Starting phenix.real_space_refine on Tue Aug 26 23:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wli_37620/08_2025/8wli_37620.map" } resolution = 3.2 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= -0.003 sd= 0.133 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): 0.05s 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: 2.79, per 1000 atoms: 0.06 Number of scatterers: 43350 At special positions: 0 Unit cell: (265.068, 265.068, 98.568, 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 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: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 229 through 258 removed outlier: 3.607A 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: 3.607A 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: 3.607A 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: 3.607A 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: 3.608A 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 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: 3.608A 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: 3.607A 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: 3.608A 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: 3.607A 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: 3.607A 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: 3.607A 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: 3.607A 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: 3.607A 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: 3.607A 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: 3.608A 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: 3.608A 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: 3.608A 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: 3.607A 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: 3.608A 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: 4.977A 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: 6.874A 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: 5.882A pdb=" N GLU A 367 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.881A 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: 5.308A 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: 5.308A 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: 5.308A 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: 5.308A 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: 5.881A pdb=" N GLU F 367 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 3.757A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.882A 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: 5.308A 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: 5.881A 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: 5.308A 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: 5.882A pdb=" N GLU J 367 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU K 293 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 5.881A 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: 5.309A 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: 5.881A 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: 5.308A 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: 5.881A 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: 5.308A 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: 3.758A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.308A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 5.371A 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: 5.307A 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: 5.882A 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: 5.308A 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: 5.882A pdb=" N GLU R 367 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.881A 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: 5.308A 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: 5.308A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 5.370A 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: 3.758A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.308A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU W 293 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU W 367 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 5.370A 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: 5.308A 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: 5.882A 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: 5.308A 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: 5.881A 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: 5.308A 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: 5.882A pdb=" N GLU a 367 " --> pdb=" O LEU a 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU b 293 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 5.881A 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: 5.309A 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: 5.881A 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: 5.308A 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: 5.881A 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: 5.308A 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: 3.758A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 5.308A 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: 5.308A 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: 3.758A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 5.307A 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: 5.882A 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: 5.308A 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: 4.977A 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=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: 6.924A 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: 4.977A 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: 4.977A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.297A 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: 4.977A 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: 6.874A 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: 4.977A 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: 6.874A 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: 4.977A 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: 6.874A 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: 6.924A 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: 6.874A 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: 4.977A 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: 6.923A 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: 4.977A 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: 4.977A 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: 4.977A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.297A 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: 4.977A 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: 6.874A 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: 6.874A 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: 4.977A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.297A 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: 4.977A 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: 6.874A 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: 6.924A 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: 4.977A 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: 7.297A 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: 4.977A 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: 6.874A 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: 4.977A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.298A 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: 4.977A 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: 6.874A 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: 6.924A 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: 6.874A 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: 4.977A 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: 4.977A 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: 4.977A 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=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: 4.977A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.297A 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: 4.977A 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: 6.874A 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: 6.874A 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: 8.91 Time building geometry restraints manager: 4.32 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: 11911 1.33 - 1.45: 6551 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 N 257 " pdb=" CA VAL N 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 e 257 " pdb=" CA VAL e 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 g 257 " pdb=" CA VAL g 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" N VAL P 257 " pdb=" CA VAL P 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" N VAL h 257 " pdb=" CA VAL h 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.19e+01 ... (remaining 43821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 57139 1.53 - 3.07: 1460 3.07 - 4.60: 427 4.60 - 6.14: 100 6.14 - 7.67: 68 Bond angle restraints: 59194 Sorted by residual: angle pdb=" N ASN X 261 " pdb=" CA ASN X 261 " pdb=" C ASN X 261 " ideal model delta sigma weight residual 113.02 106.57 6.45 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN G 261 " pdb=" CA ASN G 261 " pdb=" C ASN G 261 " ideal model delta sigma weight residual 113.02 106.57 6.45 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN M 261 " pdb=" CA ASN M 261 " pdb=" C ASN M 261 " ideal model delta sigma weight residual 113.02 106.57 6.45 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN d 261 " pdb=" CA ASN d 261 " pdb=" C ASN d 261 " ideal model delta sigma weight residual 113.02 106.57 6.45 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN g 261 " pdb=" CA ASN g 261 " pdb=" C ASN g 261 " ideal model delta sigma weight residual 113.02 106.58 6.44 1.20e+00 6.94e-01 2.88e+01 ... (remaining 59189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 22980 16.79 - 33.57: 2860 33.57 - 50.36: 1122 50.36 - 67.15: 238 67.15 - 83.94: 102 Dihedral angle restraints: 27302 sinusoidal: 11152 harmonic: 16150 Sorted by residual: dihedral pdb=" CA ARG Y 294 " pdb=" CB ARG Y 294 " pdb=" CG ARG Y 294 " pdb=" CD ARG Y 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.98 59.02 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 180.00 120.98 59.02 3 1.50e+01 4.44e-03 9.48e+00 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 180.00 120.98 59.02 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 27299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3998 0.027 - 0.053: 1824 0.053 - 0.080: 502 0.080 - 0.107: 187 0.107 - 0.133: 255 Chirality restraints: 6766 Sorted by residual: chirality pdb=" CA VAL g 257 " pdb=" N VAL g 257 " pdb=" C VAL g 257 " pdb=" CB VAL g 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL P 257 " pdb=" N VAL P 257 " pdb=" C VAL P 257 " pdb=" CB VAL P 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL h 257 " pdb=" N VAL h 257 " pdb=" C VAL h 257 " pdb=" CB VAL h 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 6763 not shown) Planarity restraints: 8024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE M 256 " -0.017 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE M 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE M 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL M 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 256 " -0.017 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE d 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE d 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL d 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 256 " -0.017 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE c 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE c 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL c 257 " -0.019 2.00e-02 2.50e+03 ... (remaining 8021 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 9032 2.80 - 3.32: 37561 3.32 - 3.85: 71520 3.85 - 4.37: 84588 4.37 - 4.90: 148893 Nonbonded interactions: 351594 Sorted by model distance: nonbonded pdb=" OG1 THR E 429 " pdb=" OE1 GLU F 418 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR V 429 " pdb=" OE1 GLU W 418 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR d 429 " pdb=" OE1 GLU e 418 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR M 429 " pdb=" OE1 GLU N 418 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR b 429 " pdb=" OE1 GLU c 418 " model vdw 2.270 3.040 ... (remaining 351589 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: 7.940 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 29.650 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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= 0.222 Angle : 0.707 7.674 59194 Z= 0.443 Chirality : 0.040 0.133 6766 Planarity : 0.004 0.032 8024 Dihedral : 18.035 83.935 16762 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.35 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: 0.83 (0.11), residues: 2482 loop : -0.98 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 296 TYR 0.004 0.001 TYR g 366 PHE 0.007 0.001 PHE h 237 HIS 0.005 0.001 HIS e 263 Details of bonding type rmsd covalent geometry : bond 0.00353 (43826) covalent geometry : angle 0.70663 (59194) hydrogen bonds : bond 0.18689 ( 2619) hydrogen bonds : angle 5.94747 ( 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 1840 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1806 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8197 (mt) cc_final: 0.7948 (mm) REVERT: A 385 LEU cc_start: 0.8823 (tp) cc_final: 0.8534 (tp) REVERT: A 405 THR cc_start: 0.8282 (p) cc_final: 0.7930 (t) REVERT: A 408 GLN cc_start: 0.8451 (mt0) cc_final: 0.8212 (mt0) REVERT: B 236 LYS cc_start: 0.7858 (mttt) cc_final: 0.7484 (pttp) REVERT: B 271 ASP cc_start: 0.7988 (t0) cc_final: 0.7665 (t70) REVERT: B 290 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8085 (mmmm) REVERT: B 303 GLN cc_start: 0.7101 (mt0) cc_final: 0.6656 (tm-30) REVERT: B 405 THR cc_start: 0.8325 (p) cc_final: 0.7915 (t) REVERT: B 408 GLN cc_start: 0.8327 (mt0) cc_final: 0.7918 (mt0) REVERT: B 414 ASP cc_start: 0.7192 (m-30) cc_final: 0.6933 (m-30) REVERT: C 271 ASP cc_start: 0.7975 (t0) cc_final: 0.7625 (t70) REVERT: C 290 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8237 (mmmm) REVERT: C 303 GLN cc_start: 0.7714 (mt0) cc_final: 0.7286 (tm-30) REVERT: C 416 THR cc_start: 0.8547 (m) cc_final: 0.8126 (p) REVERT: D 247 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7725 (mtm-85) REVERT: D 290 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8217 (mmmm) REVERT: D 303 GLN cc_start: 0.7046 (mt0) cc_final: 0.6533 (tm-30) REVERT: D 414 ASP cc_start: 0.7056 (m-30) cc_final: 0.6757 (m-30) REVERT: E 236 LYS cc_start: 0.7675 (mttt) cc_final: 0.7444 (pttp) REVERT: E 290 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8200 (mmmm) REVERT: E 367 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7865 (mt-10) REVERT: E 376 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8366 (mtpp) REVERT: E 418 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8478 (mm-30) REVERT: E 428 ASP cc_start: 0.8745 (m-30) cc_final: 0.8486 (m-30) REVERT: F 271 ASP cc_start: 0.8118 (t0) cc_final: 0.7860 (t70) REVERT: F 290 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8293 (mmmm) REVERT: F 362 GLU cc_start: 0.7790 (tt0) cc_final: 0.7575 (tt0) REVERT: G 303 GLN cc_start: 0.7324 (mt0) cc_final: 0.7015 (tm-30) REVERT: G 408 GLN cc_start: 0.8363 (mt0) cc_final: 0.8158 (mt0) REVERT: H 230 LEU cc_start: 0.7701 (tp) cc_final: 0.7412 (mp) REVERT: H 271 ASP cc_start: 0.8316 (t0) cc_final: 0.7923 (t70) REVERT: H 367 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7987 (mm-30) REVERT: H 408 GLN cc_start: 0.8164 (mt0) cc_final: 0.7868 (mt0) REVERT: I 290 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8216 (mptt) REVERT: I 367 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8100 (mm-30) REVERT: J 236 LYS cc_start: 0.7792 (mttt) cc_final: 0.7564 (pttp) REVERT: J 271 ASP cc_start: 0.8285 (t0) cc_final: 0.8079 (t70) REVERT: J 290 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8049 (mmmm) REVERT: K 236 LYS cc_start: 0.7950 (mttt) cc_final: 0.7587 (pttp) REVERT: K 271 ASP cc_start: 0.8118 (t0) cc_final: 0.7741 (t70) REVERT: K 290 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8240 (mttt) REVERT: K 303 GLN cc_start: 0.7519 (mt0) cc_final: 0.7027 (tm-30) REVERT: K 405 THR cc_start: 0.8340 (p) cc_final: 0.8125 (t) REVERT: K 414 ASP cc_start: 0.7370 (m-30) cc_final: 0.6885 (m-30) REVERT: L 236 LYS cc_start: 0.7783 (mttt) cc_final: 0.7475 (pttp) REVERT: L 247 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7846 (mtm-85) REVERT: L 367 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8053 (mt-10) REVERT: L 414 ASP cc_start: 0.7304 (m-30) cc_final: 0.6606 (m-30) REVERT: M 230 LEU cc_start: 0.7550 (tp) cc_final: 0.6937 (mp) REVERT: M 271 ASP cc_start: 0.8192 (t0) cc_final: 0.7986 (t70) REVERT: M 303 GLN cc_start: 0.7067 (mt0) cc_final: 0.6569 (tm-30) REVERT: M 366 TYR cc_start: 0.8544 (m-80) cc_final: 0.8233 (m-80) REVERT: N 290 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8167 (mmmm) REVERT: N 367 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8139 (mm-30) REVERT: N 402 LEU cc_start: 0.7717 (tp) cc_final: 0.7442 (mm) REVERT: N 405 THR cc_start: 0.8373 (p) cc_final: 0.8166 (t) REVERT: O 236 LYS cc_start: 0.7843 (mttt) cc_final: 0.7420 (pttp) REVERT: O 249 ILE cc_start: 0.8798 (mt) cc_final: 0.8559 (mt) REVERT: O 269 GLN cc_start: 0.8000 (mp10) cc_final: 0.7788 (mp10) REVERT: O 271 ASP cc_start: 0.8150 (t0) cc_final: 0.7886 (t70) REVERT: O 405 THR cc_start: 0.8619 (p) cc_final: 0.8365 (t) REVERT: O 408 GLN cc_start: 0.8092 (mt0) cc_final: 0.7653 (mt0) REVERT: P 290 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8169 (mmmm) REVERT: P 303 GLN cc_start: 0.7478 (mt0) cc_final: 0.7014 (tm-30) REVERT: P 405 THR cc_start: 0.8582 (p) cc_final: 0.8173 (t) REVERT: Q 249 ILE cc_start: 0.9000 (mt) cc_final: 0.8770 (mt) REVERT: Q 290 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8168 (mmmm) REVERT: Q 303 GLN cc_start: 0.7348 (mt0) cc_final: 0.6839 (tm-30) REVERT: Q 412 ILE cc_start: 0.8705 (mm) cc_final: 0.8495 (mm) REVERT: R 253 LEU cc_start: 0.8201 (mt) cc_final: 0.7951 (mm) REVERT: R 385 LEU cc_start: 0.8825 (tp) cc_final: 0.8533 (tp) REVERT: R 405 THR cc_start: 0.8284 (p) cc_final: 0.7930 (t) REVERT: R 408 GLN cc_start: 0.8454 (mt0) cc_final: 0.8215 (mt0) REVERT: S 236 LYS cc_start: 0.7858 (mttt) cc_final: 0.7482 (pttp) REVERT: S 271 ASP cc_start: 0.7987 (t0) cc_final: 0.7667 (t70) REVERT: S 290 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8084 (mmmm) REVERT: S 303 GLN cc_start: 0.7097 (mt0) cc_final: 0.6656 (tm-30) REVERT: S 405 THR cc_start: 0.8322 (p) cc_final: 0.7916 (t) REVERT: S 408 GLN cc_start: 0.8324 (mt0) cc_final: 0.7921 (mt0) REVERT: S 414 ASP cc_start: 0.7198 (m-30) cc_final: 0.6937 (m-30) REVERT: T 271 ASP cc_start: 0.7977 (t0) cc_final: 0.7628 (t70) REVERT: T 290 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8235 (mmmm) REVERT: T 303 GLN cc_start: 0.7722 (mt0) cc_final: 0.7289 (tm-30) REVERT: T 416 THR cc_start: 0.8546 (m) cc_final: 0.8123 (p) REVERT: U 247 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7726 (mtm-85) REVERT: U 290 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8217 (mmmm) REVERT: U 303 GLN cc_start: 0.7044 (mt0) cc_final: 0.6531 (tm-30) REVERT: U 414 ASP cc_start: 0.7056 (m-30) cc_final: 0.6752 (m-30) REVERT: V 236 LYS cc_start: 0.7674 (mttt) cc_final: 0.7442 (pttp) REVERT: V 290 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8199 (mmmm) REVERT: V 367 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7870 (mt-10) REVERT: V 376 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8363 (mtpp) REVERT: V 418 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8475 (mm-30) REVERT: V 428 ASP cc_start: 0.8746 (m-30) cc_final: 0.8484 (m-30) REVERT: W 271 ASP cc_start: 0.8119 (t0) cc_final: 0.7860 (t70) REVERT: W 290 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8296 (mmmm) REVERT: W 362 GLU cc_start: 0.7789 (tt0) cc_final: 0.7572 (tt0) REVERT: X 303 GLN cc_start: 0.7321 (mt0) cc_final: 0.7009 (tm-30) REVERT: X 408 GLN cc_start: 0.8361 (mt0) cc_final: 0.8157 (mt0) REVERT: Y 230 LEU cc_start: 0.7695 (tp) cc_final: 0.7407 (mp) REVERT: Y 271 ASP cc_start: 0.8318 (t0) cc_final: 0.7922 (t70) REVERT: Y 367 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7990 (mm-30) REVERT: Y 408 GLN cc_start: 0.8161 (mt0) cc_final: 0.7866 (mt0) REVERT: Z 290 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8216 (mptt) REVERT: Z 367 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8095 (mm-30) REVERT: a 236 LYS cc_start: 0.7797 (mttt) cc_final: 0.7568 (pttp) REVERT: a 271 ASP cc_start: 0.8286 (t0) cc_final: 0.8083 (t70) REVERT: a 290 LYS cc_start: 0.8279 (mtmt) cc_final: 0.8053 (mmmm) REVERT: b 236 LYS cc_start: 0.7943 (mttt) cc_final: 0.7581 (pttp) REVERT: b 271 ASP cc_start: 0.8118 (t0) cc_final: 0.7741 (t70) REVERT: b 290 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8244 (mttt) REVERT: b 303 GLN cc_start: 0.7522 (mt0) cc_final: 0.7028 (tm-30) REVERT: b 405 THR cc_start: 0.8336 (p) cc_final: 0.8120 (t) REVERT: b 414 ASP cc_start: 0.7370 (m-30) cc_final: 0.6881 (m-30) REVERT: c 236 LYS cc_start: 0.7788 (mttt) cc_final: 0.7478 (pttp) REVERT: c 247 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7844 (mtm-85) REVERT: c 367 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8051 (mt-10) REVERT: c 414 ASP cc_start: 0.7306 (m-30) cc_final: 0.6617 (m-30) REVERT: d 230 LEU cc_start: 0.7551 (tp) cc_final: 0.6938 (mp) REVERT: d 271 ASP cc_start: 0.8192 (t0) cc_final: 0.7987 (t70) REVERT: d 303 GLN cc_start: 0.7074 (mt0) cc_final: 0.6574 (tm-30) REVERT: d 366 TYR cc_start: 0.8547 (m-80) cc_final: 0.8237 (m-80) REVERT: e 290 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8165 (mmmm) REVERT: e 367 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8142 (mm-30) REVERT: e 402 LEU cc_start: 0.7714 (tp) cc_final: 0.7438 (mm) REVERT: e 405 THR cc_start: 0.8375 (p) cc_final: 0.8168 (t) REVERT: f 236 LYS cc_start: 0.7850 (mttt) cc_final: 0.7422 (pttp) REVERT: f 249 ILE cc_start: 0.8794 (mt) cc_final: 0.8557 (mt) REVERT: f 269 GLN cc_start: 0.7999 (mp10) cc_final: 0.7782 (mp10) REVERT: f 271 ASP cc_start: 0.8151 (t0) cc_final: 0.7887 (t70) REVERT: f 405 THR cc_start: 0.8620 (p) cc_final: 0.8366 (t) REVERT: f 408 GLN cc_start: 0.8090 (mt0) cc_final: 0.7649 (mt0) REVERT: g 290 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8168 (mmmm) REVERT: g 303 GLN cc_start: 0.7480 (mt0) cc_final: 0.7016 (tm-30) REVERT: g 405 THR cc_start: 0.8581 (p) cc_final: 0.8164 (t) REVERT: h 249 ILE cc_start: 0.8999 (mt) cc_final: 0.8770 (mt) REVERT: h 290 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8168 (mmmm) REVERT: h 303 GLN cc_start: 0.7347 (mt0) cc_final: 0.6838 (tm-30) REVERT: h 412 ILE cc_start: 0.8703 (mm) cc_final: 0.8493 (mm) outliers start: 34 outliers final: 34 residues processed: 1840 average time/residue: 0.2488 time to fit residues: 729.0606 Evaluate side-chains 1520 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1486 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 G residue 295 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain I 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 X residue 295 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Z 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: 7.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 434 ASN B 303 GLN B 374 HIS B 434 ASN C 303 GLN C 374 HIS C 434 ASN D 303 GLN D 374 HIS D 431 ASN D 434 ASN E 374 HIS E 431 ASN E 434 ASN F 374 HIS F 434 ASN G 303 GLN G 374 HIS G 431 ASN G 434 ASN H 374 HIS ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 GLN I 374 HIS I 431 ASN I 434 ASN J 374 HIS ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN K 374 HIS K 434 ASN L 374 HIS L 431 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN M 374 HIS M 431 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 HIS N 408 GLN N 431 ASN ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 HIS O 431 ASN O 434 ASN P 303 GLN P 374 HIS P 431 ASN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN Q 374 HIS Q 408 GLN Q 431 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 HIS R 434 ASN S 303 GLN S 374 HIS S 431 ASN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 303 GLN T 374 HIS T 434 ASN U 303 GLN U 374 HIS U 431 ASN U 434 ASN V 374 HIS V 431 ASN V 434 ASN W 374 HIS W 434 ASN X 303 GLN X 374 HIS X 431 ASN X 434 ASN Y 374 HIS ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 265 GLN Z 374 HIS Z 431 ASN Z 434 ASN a 374 HIS ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 303 GLN b 374 HIS b 434 ASN c 374 HIS c 431 ASN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 GLN d 374 HIS d 431 ASN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 HIS e 408 GLN e 431 ASN ** e 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 374 HIS f 431 ASN f 434 ASN g 303 GLN g 374 HIS g 431 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 303 GLN h 374 HIS h 408 GLN h 431 ASN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112210 restraints weight = 60409.872| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.75 r_work: 0.3287 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 43826 Z= 0.275 Angle : 0.684 8.274 59194 Z= 0.359 Chirality : 0.047 0.187 6766 Planarity : 0.005 0.052 8024 Dihedral : 4.622 32.374 6052 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.57 % Allowed : 25.78 % Favored : 69.65 % 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: 1.65 (0.12), residues: 5440 helix: 3.68 (0.11), residues: 1428 sheet: 0.69 (0.11), residues: 2618 loop : -0.91 (0.14), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 244 TYR 0.021 0.003 TYR F 366 PHE 0.019 0.002 PHE a 422 HIS 0.005 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00623 (43826) covalent geometry : angle 0.68423 (59194) hydrogen bonds : bond 0.05030 ( 2619) hydrogen bonds : angle 4.86739 ( 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 1740 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1521 time to evaluate : 1.435 Fit side-chains REVERT: A 249 ILE cc_start: 0.9228 (mt) cc_final: 0.8948 (mt) REVERT: A 253 LEU cc_start: 0.8749 (mt) cc_final: 0.8451 (mm) REVERT: A 276 GLU cc_start: 0.7829 (tt0) cc_final: 0.7575 (tt0) REVERT: A 408 GLN cc_start: 0.8609 (mt0) cc_final: 0.8405 (mt0) REVERT: A 413 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 271 ASP cc_start: 0.8684 (t0) cc_final: 0.8463 (t70) REVERT: B 408 GLN cc_start: 0.8477 (mt0) cc_final: 0.7844 (tt0) REVERT: C 253 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8581 (mm) REVERT: C 373 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8111 (ttt90) REVERT: C 416 THR cc_start: 0.8763 (m) cc_final: 0.8379 (p) REVERT: D 373 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8114 (ttt-90) REVERT: D 413 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 414 ASP cc_start: 0.7437 (m-30) cc_final: 0.7236 (m-30) REVERT: E 276 GLU cc_start: 0.8098 (tt0) cc_final: 0.7881 (tt0) REVERT: E 413 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7869 (tm-30) REVERT: E 428 ASP cc_start: 0.9045 (m-30) cc_final: 0.8668 (m-30) REVERT: F 276 GLU cc_start: 0.7930 (tt0) cc_final: 0.7708 (tt0) REVERT: G 242 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8474 (mt-10) REVERT: G 276 GLU cc_start: 0.8159 (tt0) cc_final: 0.7905 (tt0) REVERT: G 294 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8582 (tpp-160) REVERT: G 383 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7802 (tp30) REVERT: G 413 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7532 (tm-30) REVERT: H 290 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8895 (mttp) REVERT: H 294 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8430 (tpp-160) REVERT: H 412 ILE cc_start: 0.8928 (mm) cc_final: 0.8718 (mm) REVERT: H 413 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7844 (tm-30) REVERT: H 423 SER cc_start: 0.8753 (t) cc_final: 0.8510 (p) REVERT: I 253 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8703 (mt) REVERT: I 276 GLU cc_start: 0.7691 (tt0) cc_final: 0.7482 (tt0) REVERT: I 416 THR cc_start: 0.8805 (m) cc_final: 0.8601 (p) REVERT: J 236 LYS cc_start: 0.8233 (mttt) cc_final: 0.7996 (pttp) REVERT: J 242 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8357 (mt-10) REVERT: J 271 ASP cc_start: 0.8657 (t0) cc_final: 0.8411 (t70) REVERT: J 420 MET cc_start: 0.9318 (ptm) cc_final: 0.8972 (ptm) REVERT: J 428 ASP cc_start: 0.9142 (m-30) cc_final: 0.8795 (m-30) REVERT: K 250 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7757 (mt-10) REVERT: K 366 TYR cc_start: 0.9193 (m-80) cc_final: 0.8593 (m-80) REVERT: K 408 GLN cc_start: 0.8460 (mt0) cc_final: 0.8140 (tt0) REVERT: K 428 ASP cc_start: 0.8652 (m-30) cc_final: 0.8349 (m-30) REVERT: L 246 GLN cc_start: 0.8747 (tt0) cc_final: 0.8493 (tt0) REVERT: L 294 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8134 (tpm170) REVERT: L 302 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7513 (mp0) REVERT: L 410 LYS cc_start: 0.8568 (tppt) cc_final: 0.8107 (tppt) REVERT: L 414 ASP cc_start: 0.7757 (m-30) cc_final: 0.7248 (m-30) REVERT: M 271 ASP cc_start: 0.8529 (t0) cc_final: 0.8259 (t70) REVERT: M 276 GLU cc_start: 0.8145 (tt0) cc_final: 0.7844 (tt0) REVERT: M 290 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8582 (mttm) REVERT: M 413 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7845 (tm-30) REVERT: N 271 ASP cc_start: 0.8433 (t70) cc_final: 0.8147 (t70) REVERT: N 408 GLN cc_start: 0.8526 (mt0) cc_final: 0.8085 (mt0) REVERT: N 416 THR cc_start: 0.8864 (m) cc_final: 0.8489 (p) REVERT: O 236 LYS cc_start: 0.8364 (mttt) cc_final: 0.8147 (pttp) REVERT: O 271 ASP cc_start: 0.8603 (t0) cc_final: 0.8396 (t70) REVERT: O 276 GLU cc_start: 0.8042 (tt0) cc_final: 0.7809 (tt0) REVERT: O 290 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8749 (mttp) REVERT: P 413 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7475 (tm-30) REVERT: P 414 ASP cc_start: 0.7389 (m-30) cc_final: 0.7145 (m-30) REVERT: Q 235 LEU cc_start: 0.9003 (mt) cc_final: 0.8695 (mt) REVERT: Q 413 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7802 (tm-30) REVERT: R 249 ILE cc_start: 0.9239 (mt) cc_final: 0.8958 (mt) REVERT: R 253 LEU cc_start: 0.8749 (mt) cc_final: 0.8462 (mm) REVERT: R 276 GLU cc_start: 0.7852 (tt0) cc_final: 0.7597 (tt0) REVERT: R 413 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7715 (tm-30) REVERT: S 271 ASP cc_start: 0.8671 (t0) cc_final: 0.8458 (t70) REVERT: S 408 GLN cc_start: 0.8476 (mt0) cc_final: 0.7849 (tt0) REVERT: T 253 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8577 (mm) REVERT: T 373 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8106 (ttt90) REVERT: T 416 THR cc_start: 0.8777 (m) cc_final: 0.8380 (p) REVERT: U 373 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8112 (ttt-90) REVERT: U 413 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7769 (tm-30) REVERT: V 276 GLU cc_start: 0.8068 (tt0) cc_final: 0.7858 (tt0) REVERT: V 413 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7881 (tm-30) REVERT: V 428 ASP cc_start: 0.9050 (m-30) cc_final: 0.8676 (m-30) REVERT: W 276 GLU cc_start: 0.7949 (tt0) cc_final: 0.7724 (tt0) REVERT: X 242 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8455 (mt-10) REVERT: X 276 GLU cc_start: 0.8157 (tt0) cc_final: 0.7898 (tt0) REVERT: X 294 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8576 (tpp-160) REVERT: X 383 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7830 (tp30) REVERT: X 413 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7541 (tm-30) REVERT: Y 290 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8888 (mttp) REVERT: Y 294 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (tpp-160) REVERT: Y 412 ILE cc_start: 0.8932 (mm) cc_final: 0.8716 (mm) REVERT: Y 413 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7826 (tm-30) REVERT: Y 423 SER cc_start: 0.8764 (t) cc_final: 0.8524 (p) REVERT: Z 253 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8703 (mt) REVERT: Z 276 GLU cc_start: 0.7695 (tt0) cc_final: 0.7488 (tt0) REVERT: Z 416 THR cc_start: 0.8809 (m) cc_final: 0.8600 (p) REVERT: a 236 LYS cc_start: 0.8215 (mttt) cc_final: 0.7983 (pttp) REVERT: a 242 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8356 (mt-10) REVERT: a 271 ASP cc_start: 0.8656 (t0) cc_final: 0.8407 (t70) REVERT: a 420 MET cc_start: 0.9324 (ptm) cc_final: 0.8980 (ptm) REVERT: a 428 ASP cc_start: 0.9144 (m-30) cc_final: 0.8798 (m-30) REVERT: b 250 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7767 (mt-10) REVERT: b 366 TYR cc_start: 0.9183 (m-80) cc_final: 0.8575 (m-80) REVERT: b 408 GLN cc_start: 0.8457 (mt0) cc_final: 0.8138 (tt0) REVERT: b 428 ASP cc_start: 0.8658 (m-30) cc_final: 0.8347 (m-30) REVERT: c 246 GLN cc_start: 0.8746 (tt0) cc_final: 0.8494 (tt0) REVERT: c 294 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8127 (tpm170) REVERT: c 302 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7499 (mp0) REVERT: c 410 LYS cc_start: 0.8565 (tppt) cc_final: 0.8160 (tppt) REVERT: c 413 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7548 (tm-30) REVERT: c 414 ASP cc_start: 0.7757 (m-30) cc_final: 0.7089 (m-30) REVERT: d 271 ASP cc_start: 0.8507 (t0) cc_final: 0.8241 (t70) REVERT: d 276 GLU cc_start: 0.8119 (tt0) cc_final: 0.7826 (tt0) REVERT: d 290 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8587 (mttm) REVERT: d 413 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7831 (tm-30) REVERT: e 271 ASP cc_start: 0.8407 (t70) cc_final: 0.8129 (t70) REVERT: e 408 GLN cc_start: 0.8537 (mt0) cc_final: 0.8101 (mt0) REVERT: e 416 THR cc_start: 0.8870 (m) cc_final: 0.8490 (p) REVERT: f 236 LYS cc_start: 0.8368 (mttt) cc_final: 0.8141 (pttp) REVERT: f 271 ASP cc_start: 0.8602 (t0) cc_final: 0.8401 (t70) REVERT: f 276 GLU cc_start: 0.8033 (tt0) cc_final: 0.7804 (tt0) REVERT: f 290 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8751 (mttp) REVERT: g 413 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7453 (tm-30) REVERT: g 414 ASP cc_start: 0.7406 (m-30) cc_final: 0.7159 (m-30) REVERT: h 235 LEU cc_start: 0.9004 (mt) cc_final: 0.8699 (mt) REVERT: h 413 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 219 outliers final: 68 residues processed: 1678 average time/residue: 0.2446 time to fit residues: 656.1539 Evaluate side-chains 1271 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1189 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 294 ARG Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain K residue 358 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 294 ARG Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 356 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 433 VAL Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 415 LEU Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 373 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain X residue 294 ARG Chi-restraints excluded: chain X residue 358 THR Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain X residue 431 ASN Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 294 ARG Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Z residue 253 LEU Chi-restraints excluded: chain Z residue 358 THR Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain b residue 358 THR Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 294 ARG Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 247 ARG Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 356 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 430 LEU Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 92 optimal weight: 0.0370 chunk 271 optimal weight: 3.9990 chunk 346 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 419 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 188 optimal weight: 0.0070 chunk 351 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 234 GLN B 431 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN F 408 GLN G 434 ASN I 265 GLN J 431 ASN K 234 GLN K 265 GLN K 434 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN P 434 ASN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 431 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN S 234 GLN T 234 GLN W 408 GLN X 434 ASN Z 265 GLN a 431 ASN b 234 GLN b 265 GLN ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 234 GLN g 434 ASN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 431 ASN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115563 restraints weight = 59778.506| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.73 r_work: 0.3347 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43826 Z= 0.115 Angle : 0.534 7.109 59194 Z= 0.277 Chirality : 0.041 0.142 6766 Planarity : 0.004 0.051 8024 Dihedral : 4.034 16.047 6018 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.53 % Allowed : 23.61 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.12), residues: 5440 helix: 3.81 (0.12), residues: 1428 sheet: 0.71 (0.11), residues: 2618 loop : -0.79 (0.14), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 244 TYR 0.013 0.001 TYR F 366 PHE 0.013 0.001 PHE a 422 HIS 0.001 0.000 HIS S 263 Details of bonding type rmsd covalent geometry : bond 0.00249 (43826) covalent geometry : angle 0.53363 (59194) hydrogen bonds : bond 0.03576 ( 2619) hydrogen bonds : angle 4.37176 ( 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 1463 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1294 time to evaluate : 1.918 Fit side-chains REVERT: A 249 ILE cc_start: 0.9130 (mt) cc_final: 0.8865 (mt) REVERT: A 253 LEU cc_start: 0.8461 (mt) cc_final: 0.8196 (mm) REVERT: A 276 GLU cc_start: 0.7856 (tt0) cc_final: 0.7599 (tt0) REVERT: A 290 LYS cc_start: 0.8700 (mttp) cc_final: 0.8391 (mtpp) REVERT: A 413 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 276 GLU cc_start: 0.7831 (tt0) cc_final: 0.7483 (mt-10) REVERT: D 290 LYS cc_start: 0.8895 (mttm) cc_final: 0.8537 (mtpp) REVERT: D 410 LYS cc_start: 0.8581 (tppt) cc_final: 0.8302 (tppt) REVERT: D 414 ASP cc_start: 0.7258 (m-30) cc_final: 0.6951 (m-30) REVERT: E 242 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 276 GLU cc_start: 0.7748 (tt0) cc_final: 0.7541 (tt0) REVERT: F 290 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8767 (mttp) REVERT: G 362 GLU cc_start: 0.7975 (tt0) cc_final: 0.7768 (tt0) REVERT: G 381 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7547 (t0) REVERT: G 413 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7411 (tm-30) REVERT: G 414 ASP cc_start: 0.7461 (m-30) cc_final: 0.7031 (m-30) REVERT: H 253 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7782 (mm) REVERT: H 276 GLU cc_start: 0.7351 (tt0) cc_final: 0.7037 (tt0) REVERT: H 412 ILE cc_start: 0.8904 (mm) cc_final: 0.8665 (mm) REVERT: H 413 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7985 (tm-30) REVERT: I 271 ASP cc_start: 0.8444 (t70) cc_final: 0.8043 (t0) REVERT: I 413 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7483 (tm-30) REVERT: J 370 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7753 (ttm-80) REVERT: J 428 ASP cc_start: 0.8888 (m-30) cc_final: 0.8593 (m-30) REVERT: K 366 TYR cc_start: 0.9181 (m-80) cc_final: 0.8755 (m-80) REVERT: K 408 GLN cc_start: 0.8322 (mt0) cc_final: 0.7852 (tt0) REVERT: L 413 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7542 (tm-30) REVERT: L 414 ASP cc_start: 0.7585 (m-30) cc_final: 0.7103 (m-30) REVERT: M 276 GLU cc_start: 0.7832 (tt0) cc_final: 0.7523 (tt0) REVERT: M 290 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8639 (mttm) REVERT: M 413 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7881 (tm-30) REVERT: O 236 LYS cc_start: 0.8291 (mttt) cc_final: 0.8034 (pttp) REVERT: O 276 GLU cc_start: 0.7638 (tt0) cc_final: 0.7429 (tt0) REVERT: O 290 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8834 (mttp) REVERT: O 413 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7599 (tm-30) REVERT: P 271 ASP cc_start: 0.8565 (t70) cc_final: 0.8327 (t0) REVERT: P 414 ASP cc_start: 0.7272 (m-30) cc_final: 0.6913 (m-30) REVERT: Q 413 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7599 (tm-30) REVERT: R 242 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8560 (mt-10) REVERT: R 249 ILE cc_start: 0.9142 (mt) cc_final: 0.8868 (mt) REVERT: R 253 LEU cc_start: 0.8521 (mt) cc_final: 0.8269 (mm) REVERT: R 276 GLU cc_start: 0.7857 (tt0) cc_final: 0.7601 (tt0) REVERT: R 290 LYS cc_start: 0.8702 (mttp) cc_final: 0.8390 (mtpp) REVERT: R 413 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7629 (tm-30) REVERT: S 276 GLU cc_start: 0.7851 (tt0) cc_final: 0.7491 (mt-10) REVERT: S 394 LYS cc_start: 0.7405 (mtmm) cc_final: 0.7194 (mtmm) REVERT: U 290 LYS cc_start: 0.8901 (mttm) cc_final: 0.8543 (mtpp) REVERT: U 410 LYS cc_start: 0.8490 (tppt) cc_final: 0.8286 (tppt) REVERT: U 413 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7823 (tm-30) REVERT: V 242 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8535 (mt-10) REVERT: V 276 GLU cc_start: 0.7713 (tt0) cc_final: 0.7510 (tt0) REVERT: W 290 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8774 (mttp) REVERT: X 362 GLU cc_start: 0.7974 (tt0) cc_final: 0.7774 (tt0) REVERT: X 381 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7536 (t0) REVERT: X 413 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7390 (tm-30) REVERT: X 414 ASP cc_start: 0.7449 (m-30) cc_final: 0.7017 (m-30) REVERT: Y 253 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7786 (mm) REVERT: Y 276 GLU cc_start: 0.7337 (tt0) cc_final: 0.7025 (tt0) REVERT: Y 412 ILE cc_start: 0.8903 (mm) cc_final: 0.8661 (mm) REVERT: Y 413 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7988 (tm-30) REVERT: Z 271 ASP cc_start: 0.8455 (t70) cc_final: 0.8056 (t0) REVERT: Z 413 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7491 (tm-30) REVERT: a 370 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: a 428 ASP cc_start: 0.8890 (m-30) cc_final: 0.8597 (m-30) REVERT: b 366 TYR cc_start: 0.9175 (m-80) cc_final: 0.8742 (m-80) REVERT: b 408 GLN cc_start: 0.8320 (mt0) cc_final: 0.7852 (tt0) REVERT: c 413 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7579 (tm-30) REVERT: c 414 ASP cc_start: 0.7589 (m-30) cc_final: 0.7117 (m-30) REVERT: d 276 GLU cc_start: 0.7842 (tt0) cc_final: 0.7533 (tt0) REVERT: d 290 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8651 (mttm) REVERT: d 413 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7881 (tm-30) REVERT: f 236 LYS cc_start: 0.8295 (mttt) cc_final: 0.8026 (pttp) REVERT: f 276 GLU cc_start: 0.7642 (tt0) cc_final: 0.7436 (tt0) REVERT: f 290 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8839 (mttp) REVERT: f 413 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7612 (tm-30) REVERT: g 271 ASP cc_start: 0.8544 (t70) cc_final: 0.8299 (t0) REVERT: g 414 ASP cc_start: 0.7270 (m-30) cc_final: 0.6901 (m-30) REVERT: h 413 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7601 (tm-30) outliers start: 169 outliers final: 87 residues processed: 1377 average time/residue: 0.2860 time to fit residues: 634.8853 Evaluate side-chains 1241 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1148 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 431 ASN Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 356 ARG Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain X residue 431 ASN Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 356 ARG Chi-restraints excluded: chain e residue 278 THR Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 520 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 447 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 263 HIS C 431 ASN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 GLN G 431 ASN G 434 ASN K 234 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 431 ASN M 434 ASN N 234 GLN P 234 GLN Q 431 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 434 ASN T 234 GLN T 263 HIS T 274 ASN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 408 GLN X 431 ASN X 434 ASN b 234 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 431 ASN d 434 ASN e 234 GLN g 234 GLN h 265 GLN h 431 ASN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115033 restraints weight = 59342.699| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.66 r_work: 0.3317 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43826 Z= 0.133 Angle : 0.528 6.076 59194 Z= 0.274 Chirality : 0.041 0.147 6766 Planarity : 0.004 0.056 8024 Dihedral : 3.999 15.236 6018 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.65 % Allowed : 24.05 % Favored : 72.30 % 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: 1.74 (0.12), residues: 5440 helix: 3.72 (0.12), residues: 1428 sheet: 0.74 (0.11), residues: 2618 loop : -0.81 (0.14), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 247 TYR 0.015 0.001 TYR L 366 PHE 0.014 0.001 PHE a 422 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00298 (43826) covalent geometry : angle 0.52784 (59194) hydrogen bonds : bond 0.03446 ( 2619) hydrogen bonds : angle 4.25040 ( 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 1426 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1251 time to evaluate : 1.905 Fit side-chains REVERT: A 242 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 249 ILE cc_start: 0.9132 (mt) cc_final: 0.8856 (mt) REVERT: A 253 LEU cc_start: 0.8398 (mt) cc_final: 0.8150 (mm) REVERT: A 276 GLU cc_start: 0.7916 (tt0) cc_final: 0.7645 (tt0) REVERT: A 290 LYS cc_start: 0.8692 (mttp) cc_final: 0.8385 (mtpp) REVERT: A 413 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 276 GLU cc_start: 0.7946 (tt0) cc_final: 0.7540 (mt-10) REVERT: B 377 MET cc_start: 0.8715 (mpt) cc_final: 0.8196 (mpt) REVERT: C 416 THR cc_start: 0.8731 (m) cc_final: 0.8363 (p) REVERT: D 370 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: E 276 GLU cc_start: 0.7680 (tt0) cc_final: 0.7464 (tt0) REVERT: E 413 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7984 (tm-30) REVERT: F 290 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8800 (mttp) REVERT: F 370 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7881 (ttm-80) REVERT: G 381 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7554 (t0) REVERT: G 413 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7572 (tm-30) REVERT: H 271 ASP cc_start: 0.8520 (t70) cc_final: 0.8240 (t0) REVERT: H 276 GLU cc_start: 0.7403 (tt0) cc_final: 0.7131 (tt0) REVERT: H 370 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7825 (ttm-80) REVERT: H 413 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7733 (tm-30) REVERT: I 275 LYS cc_start: 0.8787 (mttm) cc_final: 0.8514 (mttp) REVERT: J 420 MET cc_start: 0.9215 (ptm) cc_final: 0.8753 (ptm) REVERT: J 428 ASP cc_start: 0.8924 (m-30) cc_final: 0.8559 (m-30) REVERT: K 366 TYR cc_start: 0.9197 (m-80) cc_final: 0.8836 (m-80) REVERT: K 408 GLN cc_start: 0.8345 (mt0) cc_final: 0.7933 (tt0) REVERT: M 271 ASP cc_start: 0.8208 (t70) cc_final: 0.7994 (t0) REVERT: M 276 GLU cc_start: 0.7856 (tt0) cc_final: 0.7568 (tt0) REVERT: M 290 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8674 (mttm) REVERT: M 302 GLU cc_start: 0.7836 (tt0) cc_final: 0.7481 (tp30) REVERT: M 408 GLN cc_start: 0.8259 (mt0) cc_final: 0.7975 (mt0) REVERT: N 265 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8455 (mm-40) REVERT: N 271 ASP cc_start: 0.8550 (t70) cc_final: 0.8066 (t0) REVERT: N 370 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7834 (ttm-80) REVERT: N 408 GLN cc_start: 0.8186 (mt0) cc_final: 0.7950 (mt0) REVERT: O 236 LYS cc_start: 0.8305 (mttt) cc_final: 0.8046 (pttp) REVERT: O 290 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8719 (mttp) REVERT: O 370 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: O 413 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7618 (tm-30) REVERT: P 271 ASP cc_start: 0.8558 (t70) cc_final: 0.8321 (t0) REVERT: P 414 ASP cc_start: 0.7415 (m-30) cc_final: 0.7061 (m-30) REVERT: Q 424 ASP cc_start: 0.8375 (m-30) cc_final: 0.8142 (m-30) REVERT: R 249 ILE cc_start: 0.9142 (mt) cc_final: 0.8862 (mt) REVERT: R 276 GLU cc_start: 0.7809 (tt0) cc_final: 0.7540 (tt0) REVERT: R 290 LYS cc_start: 0.8688 (mttp) cc_final: 0.8378 (mtpp) REVERT: S 276 GLU cc_start: 0.7917 (tt0) cc_final: 0.7518 (mt-10) REVERT: S 377 MET cc_start: 0.8725 (mpt) cc_final: 0.8211 (mpt) REVERT: T 416 THR cc_start: 0.8721 (m) cc_final: 0.8358 (p) REVERT: U 370 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7914 (ttm-80) REVERT: V 276 GLU cc_start: 0.7673 (tt0) cc_final: 0.7465 (tt0) REVERT: V 413 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7962 (tm-30) REVERT: W 290 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8811 (mttp) REVERT: W 370 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7883 (ttm-80) REVERT: X 381 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7521 (t0) REVERT: X 413 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7578 (tm-30) REVERT: Y 271 ASP cc_start: 0.8506 (t70) cc_final: 0.8227 (t0) REVERT: Y 276 GLU cc_start: 0.7389 (tt0) cc_final: 0.7120 (tt0) REVERT: Y 370 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7819 (ttm-80) REVERT: Y 413 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7731 (tm-30) REVERT: Z 275 LYS cc_start: 0.8789 (mttm) cc_final: 0.8519 (mttp) REVERT: Z 383 GLU cc_start: 0.8213 (mm-30) cc_final: 0.8012 (mm-30) REVERT: a 420 MET cc_start: 0.9210 (ptm) cc_final: 0.8746 (ptm) REVERT: a 428 ASP cc_start: 0.8920 (m-30) cc_final: 0.8555 (m-30) REVERT: b 366 TYR cc_start: 0.9184 (m-80) cc_final: 0.8823 (m-80) REVERT: b 408 GLN cc_start: 0.8353 (mt0) cc_final: 0.7937 (tt0) REVERT: c 302 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: d 271 ASP cc_start: 0.8190 (t70) cc_final: 0.7978 (t0) REVERT: d 276 GLU cc_start: 0.7843 (tt0) cc_final: 0.7558 (tt0) REVERT: d 290 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8682 (mttm) REVERT: d 302 GLU cc_start: 0.7852 (tt0) cc_final: 0.7501 (tp30) REVERT: d 408 GLN cc_start: 0.8235 (mt0) cc_final: 0.7949 (mt0) REVERT: e 265 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8447 (mm-40) REVERT: e 271 ASP cc_start: 0.8548 (t70) cc_final: 0.8065 (t0) REVERT: e 370 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7849 (ttm-80) REVERT: e 408 GLN cc_start: 0.8189 (mt0) cc_final: 0.7950 (mt0) REVERT: f 236 LYS cc_start: 0.8298 (mttt) cc_final: 0.8040 (pttp) REVERT: f 290 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8715 (mttp) REVERT: f 370 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7936 (ttm-80) REVERT: f 413 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7616 (tm-30) REVERT: g 271 ASP cc_start: 0.8546 (t70) cc_final: 0.8302 (t0) REVERT: g 414 ASP cc_start: 0.7422 (m-30) cc_final: 0.7062 (m-30) REVERT: h 424 ASP cc_start: 0.8388 (m-30) cc_final: 0.8154 (m-30) outliers start: 175 outliers final: 101 residues processed: 1347 average time/residue: 0.2925 time to fit residues: 627.9920 Evaluate side-chains 1289 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1175 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 356 ARG Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 236 LYS Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 302 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 356 ARG Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 200 optimal weight: 3.9990 chunk 488 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 533 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 539 optimal weight: 0.9990 chunk 450 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 234 GLN E 234 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 ASN J 434 ASN K 234 GLN K 265 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN P 234 GLN Q 431 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN U 234 GLN V 234 GLN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 408 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 434 ASN a 434 ASN b 234 GLN b 265 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 234 GLN g 234 GLN h 265 GLN h 431 ASN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113341 restraints weight = 59791.888| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.76 r_work: 0.3316 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43826 Z= 0.128 Angle : 0.519 6.254 59194 Z= 0.268 Chirality : 0.041 0.132 6766 Planarity : 0.005 0.058 8024 Dihedral : 3.961 15.191 6018 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.46 % Allowed : 25.05 % 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: 1.76 (0.12), residues: 5440 helix: 3.74 (0.12), residues: 1428 sheet: 0.90 (0.11), residues: 2482 loop : -0.95 (0.13), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 356 TYR 0.015 0.001 TYR c 366 PHE 0.013 0.001 PHE a 422 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00289 (43826) covalent geometry : angle 0.51909 (59194) hydrogen bonds : bond 0.03290 ( 2619) hydrogen bonds : angle 4.18511 ( 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 1412 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1246 time to evaluate : 2.081 Fit side-chains REVERT: A 249 ILE cc_start: 0.9115 (mt) cc_final: 0.8850 (mt) REVERT: A 253 LEU cc_start: 0.8252 (mt) cc_final: 0.7996 (mm) REVERT: A 276 GLU cc_start: 0.7874 (tt0) cc_final: 0.7602 (tt0) REVERT: A 290 LYS cc_start: 0.8725 (mttp) cc_final: 0.8417 (mtpp) REVERT: B 276 GLU cc_start: 0.7946 (tt0) cc_final: 0.7584 (mt-10) REVERT: B 370 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7625 (ttm-80) REVERT: B 377 MET cc_start: 0.8759 (mpt) cc_final: 0.8233 (mpt) REVERT: C 416 THR cc_start: 0.8745 (m) cc_final: 0.8360 (p) REVERT: D 250 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7331 (mp0) REVERT: D 370 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7956 (ttm-80) REVERT: E 413 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7961 (tm-30) REVERT: F 256 ILE cc_start: 0.7585 (pt) cc_final: 0.7235 (pp) REVERT: F 290 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8831 (mttp) REVERT: F 370 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7911 (ttm-80) REVERT: F 413 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7468 (tm-30) REVERT: G 413 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7497 (tm-30) REVERT: G 414 ASP cc_start: 0.7524 (m-30) cc_final: 0.7134 (m-30) REVERT: H 276 GLU cc_start: 0.7357 (tt0) cc_final: 0.7115 (tt0) REVERT: H 290 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8543 (mttp) REVERT: H 370 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7827 (ttm-80) REVERT: H 412 ILE cc_start: 0.8946 (mm) cc_final: 0.8743 (mm) REVERT: I 275 LYS cc_start: 0.8812 (mttm) cc_final: 0.8537 (mttp) REVERT: I 413 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7550 (tm-30) REVERT: J 370 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7783 (ttm-80) REVERT: J 428 ASP cc_start: 0.8907 (m-30) cc_final: 0.8617 (m-30) REVERT: K 250 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7444 (mt-10) REVERT: K 276 GLU cc_start: 0.7618 (tt0) cc_final: 0.7383 (tt0) REVERT: K 366 TYR cc_start: 0.9195 (m-80) cc_final: 0.8855 (m-80) REVERT: K 370 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7868 (ttm-80) REVERT: K 408 GLN cc_start: 0.8347 (mt0) cc_final: 0.7942 (tt0) REVERT: M 276 GLU cc_start: 0.7905 (tt0) cc_final: 0.7605 (tt0) REVERT: M 290 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8732 (mtpp) REVERT: M 302 GLU cc_start: 0.7866 (tt0) cc_final: 0.7609 (tp30) REVERT: M 408 GLN cc_start: 0.8288 (mt0) cc_final: 0.7977 (mt0) REVERT: N 265 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8592 (mm-40) REVERT: N 271 ASP cc_start: 0.8615 (t70) cc_final: 0.8164 (t0) REVERT: N 370 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: N 408 GLN cc_start: 0.8223 (mt0) cc_final: 0.7949 (mt0) REVERT: O 236 LYS cc_start: 0.8281 (mttt) cc_final: 0.8035 (pttp) REVERT: O 271 ASP cc_start: 0.8513 (t70) cc_final: 0.8211 (t70) REVERT: O 290 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8716 (mttp) REVERT: O 370 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7971 (ttm-80) REVERT: O 383 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8129 (mt-10) REVERT: O 413 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7618 (tm-30) REVERT: P 271 ASP cc_start: 0.8577 (t70) cc_final: 0.8274 (t0) REVERT: P 414 ASP cc_start: 0.7455 (m-30) cc_final: 0.7101 (m-30) REVERT: Q 413 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7687 (tm-30) REVERT: R 276 GLU cc_start: 0.7870 (tt0) cc_final: 0.7595 (tt0) REVERT: R 290 LYS cc_start: 0.8728 (mttp) cc_final: 0.8420 (mtpp) REVERT: R 413 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7717 (tm-30) REVERT: S 276 GLU cc_start: 0.7928 (tt0) cc_final: 0.7576 (mt-10) REVERT: S 370 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7635 (ttm-80) REVERT: S 377 MET cc_start: 0.8775 (mpt) cc_final: 0.8254 (mpt) REVERT: T 416 THR cc_start: 0.8732 (m) cc_final: 0.8352 (p) REVERT: U 370 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7956 (ttm-80) REVERT: U 413 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7775 (tm-30) REVERT: U 414 ASP cc_start: 0.7307 (m-30) cc_final: 0.7060 (m-30) REVERT: V 413 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7963 (tm-30) REVERT: W 256 ILE cc_start: 0.7583 (pt) cc_final: 0.7236 (pp) REVERT: W 290 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8833 (mttp) REVERT: W 370 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: W 413 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7445 (tm-30) REVERT: X 413 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7503 (tm-30) REVERT: X 414 ASP cc_start: 0.7538 (m-30) cc_final: 0.7150 (m-30) REVERT: Y 271 ASP cc_start: 0.8523 (t70) cc_final: 0.8237 (t0) REVERT: Y 275 LYS cc_start: 0.8773 (mttp) cc_final: 0.8513 (mttm) REVERT: Y 276 GLU cc_start: 0.7322 (tt0) cc_final: 0.7079 (tt0) REVERT: Y 290 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8538 (mttp) REVERT: Y 370 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7812 (ttm-80) REVERT: Y 412 ILE cc_start: 0.8938 (mm) cc_final: 0.8732 (mm) REVERT: Z 275 LYS cc_start: 0.8796 (mttm) cc_final: 0.8566 (mttp) REVERT: Z 413 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7557 (tm-30) REVERT: a 370 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7758 (ttm-80) REVERT: a 428 ASP cc_start: 0.8894 (m-30) cc_final: 0.8606 (m-30) REVERT: b 250 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7456 (mt-10) REVERT: b 276 GLU cc_start: 0.7608 (tt0) cc_final: 0.7372 (tt0) REVERT: b 366 TYR cc_start: 0.9183 (m-80) cc_final: 0.8840 (m-80) REVERT: b 370 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7874 (ttm-80) REVERT: b 408 GLN cc_start: 0.8355 (mt0) cc_final: 0.7948 (tt0) REVERT: d 276 GLU cc_start: 0.7875 (tt0) cc_final: 0.7579 (tt0) REVERT: d 290 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8753 (mtpp) REVERT: d 302 GLU cc_start: 0.7872 (tt0) cc_final: 0.7612 (tp30) REVERT: d 408 GLN cc_start: 0.8275 (mt0) cc_final: 0.7968 (mt0) REVERT: e 265 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8591 (mm-40) REVERT: e 271 ASP cc_start: 0.8618 (t70) cc_final: 0.8165 (t0) REVERT: e 370 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7761 (ttm-80) REVERT: e 408 GLN cc_start: 0.8225 (mt0) cc_final: 0.7950 (mt0) REVERT: f 236 LYS cc_start: 0.8265 (mttt) cc_final: 0.8028 (pttp) REVERT: f 271 ASP cc_start: 0.8520 (t70) cc_final: 0.8213 (t70) REVERT: f 290 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8713 (mttp) REVERT: f 370 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7986 (ttm-80) REVERT: f 383 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8121 (mt-10) REVERT: f 413 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7621 (tm-30) REVERT: g 271 ASP cc_start: 0.8578 (t70) cc_final: 0.8280 (t0) REVERT: g 414 ASP cc_start: 0.7451 (m-30) cc_final: 0.7093 (m-30) REVERT: h 413 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7686 (tm-30) outliers start: 166 outliers final: 107 residues processed: 1336 average time/residue: 0.2917 time to fit residues: 617.1597 Evaluate side-chains 1338 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1215 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 370 ARG Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 420 MET Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 251 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 chunk 398 optimal weight: 0.9980 chunk 375 optimal weight: 0.3980 chunk 327 optimal weight: 6.9990 chunk 426 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN N 234 GLN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN e 234 GLN h 265 GLN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111909 restraints weight = 60217.042| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.76 r_work: 0.3314 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43826 Z= 0.122 Angle : 0.514 6.235 59194 Z= 0.265 Chirality : 0.041 0.136 6766 Planarity : 0.005 0.059 8024 Dihedral : 3.924 14.762 6018 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.01 % Allowed : 25.20 % Favored : 70.80 % 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: 1.78 (0.12), residues: 5440 helix: 3.72 (0.12), residues: 1428 sheet: 0.74 (0.10), residues: 2618 loop : -0.68 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 356 TYR 0.014 0.001 TYR L 366 PHE 0.013 0.001 PHE a 422 HIS 0.001 0.000 HIS Z 263 Details of bonding type rmsd covalent geometry : bond 0.00275 (43826) covalent geometry : angle 0.51431 (59194) hydrogen bonds : bond 0.03164 ( 2619) hydrogen bonds : angle 4.12585 ( 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 1441 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1249 time to evaluate : 1.927 Fit side-chains REVERT: A 249 ILE cc_start: 0.9101 (mt) cc_final: 0.8855 (mt) REVERT: A 253 LEU cc_start: 0.8240 (mt) cc_final: 0.8024 (mm) REVERT: A 276 GLU cc_start: 0.7963 (tt0) cc_final: 0.7696 (tt0) REVERT: A 290 LYS cc_start: 0.8875 (mttp) cc_final: 0.8595 (mtpp) REVERT: A 370 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7945 (ttm-80) REVERT: A 413 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 275 LYS cc_start: 0.8901 (mttm) cc_final: 0.8617 (mttp) REVERT: B 276 GLU cc_start: 0.7894 (tt0) cc_final: 0.7511 (mt-10) REVERT: B 370 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7679 (ttm-80) REVERT: C 370 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7791 (ttm-80) REVERT: C 408 GLN cc_start: 0.8493 (mt0) cc_final: 0.8211 (mt0) REVERT: C 416 THR cc_start: 0.8746 (m) cc_final: 0.8368 (p) REVERT: D 290 LYS cc_start: 0.9071 (mttm) cc_final: 0.8729 (mtpp) REVERT: D 370 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: F 256 ILE cc_start: 0.7570 (pt) cc_final: 0.7257 (pp) REVERT: F 290 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8834 (mttp) REVERT: F 370 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: G 413 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7485 (tm-30) REVERT: G 414 ASP cc_start: 0.7558 (m-30) cc_final: 0.7141 (m-30) REVERT: H 370 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7846 (ttm-80) REVERT: I 413 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7253 (tm-30) REVERT: J 370 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7718 (ttm-80) REVERT: J 420 MET cc_start: 0.9004 (ptm) cc_final: 0.8657 (ptm) REVERT: J 428 ASP cc_start: 0.8909 (m-30) cc_final: 0.8652 (m-30) REVERT: K 250 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7414 (mt-10) REVERT: K 276 GLU cc_start: 0.7642 (tt0) cc_final: 0.7412 (tt0) REVERT: K 356 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6228 (ptp-170) REVERT: K 366 TYR cc_start: 0.9218 (m-80) cc_final: 0.8929 (m-80) REVERT: K 367 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8671 (mm-30) REVERT: K 370 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7870 (ttm-80) REVERT: K 408 GLN cc_start: 0.8337 (mt0) cc_final: 0.7950 (tt0) REVERT: L 256 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7571 (pt) REVERT: L 370 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8175 (ttm-80) REVERT: L 377 MET cc_start: 0.8547 (mpt) cc_final: 0.8112 (mpt) REVERT: L 383 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: L 413 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7582 (tm-30) REVERT: L 428 ASP cc_start: 0.8618 (m-30) cc_final: 0.8331 (m-30) REVERT: M 242 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8371 (mt-10) REVERT: M 246 GLN cc_start: 0.8804 (tt0) cc_final: 0.8535 (tt0) REVERT: M 276 GLU cc_start: 0.7900 (tt0) cc_final: 0.7581 (tt0) REVERT: M 302 GLU cc_start: 0.7924 (tt0) cc_final: 0.7627 (tp30) REVERT: M 408 GLN cc_start: 0.8358 (mt0) cc_final: 0.8096 (mt0) REVERT: N 265 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8624 (mm-40) REVERT: N 271 ASP cc_start: 0.8772 (t70) cc_final: 0.8378 (t0) REVERT: N 276 GLU cc_start: 0.8092 (tt0) cc_final: 0.7763 (tt0) REVERT: N 370 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7799 (ttm-80) REVERT: O 271 ASP cc_start: 0.8354 (t70) cc_final: 0.8121 (t0) REVERT: O 290 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8730 (mttp) REVERT: O 370 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: O 413 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7577 (tm-30) REVERT: P 271 ASP cc_start: 0.8581 (t70) cc_final: 0.8345 (t0) REVERT: P 370 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7871 (ttm-80) REVERT: P 414 ASP cc_start: 0.7466 (m-30) cc_final: 0.7064 (m-30) REVERT: Q 370 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7643 (ttm-80) REVERT: Q 413 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7742 (tm-30) REVERT: Q 424 ASP cc_start: 0.8237 (m-30) cc_final: 0.7900 (m-30) REVERT: R 265 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8054 (mm-40) REVERT: R 276 GLU cc_start: 0.7960 (tt0) cc_final: 0.7689 (tt0) REVERT: R 290 LYS cc_start: 0.8871 (mttp) cc_final: 0.8587 (mtpp) REVERT: R 370 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: S 275 LYS cc_start: 0.8887 (mttm) cc_final: 0.8599 (mttp) REVERT: S 276 GLU cc_start: 0.7911 (tt0) cc_final: 0.7517 (mt-10) REVERT: S 370 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7681 (ttm-80) REVERT: T 370 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7800 (ttm-80) REVERT: T 408 GLN cc_start: 0.8492 (mt0) cc_final: 0.8210 (mt0) REVERT: T 416 THR cc_start: 0.8732 (m) cc_final: 0.8362 (p) REVERT: U 290 LYS cc_start: 0.9060 (mttm) cc_final: 0.8730 (mtpp) REVERT: U 370 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7993 (ttm-80) REVERT: U 410 LYS cc_start: 0.8577 (tppt) cc_final: 0.8312 (tppt) REVERT: U 414 ASP cc_start: 0.7312 (m-30) cc_final: 0.7072 (m-30) REVERT: W 244 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7420 (ttp-170) REVERT: W 256 ILE cc_start: 0.7570 (pt) cc_final: 0.7254 (pp) REVERT: W 290 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8841 (mttp) REVERT: W 370 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7894 (ttm-80) REVERT: X 413 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7495 (tm-30) REVERT: X 414 ASP cc_start: 0.7555 (m-30) cc_final: 0.7137 (m-30) REVERT: Y 271 ASP cc_start: 0.8522 (t70) cc_final: 0.8061 (t0) REVERT: Y 275 LYS cc_start: 0.8728 (mttp) cc_final: 0.8247 (mttp) REVERT: Y 276 GLU cc_start: 0.7350 (tt0) cc_final: 0.7136 (tt0) REVERT: Y 370 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7835 (ttm-80) REVERT: Z 275 LYS cc_start: 0.8789 (mttm) cc_final: 0.8540 (mttp) REVERT: Z 373 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8104 (ttt180) REVERT: Z 413 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7492 (tm-30) REVERT: a 370 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7698 (ttm-80) REVERT: a 420 MET cc_start: 0.9001 (ptm) cc_final: 0.8652 (ptm) REVERT: a 428 ASP cc_start: 0.8900 (m-30) cc_final: 0.8653 (m-30) REVERT: b 250 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7446 (mt-10) REVERT: b 276 GLU cc_start: 0.7597 (tt0) cc_final: 0.7364 (tt0) REVERT: b 356 ARG cc_start: 0.6707 (ttp-110) cc_final: 0.6178 (ptp-170) REVERT: b 366 TYR cc_start: 0.9210 (m-80) cc_final: 0.8922 (m-80) REVERT: b 367 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8673 (mm-30) REVERT: b 370 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7874 (ttm-80) REVERT: b 408 GLN cc_start: 0.8346 (mt0) cc_final: 0.7960 (tt0) REVERT: c 256 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7575 (pt) REVERT: c 370 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: c 383 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: c 413 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7581 (tm-30) REVERT: c 428 ASP cc_start: 0.8630 (m-30) cc_final: 0.8340 (m-30) REVERT: d 242 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8363 (mt-10) REVERT: d 246 GLN cc_start: 0.8788 (tt0) cc_final: 0.8518 (tt0) REVERT: d 276 GLU cc_start: 0.7891 (tt0) cc_final: 0.7570 (tt0) REVERT: d 302 GLU cc_start: 0.7926 (tt0) cc_final: 0.7641 (tp30) REVERT: d 408 GLN cc_start: 0.8355 (mt0) cc_final: 0.8094 (mt0) REVERT: e 265 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8626 (mm-40) REVERT: e 271 ASP cc_start: 0.8756 (t70) cc_final: 0.8368 (t0) REVERT: e 276 GLU cc_start: 0.8052 (tt0) cc_final: 0.7729 (tt0) REVERT: e 370 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: f 271 ASP cc_start: 0.8352 (t70) cc_final: 0.8122 (t0) REVERT: f 290 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8728 (mttp) REVERT: f 370 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7994 (ttm-80) REVERT: f 413 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7586 (tm-30) REVERT: g 271 ASP cc_start: 0.8568 (t70) cc_final: 0.8333 (t0) REVERT: g 370 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7891 (ttm-80) REVERT: g 414 ASP cc_start: 0.7457 (m-30) cc_final: 0.7056 (m-30) REVERT: h 370 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7586 (ttm-80) REVERT: h 413 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7748 (tm-30) REVERT: h 424 ASP cc_start: 0.8241 (m-30) cc_final: 0.7907 (m-30) outliers start: 192 outliers final: 122 residues processed: 1364 average time/residue: 0.3068 time to fit residues: 659.3891 Evaluate side-chains 1337 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1183 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 385 LEU Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 370 ARG Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 370 ARG Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 370 ARG Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 236 LYS Chi-restraints excluded: chain T residue 370 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 356 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 244 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 394 LYS Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 236 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 373 ARG Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 359 GLN Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 370 ARG Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 278 THR Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 370 ARG Chi-restraints excluded: chain h residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 267 optimal weight: 0.9990 chunk 445 optimal weight: 0.0470 chunk 235 optimal weight: 0.7980 chunk 423 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 290 optimal weight: 0.3980 chunk 240 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN L 234 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN P 234 GLN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 246 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 234 GLN g 234 GLN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108495 restraints weight = 60721.539| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.80 r_work: 0.3297 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5627 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= 0.106 Angle : 0.509 6.671 59194 Z= 0.261 Chirality : 0.041 0.128 6766 Planarity : 0.005 0.059 8024 Dihedral : 3.866 15.162 6018 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.55 % Allowed : 26.07 % Favored : 70.38 % 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: 1.74 (0.12), residues: 5440 helix: 3.76 (0.13), residues: 1394 sheet: 0.90 (0.11), residues: 2516 loop : -0.96 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 247 TYR 0.013 0.001 TYR c 366 PHE 0.011 0.001 PHE J 422 HIS 0.001 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00238 (43826) covalent geometry : angle 0.50893 (59194) hydrogen bonds : bond 0.02936 ( 2619) hydrogen bonds : angle 4.02697 ( 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 1423 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1253 time to evaluate : 1.846 Fit side-chains REVERT: A 249 ILE cc_start: 0.9089 (mt) cc_final: 0.8840 (mt) REVERT: A 276 GLU cc_start: 0.8052 (tt0) cc_final: 0.7754 (tt0) REVERT: A 290 LYS cc_start: 0.8914 (mttp) cc_final: 0.8596 (mtpp) REVERT: A 370 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8024 (ttm-80) REVERT: A 413 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 275 LYS cc_start: 0.8927 (mttm) cc_final: 0.8620 (mttp) REVERT: B 276 GLU cc_start: 0.7809 (tt0) cc_final: 0.7343 (mt-10) REVERT: B 370 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7677 (ttm-80) REVERT: C 370 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7821 (ttm-80) REVERT: C 408 GLN cc_start: 0.8531 (mt0) cc_final: 0.8204 (mt0) REVERT: C 416 THR cc_start: 0.8728 (m) cc_final: 0.8335 (p) REVERT: D 370 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8029 (ttm-80) REVERT: E 423 SER cc_start: 0.8672 (t) cc_final: 0.8441 (p) REVERT: F 244 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7442 (ttp-170) REVERT: F 256 ILE cc_start: 0.7460 (pt) cc_final: 0.7241 (pp) REVERT: F 290 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8788 (mttp) REVERT: F 370 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: G 367 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8466 (mm-30) REVERT: G 413 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7489 (tm-30) REVERT: G 414 ASP cc_start: 0.7581 (m-30) cc_final: 0.7174 (m-30) REVERT: H 276 GLU cc_start: 0.7445 (tt0) cc_final: 0.7127 (mt-10) REVERT: H 370 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7882 (ttm-80) REVERT: H 412 ILE cc_start: 0.8984 (mm) cc_final: 0.8727 (mm) REVERT: J 370 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7767 (ttm-80) REVERT: J 420 MET cc_start: 0.8915 (ptm) cc_final: 0.8580 (ptm) REVERT: K 250 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7470 (mt-10) REVERT: K 276 GLU cc_start: 0.7673 (tt0) cc_final: 0.7446 (tt0) REVERT: K 356 ARG cc_start: 0.6792 (ttp-110) cc_final: 0.6296 (ptp-170) REVERT: K 366 TYR cc_start: 0.9219 (m-80) cc_final: 0.8934 (m-80) REVERT: K 370 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: K 408 GLN cc_start: 0.8338 (mt0) cc_final: 0.7982 (tt0) REVERT: L 256 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7624 (pt) REVERT: L 271 ASP cc_start: 0.8495 (t0) cc_final: 0.8201 (t70) REVERT: L 370 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8164 (ttm-80) REVERT: L 377 MET cc_start: 0.8570 (mpt) cc_final: 0.8126 (mpt) REVERT: L 383 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: L 413 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7574 (tm-30) REVERT: L 428 ASP cc_start: 0.8572 (m-30) cc_final: 0.8298 (m-30) REVERT: M 242 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8378 (mt-10) REVERT: M 246 GLN cc_start: 0.8796 (tt0) cc_final: 0.8125 (tt0) REVERT: M 250 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7331 (mp0) REVERT: M 276 GLU cc_start: 0.7958 (tt0) cc_final: 0.7615 (tt0) REVERT: M 302 GLU cc_start: 0.7959 (tt0) cc_final: 0.7581 (tp30) REVERT: M 408 GLN cc_start: 0.8258 (mt0) cc_final: 0.7949 (mt0) REVERT: M 413 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7915 (tm-30) REVERT: N 265 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8605 (mm-40) REVERT: N 271 ASP cc_start: 0.8693 (t70) cc_final: 0.8305 (t0) REVERT: N 276 GLU cc_start: 0.8145 (tt0) cc_final: 0.7798 (tt0) REVERT: N 370 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7837 (ttm-80) REVERT: O 290 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8773 (mttp) REVERT: O 370 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: O 413 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7587 (tm-30) REVERT: P 370 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7828 (ttm-80) REVERT: P 413 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7518 (tm-30) REVERT: P 414 ASP cc_start: 0.7279 (m-30) cc_final: 0.6850 (m-30) REVERT: Q 370 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7639 (ttm-80) REVERT: Q 413 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7751 (tm-30) REVERT: R 265 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8069 (mm-40) REVERT: R 276 GLU cc_start: 0.8010 (tt0) cc_final: 0.7710 (tt0) REVERT: R 290 LYS cc_start: 0.8918 (mttp) cc_final: 0.8596 (mtpp) REVERT: R 370 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7979 (ttm-80) REVERT: S 275 LYS cc_start: 0.8923 (mttm) cc_final: 0.8608 (mttp) REVERT: S 276 GLU cc_start: 0.7822 (tt0) cc_final: 0.7344 (mt-10) REVERT: S 370 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7685 (ttm-80) REVERT: T 370 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7817 (ttm-80) REVERT: T 408 GLN cc_start: 0.8532 (mt0) cc_final: 0.8204 (mt0) REVERT: T 416 THR cc_start: 0.8714 (m) cc_final: 0.8321 (p) REVERT: U 370 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8036 (ttm-80) REVERT: U 410 LYS cc_start: 0.8582 (tppt) cc_final: 0.8263 (tppt) REVERT: V 423 SER cc_start: 0.8665 (t) cc_final: 0.8437 (p) REVERT: W 244 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7451 (ttp-170) REVERT: W 256 ILE cc_start: 0.7463 (pt) cc_final: 0.7245 (pp) REVERT: W 290 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8788 (mttp) REVERT: W 370 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7930 (ttm-80) REVERT: X 367 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8477 (mm-30) REVERT: X 413 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7495 (tm-30) REVERT: X 414 ASP cc_start: 0.7574 (m-30) cc_final: 0.7163 (m-30) REVERT: Y 271 ASP cc_start: 0.8580 (t70) cc_final: 0.8354 (t0) REVERT: Y 275 LYS cc_start: 0.8714 (mttp) cc_final: 0.8438 (mttp) REVERT: Y 276 GLU cc_start: 0.7391 (tt0) cc_final: 0.7174 (tt0) REVERT: Y 370 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7878 (ttm-80) REVERT: Y 412 ILE cc_start: 0.8980 (mm) cc_final: 0.8724 (mm) REVERT: Z 275 LYS cc_start: 0.8798 (mttm) cc_final: 0.8548 (mttp) REVERT: Z 373 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8196 (ttt180) REVERT: a 370 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7769 (ttm-80) REVERT: a 420 MET cc_start: 0.8926 (ptm) cc_final: 0.8593 (ptm) REVERT: b 250 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7490 (mt-10) REVERT: b 276 GLU cc_start: 0.7591 (tt0) cc_final: 0.7370 (tt0) REVERT: b 356 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6207 (ptp-170) REVERT: b 366 TYR cc_start: 0.9211 (m-80) cc_final: 0.8930 (m-80) REVERT: b 367 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8622 (mm-30) REVERT: b 370 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7967 (ttm-80) REVERT: b 408 GLN cc_start: 0.8346 (mt0) cc_final: 0.7986 (tt0) REVERT: c 256 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7635 (pt) REVERT: c 271 ASP cc_start: 0.8503 (t0) cc_final: 0.8209 (t70) REVERT: c 370 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8182 (ttm-80) REVERT: c 377 MET cc_start: 0.8580 (mpt) cc_final: 0.8132 (mpt) REVERT: c 383 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: c 413 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7567 (tm-30) REVERT: c 428 ASP cc_start: 0.8593 (m-30) cc_final: 0.8312 (m-30) REVERT: d 242 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8347 (mt-10) REVERT: d 246 GLN cc_start: 0.8780 (tt0) cc_final: 0.8111 (tt0) REVERT: d 250 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7308 (mp0) REVERT: d 276 GLU cc_start: 0.7947 (tt0) cc_final: 0.7601 (tt0) REVERT: d 302 GLU cc_start: 0.7970 (tt0) cc_final: 0.7611 (tp30) REVERT: d 408 GLN cc_start: 0.8252 (mt0) cc_final: 0.7945 (mt0) REVERT: d 413 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7909 (tm-30) REVERT: e 265 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8614 (mm-40) REVERT: e 271 ASP cc_start: 0.8672 (t70) cc_final: 0.8292 (t0) REVERT: e 276 GLU cc_start: 0.8109 (tt0) cc_final: 0.7765 (tt0) REVERT: e 370 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7906 (ttm-80) REVERT: f 290 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8775 (mttp) REVERT: f 370 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8016 (ttm-80) REVERT: f 413 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7604 (tm-30) REVERT: g 370 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7837 (ttm-80) REVERT: g 413 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7549 (tm-30) REVERT: g 414 ASP cc_start: 0.7269 (m-30) cc_final: 0.6851 (m-30) REVERT: h 370 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7614 (ttm-80) REVERT: h 413 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7730 (tm-30) outliers start: 170 outliers final: 110 residues processed: 1355 average time/residue: 0.2984 time to fit residues: 637.3314 Evaluate side-chains 1359 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1216 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 370 ARG Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 370 ARG Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 370 ARG Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 370 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 356 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 230 LEU Chi-restraints excluded: chain W residue 244 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 394 LYS Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 373 ARG Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 370 ARG Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 278 THR Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 420 MET Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 370 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 275 optimal weight: 3.9990 chunk 441 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 404 optimal weight: 0.3980 chunk 350 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 518 optimal weight: 6.9990 chunk 367 optimal weight: 8.9990 chunk 539 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN K 431 ASN K 434 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 GLN ** P 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 274 ASN ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN b 431 ASN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 234 GLN ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110199 restraints weight = 60282.934| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.71 r_work: 0.3260 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43826 Z= 0.222 Angle : 0.600 7.893 59194 Z= 0.309 Chirality : 0.045 0.188 6766 Planarity : 0.005 0.064 8024 Dihedral : 4.190 15.485 6018 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.17 % Allowed : 25.70 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.11), residues: 5440 helix: 3.48 (0.12), residues: 1428 sheet: 1.05 (0.11), residues: 2380 loop : -0.78 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 356 TYR 0.020 0.002 TYR c 366 PHE 0.015 0.002 PHE c 422 HIS 0.003 0.001 HIS L 374 Details of bonding type rmsd covalent geometry : bond 0.00512 (43826) covalent geometry : angle 0.60016 (59194) hydrogen bonds : bond 0.03846 ( 2619) hydrogen bonds : angle 4.39358 ( 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 1451 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1251 time to evaluate : 1.802 Fit side-chains REVERT: A 276 GLU cc_start: 0.7896 (tt0) cc_final: 0.7629 (tt0) REVERT: A 290 LYS cc_start: 0.8913 (mttp) cc_final: 0.8577 (mtpp) REVERT: A 370 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7939 (ttm-80) REVERT: A 413 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 370 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7625 (ttm-80) REVERT: B 377 MET cc_start: 0.8823 (mpt) cc_final: 0.8454 (mpt) REVERT: C 240 ASP cc_start: 0.7751 (m-30) cc_final: 0.7543 (m-30) REVERT: C 416 THR cc_start: 0.8809 (m) cc_final: 0.8484 (p) REVERT: D 290 LYS cc_start: 0.8956 (mttm) cc_final: 0.8611 (mtpp) REVERT: D 370 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7972 (ttm-80) REVERT: D 414 ASP cc_start: 0.7454 (m-30) cc_final: 0.7153 (m-30) REVERT: E 356 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.6612 (ttm-80) REVERT: F 244 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8164 (ttp-110) REVERT: F 290 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8805 (mttp) REVERT: F 370 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7802 (ttm-80) REVERT: F 383 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: G 356 ARG cc_start: 0.7238 (ttm-80) cc_final: 0.6670 (ttt-90) REVERT: G 413 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7488 (tm-30) REVERT: G 414 ASP cc_start: 0.7609 (m-30) cc_final: 0.7186 (m-30) REVERT: H 370 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7836 (ttm-80) REVERT: H 412 ILE cc_start: 0.9012 (mm) cc_final: 0.8810 (mm) REVERT: I 413 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7555 (tm-30) REVERT: I 416 THR cc_start: 0.8642 (m) cc_final: 0.8387 (p) REVERT: J 370 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7719 (ttm-80) REVERT: J 420 MET cc_start: 0.9174 (ptm) cc_final: 0.8897 (ptm) REVERT: J 428 ASP cc_start: 0.8988 (m-30) cc_final: 0.8755 (m-30) REVERT: K 250 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7576 (mt-10) REVERT: K 356 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6357 (ptp-170) REVERT: K 370 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7730 (ttm-80) REVERT: K 408 GLN cc_start: 0.8396 (mt0) cc_final: 0.8072 (tt0) REVERT: L 370 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8102 (ttm-80) REVERT: L 383 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: L 413 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7720 (tm-30) REVERT: M 242 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8374 (mt-10) REVERT: M 276 GLU cc_start: 0.7959 (tt0) cc_final: 0.7651 (tt0) REVERT: M 408 GLN cc_start: 0.8427 (mt0) cc_final: 0.8138 (mt0) REVERT: M 413 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7917 (tm-30) REVERT: M 429 THR cc_start: 0.9261 (m) cc_final: 0.9030 (m) REVERT: N 250 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7639 (mt-10) REVERT: N 265 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8617 (mm-40) REVERT: N 271 ASP cc_start: 0.8653 (t70) cc_final: 0.8215 (t0) REVERT: N 276 GLU cc_start: 0.8157 (tt0) cc_final: 0.7897 (tt0) REVERT: N 370 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7815 (ttm-80) REVERT: N 416 THR cc_start: 0.8760 (m) cc_final: 0.8464 (p) REVERT: O 275 LYS cc_start: 0.8675 (mttm) cc_final: 0.8464 (mttp) REVERT: O 290 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8850 (mttp) REVERT: O 370 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7958 (ttm-80) REVERT: O 413 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7597 (tm-30) REVERT: P 414 ASP cc_start: 0.7439 (m-30) cc_final: 0.7100 (m-30) REVERT: Q 370 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7631 (ttm-80) REVERT: Q 424 ASP cc_start: 0.8248 (m-30) cc_final: 0.7894 (m-30) REVERT: R 276 GLU cc_start: 0.7886 (tt0) cc_final: 0.7612 (tt0) REVERT: R 290 LYS cc_start: 0.8926 (mttp) cc_final: 0.8588 (mtpp) REVERT: R 370 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: S 377 MET cc_start: 0.8810 (mpt) cc_final: 0.8440 (mpt) REVERT: T 240 ASP cc_start: 0.7749 (m-30) cc_final: 0.7544 (m-30) REVERT: T 416 THR cc_start: 0.8799 (m) cc_final: 0.8477 (p) REVERT: U 290 LYS cc_start: 0.8946 (mttm) cc_final: 0.8611 (mtpp) REVERT: U 370 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8065 (ttm-80) REVERT: U 410 LYS cc_start: 0.8529 (tppt) cc_final: 0.8269 (tppt) REVERT: V 356 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6612 (ttm-80) REVERT: W 244 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8143 (ttp-110) REVERT: W 290 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8803 (mttp) REVERT: W 370 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7801 (ttm-80) REVERT: W 383 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: X 356 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6661 (ttt-90) REVERT: X 413 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7507 (tm-30) REVERT: X 414 ASP cc_start: 0.7597 (m-30) cc_final: 0.7171 (m-30) REVERT: Y 271 ASP cc_start: 0.8593 (t70) cc_final: 0.8311 (t0) REVERT: Y 275 LYS cc_start: 0.8696 (mttp) cc_final: 0.8408 (mttm) REVERT: Y 370 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7823 (ttm-80) REVERT: Y 412 ILE cc_start: 0.9016 (mm) cc_final: 0.8813 (mm) REVERT: Z 275 LYS cc_start: 0.8847 (mttm) cc_final: 0.8597 (mttp) REVERT: Z 413 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7535 (tm-30) REVERT: Z 416 THR cc_start: 0.8638 (m) cc_final: 0.8389 (p) REVERT: a 370 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7678 (ttm-80) REVERT: a 420 MET cc_start: 0.9181 (ptm) cc_final: 0.8903 (ptm) REVERT: a 428 ASP cc_start: 0.8984 (m-30) cc_final: 0.8757 (m-30) REVERT: b 250 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7593 (mt-10) REVERT: b 276 GLU cc_start: 0.7809 (tt0) cc_final: 0.7607 (tt0) REVERT: b 356 ARG cc_start: 0.6858 (ttp-110) cc_final: 0.6258 (ptp-170) REVERT: b 366 TYR cc_start: 0.9229 (m-80) cc_final: 0.8958 (m-80) REVERT: b 370 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7861 (ttm-80) REVERT: b 408 GLN cc_start: 0.8421 (mt0) cc_final: 0.8104 (tt0) REVERT: c 370 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8113 (ttm-80) REVERT: c 377 MET cc_start: 0.8642 (mpt) cc_final: 0.8227 (mpt) REVERT: c 383 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: c 413 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7720 (tm-30) REVERT: d 242 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8355 (mt-10) REVERT: d 276 GLU cc_start: 0.7970 (tt0) cc_final: 0.7663 (tt0) REVERT: d 302 GLU cc_start: 0.7927 (tt0) cc_final: 0.7696 (tp30) REVERT: d 408 GLN cc_start: 0.8417 (mt0) cc_final: 0.8122 (mt0) REVERT: d 413 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7898 (tm-30) REVERT: d 429 THR cc_start: 0.9269 (m) cc_final: 0.9036 (m) REVERT: e 250 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7639 (mt-10) REVERT: e 265 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8620 (mm-40) REVERT: e 271 ASP cc_start: 0.8630 (t70) cc_final: 0.8197 (t0) REVERT: e 276 GLU cc_start: 0.8170 (tt0) cc_final: 0.7911 (tt0) REVERT: e 370 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: e 416 THR cc_start: 0.8756 (m) cc_final: 0.8455 (p) REVERT: f 275 LYS cc_start: 0.8665 (mttm) cc_final: 0.8455 (mttp) REVERT: f 290 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8852 (mttp) REVERT: f 370 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: f 413 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7582 (tm-30) REVERT: g 414 ASP cc_start: 0.7460 (m-30) cc_final: 0.7121 (m-30) REVERT: h 370 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7632 (ttm-80) REVERT: h 424 ASP cc_start: 0.8234 (m-30) cc_final: 0.7881 (m-30) outliers start: 200 outliers final: 132 residues processed: 1369 average time/residue: 0.3039 time to fit residues: 654.6326 Evaluate side-chains 1329 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1170 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 409 MET Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 370 ARG Chi-restraints excluded: chain Q residue 383 GLU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 356 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 356 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 230 LEU Chi-restraints excluded: chain W residue 244 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 383 GLU Chi-restraints excluded: chain W residue 394 LYS Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 358 THR Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 236 LYS Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 409 MET Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 390 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 370 ARG Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 358 THR Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 370 ARG Chi-restraints excluded: chain h residue 383 GLU Chi-restraints excluded: chain h residue 420 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 103 optimal weight: 0.0000 chunk 262 optimal weight: 0.7980 chunk 368 optimal weight: 2.9990 chunk 477 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 335 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 417 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN E 408 GLN G 246 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 GLN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN ** P 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 234 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN V 408 GLN X 246 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 234 GLN ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 234 GLN ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112798 restraints weight = 59478.371| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.76 r_work: 0.3304 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5897 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= 0.123 Angle : 0.542 7.951 59194 Z= 0.278 Chirality : 0.042 0.152 6766 Planarity : 0.005 0.062 8024 Dihedral : 4.000 15.547 6018 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.36 % Allowed : 26.68 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.11), residues: 5440 helix: 3.54 (0.13), residues: 1394 sheet: 1.03 (0.11), residues: 2380 loop : -0.89 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 356 TYR 0.015 0.001 TYR c 366 PHE 0.010 0.001 PHE J 422 HIS 0.001 0.000 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (43826) covalent geometry : angle 0.54222 (59194) hydrogen bonds : bond 0.03088 ( 2619) hydrogen bonds : angle 4.17307 ( 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 1387 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1226 time to evaluate : 1.883 Fit side-chains REVERT: A 242 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8312 (mt-10) REVERT: A 276 GLU cc_start: 0.7870 (tt0) cc_final: 0.7611 (tt0) REVERT: A 290 LYS cc_start: 0.8932 (mttp) cc_final: 0.8616 (mtpp) REVERT: A 370 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8022 (ttm-80) REVERT: A 413 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 275 LYS cc_start: 0.8930 (mttm) cc_final: 0.8560 (mtmm) REVERT: B 276 GLU cc_start: 0.7663 (tt0) cc_final: 0.7344 (mt-10) REVERT: B 370 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7654 (ttm-80) REVERT: B 377 MET cc_start: 0.8829 (mpt) cc_final: 0.8328 (mpt) REVERT: B 409 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: C 370 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7794 (ttm-80) REVERT: C 416 THR cc_start: 0.8716 (m) cc_final: 0.8335 (p) REVERT: D 290 LYS cc_start: 0.8914 (mttm) cc_final: 0.8705 (mttm) REVERT: D 370 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: D 414 ASP cc_start: 0.7368 (m-30) cc_final: 0.7072 (m-30) REVERT: E 423 SER cc_start: 0.8689 (t) cc_final: 0.8432 (p) REVERT: F 244 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8078 (ttp-110) REVERT: F 290 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8821 (mttp) REVERT: F 370 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7882 (ttm-80) REVERT: F 383 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: G 356 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.6619 (ttt-90) REVERT: G 367 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8518 (mm-30) REVERT: G 413 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7473 (tm-30) REVERT: G 414 ASP cc_start: 0.7603 (m-30) cc_final: 0.7161 (m-30) REVERT: H 234 GLN cc_start: 0.8559 (mt0) cc_final: 0.8335 (mt0) REVERT: H 356 ARG cc_start: 0.6786 (ttp-110) cc_final: 0.5521 (mtm110) REVERT: H 370 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7881 (ttm-80) REVERT: H 412 ILE cc_start: 0.9010 (mm) cc_final: 0.8772 (mm) REVERT: I 413 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7454 (tm-30) REVERT: I 414 ASP cc_start: 0.7444 (m-30) cc_final: 0.6945 (m-30) REVERT: J 370 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7796 (ttm-80) REVERT: J 420 MET cc_start: 0.8945 (ptm) cc_final: 0.8620 (ptm) REVERT: K 250 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7405 (mt-10) REVERT: K 356 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.6324 (ptp-170) REVERT: K 370 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7894 (ttm-80) REVERT: K 408 GLN cc_start: 0.8386 (mt0) cc_final: 0.8033 (tt0) REVERT: L 370 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8161 (ttm-80) REVERT: L 377 MET cc_start: 0.8647 (mpt) cc_final: 0.8224 (mpt) REVERT: L 383 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: L 413 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7701 (tm-30) REVERT: M 242 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8399 (mt-10) REVERT: M 271 ASP cc_start: 0.8373 (t70) cc_final: 0.8127 (t0) REVERT: M 276 GLU cc_start: 0.7883 (tt0) cc_final: 0.7563 (tt0) REVERT: M 408 GLN cc_start: 0.8280 (mt0) cc_final: 0.8036 (mt0) REVERT: M 413 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7901 (tm-30) REVERT: M 425 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8947 (mmtt) REVERT: N 250 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7492 (mt-10) REVERT: N 265 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8636 (mm-40) REVERT: N 271 ASP cc_start: 0.8651 (t70) cc_final: 0.8233 (t0) REVERT: N 276 GLU cc_start: 0.8094 (tt0) cc_final: 0.7770 (tt0) REVERT: N 370 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7807 (ttm-80) REVERT: O 275 LYS cc_start: 0.8604 (mttm) cc_final: 0.8397 (mttp) REVERT: O 370 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7961 (ttm-80) REVERT: O 413 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7557 (tm-30) REVERT: P 250 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7697 (mt-10) REVERT: P 271 ASP cc_start: 0.8552 (t70) cc_final: 0.8261 (t0) REVERT: P 413 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7518 (tm-30) REVERT: P 414 ASP cc_start: 0.7380 (m-30) cc_final: 0.6968 (m-30) REVERT: Q 370 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7627 (ttm-80) REVERT: Q 413 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7639 (tm-30) REVERT: Q 424 ASP cc_start: 0.8317 (m-30) cc_final: 0.7941 (m-30) REVERT: R 276 GLU cc_start: 0.7865 (tt0) cc_final: 0.7601 (tt0) REVERT: R 290 LYS cc_start: 0.8947 (mttp) cc_final: 0.8611 (mtpp) REVERT: R 370 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8007 (ttm-80) REVERT: S 275 LYS cc_start: 0.8926 (mttm) cc_final: 0.8553 (mtmm) REVERT: S 276 GLU cc_start: 0.7661 (tt0) cc_final: 0.7347 (mt-10) REVERT: S 370 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7665 (ttm-80) REVERT: S 377 MET cc_start: 0.8814 (mpt) cc_final: 0.8355 (mpt) REVERT: T 370 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7817 (ttm-80) REVERT: T 416 THR cc_start: 0.8711 (m) cc_final: 0.8336 (p) REVERT: U 290 LYS cc_start: 0.8907 (mttm) cc_final: 0.8701 (mttm) REVERT: U 370 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8100 (ttm-80) REVERT: U 410 LYS cc_start: 0.8505 (tppt) cc_final: 0.8268 (tppt) REVERT: V 423 SER cc_start: 0.8675 (t) cc_final: 0.8429 (p) REVERT: W 244 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8076 (ttp-110) REVERT: W 290 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8823 (mttp) REVERT: W 370 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7892 (ttm-80) REVERT: W 383 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: X 356 ARG cc_start: 0.7209 (ttm-80) cc_final: 0.6587 (ttt-90) REVERT: X 367 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8508 (mm-30) REVERT: X 413 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7488 (tm-30) REVERT: X 414 ASP cc_start: 0.7601 (m-30) cc_final: 0.7151 (m-30) REVERT: Y 234 GLN cc_start: 0.8547 (mt0) cc_final: 0.8318 (mt0) REVERT: Y 271 ASP cc_start: 0.8408 (t70) cc_final: 0.7937 (t0) REVERT: Y 275 LYS cc_start: 0.8616 (mttp) cc_final: 0.8176 (mttp) REVERT: Y 356 ARG cc_start: 0.6914 (ttp-110) cc_final: 0.5686 (mtm110) REVERT: Y 370 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7855 (ttm-80) REVERT: Y 412 ILE cc_start: 0.9010 (mm) cc_final: 0.8766 (mm) REVERT: Z 275 LYS cc_start: 0.8777 (mttm) cc_final: 0.8502 (mttp) REVERT: Z 413 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7468 (tm-30) REVERT: Z 414 ASP cc_start: 0.7461 (m-30) cc_final: 0.6951 (m-30) REVERT: a 370 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: a 420 MET cc_start: 0.8951 (ptm) cc_final: 0.8632 (ptm) REVERT: b 250 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7422 (mt-10) REVERT: b 356 ARG cc_start: 0.6952 (ttp-110) cc_final: 0.6307 (ptp-170) REVERT: b 366 TYR cc_start: 0.9206 (m-80) cc_final: 0.8947 (m-80) REVERT: b 370 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7934 (ttm-80) REVERT: b 408 GLN cc_start: 0.8384 (mt0) cc_final: 0.8032 (tt0) REVERT: c 370 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8138 (ttm-80) REVERT: c 377 MET cc_start: 0.8634 (mpt) cc_final: 0.8190 (mpt) REVERT: c 383 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: c 413 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7687 (tm-30) REVERT: d 242 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8382 (mt-10) REVERT: d 271 ASP cc_start: 0.8385 (t70) cc_final: 0.8131 (t0) REVERT: d 276 GLU cc_start: 0.7896 (tt0) cc_final: 0.7577 (tt0) REVERT: d 302 GLU cc_start: 0.7994 (tt0) cc_final: 0.7687 (tp30) REVERT: d 408 GLN cc_start: 0.8269 (mt0) cc_final: 0.8026 (mt0) REVERT: d 413 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7884 (tm-30) REVERT: d 425 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8930 (mmtt) REVERT: e 250 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7506 (mt-10) REVERT: e 265 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8631 (mm-40) REVERT: e 271 ASP cc_start: 0.8619 (t70) cc_final: 0.8210 (t0) REVERT: e 276 GLU cc_start: 0.8100 (tt0) cc_final: 0.7774 (tt0) REVERT: e 370 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7800 (ttm-80) REVERT: f 275 LYS cc_start: 0.8607 (mttm) cc_final: 0.8399 (mttp) REVERT: f 370 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: f 413 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7556 (tm-30) REVERT: g 250 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7701 (mt-10) REVERT: g 413 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7533 (tm-30) REVERT: g 414 ASP cc_start: 0.7389 (m-30) cc_final: 0.6974 (m-30) REVERT: h 370 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7602 (ttm-80) REVERT: h 413 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7646 (tm-30) REVERT: h 424 ASP cc_start: 0.8322 (m-30) cc_final: 0.7956 (m-30) outliers start: 161 outliers final: 116 residues processed: 1319 average time/residue: 0.2967 time to fit residues: 615.2344 Evaluate side-chains 1348 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1201 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 370 ARG Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain Q residue 383 GLU Chi-restraints excluded: chain Q residue 420 MET Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 370 ARG Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 356 ARG Chi-restraints excluded: chain T residue 370 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 356 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 230 LEU Chi-restraints excluded: chain W residue 244 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 383 GLU Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 229 ASP Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 370 ARG Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 409 MET Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 370 ARG Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 420 MET Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 358 THR Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 370 ARG Chi-restraints excluded: chain h residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 28 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 540 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 220 optimal weight: 0.5980 chunk 211 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN ** P 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 234 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN X 246 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN c 234 GLN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 234 GLN ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114344 restraints weight = 59721.285| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.73 r_work: 0.3328 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43826 Z= 0.116 Angle : 0.540 8.286 59194 Z= 0.276 Chirality : 0.042 0.153 6766 Planarity : 0.005 0.063 8024 Dihedral : 3.945 15.820 6018 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.05 % Allowed : 27.28 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.12), residues: 5440 helix: 3.58 (0.13), residues: 1394 sheet: 0.89 (0.11), residues: 2516 loop : -0.80 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 356 TYR 0.016 0.001 TYR F 366 PHE 0.010 0.001 PHE a 422 HIS 0.001 0.000 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (43826) covalent geometry : angle 0.53988 (59194) hydrogen bonds : bond 0.02993 ( 2619) hydrogen bonds : angle 4.08216 ( 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 1380 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1234 time to evaluate : 1.689 Fit side-chains REVERT: A 242 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 276 GLU cc_start: 0.7939 (tt0) cc_final: 0.7673 (tt0) REVERT: A 356 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.7038 (ptm-80) REVERT: A 370 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8010 (ttm-80) REVERT: A 413 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 275 LYS cc_start: 0.8923 (mttm) cc_final: 0.8659 (mttp) REVERT: B 276 GLU cc_start: 0.7669 (tt0) cc_final: 0.7359 (mt-10) REVERT: B 370 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7625 (ttm-80) REVERT: B 377 MET cc_start: 0.8803 (mpt) cc_final: 0.8229 (mpt) REVERT: B 409 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8232 (mmm) REVERT: C 370 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7747 (ttm-80) REVERT: C 416 THR cc_start: 0.8734 (m) cc_final: 0.8358 (p) REVERT: D 370 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: D 414 ASP cc_start: 0.7339 (m-30) cc_final: 0.7060 (m-30) REVERT: E 423 SER cc_start: 0.8558 (t) cc_final: 0.8351 (p) REVERT: F 244 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8066 (ttp-110) REVERT: F 290 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8829 (mttp) REVERT: F 370 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7886 (ttm-80) REVERT: F 383 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: G 356 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6696 (ttt-90) REVERT: G 367 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8419 (mm-30) REVERT: G 413 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7498 (tm-30) REVERT: G 414 ASP cc_start: 0.7462 (m-30) cc_final: 0.7043 (m-30) REVERT: H 276 GLU cc_start: 0.7425 (tt0) cc_final: 0.7161 (mt-10) REVERT: H 356 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.5609 (mtm110) REVERT: H 412 ILE cc_start: 0.9020 (mm) cc_final: 0.8781 (mm) REVERT: I 413 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7489 (tm-30) REVERT: I 414 ASP cc_start: 0.7356 (m-30) cc_final: 0.6925 (m-30) REVERT: J 370 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7755 (ttm-80) REVERT: J 420 MET cc_start: 0.9016 (ptm) cc_final: 0.8697 (ptm) REVERT: K 250 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7286 (mt-10) REVERT: K 356 ARG cc_start: 0.7001 (ttp-110) cc_final: 0.6335 (ptp-170) REVERT: K 370 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7814 (ttm-80) REVERT: K 373 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8050 (ttt90) REVERT: K 408 GLN cc_start: 0.8386 (mt0) cc_final: 0.8026 (tt0) REVERT: L 370 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: L 383 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: L 414 ASP cc_start: 0.7624 (m-30) cc_final: 0.7225 (m-30) REVERT: M 242 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8356 (mt-10) REVERT: M 276 GLU cc_start: 0.7903 (tt0) cc_final: 0.7583 (tt0) REVERT: N 250 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7382 (mt-10) REVERT: N 265 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8644 (mm-40) REVERT: N 271 ASP cc_start: 0.8649 (t70) cc_final: 0.8295 (t0) REVERT: N 276 GLU cc_start: 0.8127 (tt0) cc_final: 0.7795 (tt0) REVERT: N 370 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7805 (ttm-80) REVERT: O 370 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7959 (ttm-80) REVERT: O 413 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7547 (tm-30) REVERT: P 250 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7656 (mt-10) REVERT: P 271 ASP cc_start: 0.8581 (t70) cc_final: 0.8257 (t70) REVERT: P 367 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8569 (mm-30) REVERT: P 413 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7487 (tm-30) REVERT: P 414 ASP cc_start: 0.7403 (m-30) cc_final: 0.6968 (m-30) REVERT: Q 370 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7619 (ttm-80) REVERT: Q 413 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7695 (tm-30) REVERT: Q 424 ASP cc_start: 0.8294 (m-30) cc_final: 0.7934 (m-30) REVERT: R 242 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8363 (mt-10) REVERT: R 276 GLU cc_start: 0.7933 (tt0) cc_final: 0.7666 (tt0) REVERT: R 370 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: R 413 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7782 (tm-30) REVERT: S 275 LYS cc_start: 0.8926 (mttm) cc_final: 0.8667 (mttp) REVERT: S 370 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7627 (ttm-80) REVERT: S 377 MET cc_start: 0.8789 (mpt) cc_final: 0.8296 (mpt) REVERT: T 370 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: T 416 THR cc_start: 0.8733 (m) cc_final: 0.8367 (p) REVERT: U 370 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8076 (ttm-80) REVERT: U 414 ASP cc_start: 0.7196 (m-30) cc_final: 0.6960 (m-30) REVERT: W 244 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8057 (ttp-110) REVERT: W 290 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8835 (mttp) REVERT: W 370 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7888 (ttm-80) REVERT: W 383 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: X 356 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6669 (ttt-90) REVERT: X 367 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8437 (mm-30) REVERT: X 413 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7511 (tm-30) REVERT: X 414 ASP cc_start: 0.7447 (m-30) cc_final: 0.7023 (m-30) REVERT: Y 271 ASP cc_start: 0.8507 (t70) cc_final: 0.7993 (t0) REVERT: Y 275 LYS cc_start: 0.8631 (mttp) cc_final: 0.8202 (mttp) REVERT: Y 276 GLU cc_start: 0.7395 (tt0) cc_final: 0.7121 (mt-10) REVERT: Y 356 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.5719 (mtm110) REVERT: Y 412 ILE cc_start: 0.9016 (mm) cc_final: 0.8774 (mm) REVERT: Y 428 ASP cc_start: 0.8261 (m-30) cc_final: 0.7931 (m-30) REVERT: Z 275 LYS cc_start: 0.8785 (mttm) cc_final: 0.8517 (mttp) REVERT: Z 383 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7782 (mm-30) REVERT: Z 413 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7528 (tm-30) REVERT: a 370 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7714 (ttm-80) REVERT: a 420 MET cc_start: 0.8985 (ptm) cc_final: 0.8676 (ptm) REVERT: b 250 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7320 (mt-10) REVERT: b 356 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.6305 (ptp-170) REVERT: b 366 TYR cc_start: 0.9198 (m-80) cc_final: 0.8947 (m-80) REVERT: b 370 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7891 (ttm-80) REVERT: b 408 GLN cc_start: 0.8395 (mt0) cc_final: 0.8065 (tt0) REVERT: b 425 LYS cc_start: 0.9238 (mmtt) cc_final: 0.9036 (mmtt) REVERT: c 370 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8210 (ttm-80) REVERT: c 383 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: c 414 ASP cc_start: 0.7594 (m-30) cc_final: 0.7198 (m-30) REVERT: d 242 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8360 (mt-10) REVERT: d 276 GLU cc_start: 0.7914 (tt0) cc_final: 0.7595 (tt0) REVERT: d 302 GLU cc_start: 0.7997 (tt0) cc_final: 0.7692 (tp30) REVERT: d 425 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8985 (mmtt) REVERT: e 250 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7382 (mt-10) REVERT: e 265 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8643 (mm-40) REVERT: e 271 ASP cc_start: 0.8615 (t70) cc_final: 0.8276 (t0) REVERT: e 276 GLU cc_start: 0.8096 (tt0) cc_final: 0.7774 (tt0) REVERT: e 370 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7795 (ttm-80) REVERT: f 370 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: f 413 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7536 (tm-30) REVERT: g 250 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7657 (mt-10) REVERT: g 367 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8566 (mm-30) REVERT: g 413 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7505 (tm-30) REVERT: g 414 ASP cc_start: 0.7413 (m-30) cc_final: 0.6972 (m-30) REVERT: h 370 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7594 (ttm-80) REVERT: h 413 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7647 (tm-30) REVERT: h 424 ASP cc_start: 0.8298 (m-30) cc_final: 0.7924 (m-30) outliers start: 146 outliers final: 105 residues processed: 1319 average time/residue: 0.2687 time to fit residues: 557.7068 Evaluate side-chains 1316 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1181 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 370 ARG Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 373 ARG Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 229 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 279 GLU Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 247 ARG Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 GLU Chi-restraints excluded: chain Q residue 370 ARG Chi-restraints excluded: chain Q residue 377 MET Chi-restraints excluded: chain Q residue 383 GLU Chi-restraints excluded: chain Q residue 420 MET Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 236 LYS Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 370 ARG Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 370 ARG Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 230 LEU Chi-restraints excluded: chain W residue 244 ARG Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 383 GLU Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 412 ILE Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 390 VAL Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 390 VAL Chi-restraints excluded: chain Z residue 409 MET Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 229 ASP Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 278 THR Chi-restraints excluded: chain b residue 370 ARG Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 370 ARG Chi-restraints excluded: chain c residue 381 ASP Chi-restraints excluded: chain c residue 383 GLU Chi-restraints excluded: chain d residue 229 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain e residue 279 GLU Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 420 MET Chi-restraints excluded: chain f residue 247 ARG Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 390 VAL Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 358 THR Chi-restraints excluded: chain g residue 412 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain h residue 267 THR Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 370 ARG Chi-restraints excluded: chain h residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 8 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 446 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 507 optimal weight: 0.8980 chunk 479 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 367 optimal weight: 8.9990 chunk 52 optimal weight: 0.0000 chunk 34 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN G 246 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN N 234 GLN ** P 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 234 GLN X 246 GLN ** X 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 234 GLN c 434 ASN d 234 GLN e 234 GLN ** g 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113853 restraints weight = 60088.424| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.78 r_work: 0.3326 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43826 Z= 0.117 Angle : 0.548 8.401 59194 Z= 0.279 Chirality : 0.042 0.148 6766 Planarity : 0.005 0.066 8024 Dihedral : 3.924 15.543 6018 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.00 % Allowed : 27.28 % Favored : 69.71 % 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: 1.86 (0.12), residues: 5440 helix: 3.58 (0.12), residues: 1428 sheet: 0.90 (0.10), residues: 2584 loop : -0.60 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 247 TYR 0.015 0.001 TYR F 366 PHE 0.010 0.001 PHE J 422 HIS 0.001 0.000 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (43826) covalent geometry : angle 0.54791 (59194) hydrogen bonds : bond 0.02960 ( 2619) hydrogen bonds : angle 4.05569 ( 7245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15651.90 seconds wall clock time: 266 minutes 55.35 seconds (16015.35 seconds total)