0.8412 (tt0) cc_final: 0.8101 (tt0) REVERT: K 361 ASN cc_start: 0.8687 (m-40) cc_final: 0.8430 (m-40) REVERT: K 383 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: K 394 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6553 (ttpp) REVERT: K 415 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7501 (mt) REVERT: L 244 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7583 (mtp85) REVERT: L 246 GLN cc_start: 0.8385 (tt0) cc_final: 0.7951 (pt0) REVERT: L 383 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: L 394 LYS cc_start: 0.7297 (mmmt) cc_final: 0.6869 (ttpp) REVERT: M 246 GLN cc_start: 0.8019 (tt0) cc_final: 0.7638 (tt0) REVERT: M 394 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6838 (ttpt) REVERT: N 244 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7333 (mtt-85) REVERT: N 246 GLN cc_start: 0.8437 (tt0) cc_final: 0.8153 (tt0) REVERT: N 275 LYS cc_start: 0.8686 (mtmp) cc_final: 0.8390 (mttm) REVERT: N 370 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7664 (ttm-80) REVERT: N 394 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6664 (ttpp) REVERT: O 244 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7638 (mtm110) REVERT: O 246 GLN cc_start: 0.8185 (tt0) cc_final: 0.7831 (tt0) REVERT: O 295 SER cc_start: 0.8793 (p) cc_final: 0.8567 (t) REVERT: O 370 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.8208 (ttm170) REVERT: P 244 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7479 (mtp85) REVERT: P 246 GLN cc_start: 0.8436 (tt0) cc_final: 0.8083 (tt0) REVERT: P 377 MET cc_start: 0.8529 (mpt) cc_final: 0.8268 (mpt) REVERT: P 394 LYS cc_start: 0.6985 (mmmt) cc_final: 0.6624 (ttpp) REVERT: Q 246 GLN cc_start: 0.8153 (tt0) cc_final: 0.7882 (tt0) REVERT: Q 275 LYS cc_start: 0.8627 (mtmp) cc_final: 0.8341 (mttm) REVERT: Q 276 GLU cc_start: 0.8057 (tt0) cc_final: 0.7784 (mt-10) REVERT: Q 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6770 (ttpp) REVERT: R 244 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7597 (mtm110) REVERT: R 290 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7929 (ptpp) REVERT: R 373 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7668 (ttp-170) REVERT: R 394 LYS cc_start: 0.7337 (mmmt) cc_final: 0.6986 (ttpp) REVERT: S 244 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7786 (mtt-85) REVERT: S 246 GLN cc_start: 0.8330 (tt0) cc_final: 0.7941 (tt0) REVERT: S 275 LYS cc_start: 0.8882 (mtmp) cc_final: 0.8618 (mtmp) REVERT: S 276 GLU cc_start: 0.7968 (tt0) cc_final: 0.7747 (mt-10) REVERT: S 376 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8319 (mtpp) REVERT: S 394 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6903 (ttpp) REVERT: T 244 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7355 (mtp85) REVERT: T 246 GLN cc_start: 0.7981 (tt0) cc_final: 0.7451 (tt0) REVERT: T 394 LYS cc_start: 0.7358 (mmmt) cc_final: 0.6725 (ttpp) REVERT: U 244 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7297 (mtt-85) REVERT: U 246 GLN cc_start: 0.8097 (tt0) cc_final: 0.7837 (tt0) REVERT: U 377 MET cc_start: 0.8557 (mpt) cc_final: 0.8173 (mpt) REVERT: U 394 LYS cc_start: 0.7322 (mmmt) cc_final: 0.6853 (ttpp) REVERT: V 244 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7670 (mtp85) REVERT: V 373 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (tpp-160) REVERT: V 394 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6527 (ttpp) REVERT: W 246 GLN cc_start: 0.8285 (tt0) cc_final: 0.7981 (tt0) REVERT: W 247 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7224 (mpp-170) REVERT: W 275 LYS cc_start: 0.8753 (mtmp) cc_final: 0.8318 (mttt) REVERT: W 370 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7328 (ttm-80) REVERT: W 373 ARG cc_start: 0.8305 (ttt90) cc_final: 0.7982 (tpp80) REVERT: W 376 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8277 (mtpt) REVERT: W 394 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6652 (ttpp) REVERT: X 244 ARG cc_start: 0.7682 (mtt90) cc_final: 0.7219 (mtp85) REVERT: X 246 GLN cc_start: 0.8055 (tt0) cc_final: 0.7582 (tt0) REVERT: X 247 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7730 (mtm180) REVERT: X 394 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6692 (ttpp) REVERT: Y 244 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7697 (mtp85) REVERT: Y 376 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8402 (mtpp) REVERT: Y 394 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6929 (ttpp) REVERT: Z 244 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7339 (mtp85) REVERT: Z 290 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7982 (ptmt) REVERT: Z 394 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6469 (mtpp) REVERT: a 244 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7412 (mtp85) REVERT: a 246 GLN cc_start: 0.8280 (tt0) cc_final: 0.7938 (tt0) REVERT: a 281 HIS cc_start: 0.7920 (m90) cc_final: 0.7665 (m90) REVERT: a 290 LYS cc_start: 0.8505 (pttm) cc_final: 0.8143 (pmtt) REVERT: a 376 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: a 394 LYS cc_start: 0.7394 (mmmt) cc_final: 0.6910 (ttpp) REVERT: b 244 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7627 (mtp85) REVERT: b 246 GLN cc_start: 0.8417 (tt0) cc_final: 0.7921 (tt0) REVERT: b 361 ASN cc_start: 0.8691 (m-40) cc_final: 0.8426 (m-40) REVERT: b 383 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: b 394 LYS cc_start: 0.7260 (mmmt) cc_final: 0.6551 (ttpp) REVERT: b 415 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7482 (mt) REVERT: c 244 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7580 (mtp85) REVERT: c 246 GLN cc_start: 0.8395 (tt0) cc_final: 0.7956 (pt0) REVERT: c 383 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: c 394 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6867 (ttpp) REVERT: d 244 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7149 (ttp-110) REVERT: d 246 GLN cc_start: 0.7944 (tt0) cc_final: 0.7550 (tt0) REVERT: d 394 LYS cc_start: 0.7381 (mmmt) cc_final: 0.6834 (ttpt) REVERT: e 244 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7338 (mtt-85) REVERT: e 246 GLN cc_start: 0.8433 (tt0) cc_final: 0.8155 (tt0) REVERT: e 275 LYS cc_start: 0.8686 (mtmp) cc_final: 0.8390 (mttm) REVERT: e 356 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6504 (ttp-170) REVERT: e 370 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7650 (ttm-80) REVERT: e 394 LYS cc_start: 0.7122 (mmmt) cc_final: 0.6663 (ttpp) REVERT: f 244 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7633 (mtm110) REVERT: f 246 GLN cc_start: 0.8174 (tt0) cc_final: 0.7822 (tt0) REVERT: f 295 SER cc_start: 0.8788 (p) cc_final: 0.8570 (t) REVERT: f 370 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8245 (ttm170) REVERT: g 244 ARG cc_start: 0.7747 (mtt90) cc_final: 0.7463 (mtp85) REVERT: g 246 GLN cc_start: 0.8396 (tt0) cc_final: 0.8060 (tt0) REVERT: g 394 LYS cc_start: 0.7001 (mmmt) cc_final: 0.6622 (ttpp) REVERT: h 244 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7415 (mtm110) REVERT: h 246 GLN cc_start: 0.8160 (tt0) cc_final: 0.7846 (tt0) REVERT: h 275 LYS cc_start: 0.8612 (mtmp) cc_final: 0.8317 (mttm) REVERT: h 276 GLU cc_start: 0.8053 (tt0) cc_final: 0.7770 (mt-10) REVERT: h 394 LYS cc_start: 0.7215 (mmmt) cc_final: 0.6773 (ttpp) outliers start: 91 outliers final: 61 residues processed: 841 average time/residue: 0.6676 time to fit residues: 654.7426 Evaluate side-chains 845 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 759 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain P residue 275 LYS Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 373 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 253 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain g residue 275 LYS Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 381 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 8 optimal weight: 4.9990 chunk 182 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 446 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 507 optimal weight: 1.9990 chunk 479 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN D 303 GLN E 274 ASN E 303 GLN G 269 GLN G 431 ASN J 303 GLN K 303 GLN L 274 ASN N 269 GLN O 269 GLN O 431 ASN P 269 GLN V 274 ASN V 303 GLN W 303 GLN X 269 GLN X 431 ASN a 303 GLN b 277 GLN b 303 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121959 restraints weight = 49222.461| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.58 r_work: 0.3279 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43826 Z= 0.129 Angle : 0.481 8.116 59194 Z= 0.252 Chirality : 0.040 0.120 6766 Planarity : 0.003 0.060 8024 Dihedral : 3.832 19.116 6018 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.17 % Allowed : 26.60 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.12), residues: 5440 helix: 4.16 (0.13), residues: 1428 sheet: 0.99 (0.10), residues: 2618 loop : -0.10 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 356 TYR 0.005 0.001 TYR X 366 PHE 0.009 0.001 PHE U 422 HIS 0.002 0.000 HIS a 263 Details of bonding type rmsd covalent geometry : bond 0.00305 (43826) covalent geometry : angle 0.48089 (59194) hydrogen bonds : bond 0.03324 ( 2619) hydrogen bonds : angle 3.99735 ( 7245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19989.93 seconds wall clock time: 339 minutes 16.00 seconds (20356.00 seconds total)