Starting phenix.real_space_refine on Thu Dec 26 05:33:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjr_37590/12_2024/8wjr_37590.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 26384 2.51 5 N 8058 2.21 5 O 8806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 408 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, h Time building chain proxies: 8.60, per 1000 atoms: 0.20 Number of scatterers: 43350 At special positions: 0 Unit cell: (265.2, 265.2, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 8806 8.00 N 8058 7.00 C 26384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.84 Conformation dependent library (CDL) restraints added in 5.9 seconds 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: 5.94 Creating SS restraints... Processing helix chain 'A' and resid 229 through 258 removed outlier: 3.608A pdb=" N ILE A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'D' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 Processing helix chain 'E' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE E 252 " --> pdb=" O ARG E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 Processing helix chain 'F' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 Processing helix chain 'G' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 Processing helix chain 'H' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE H 252 " --> pdb=" O ARG H 248 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 Processing helix chain 'I' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE I 252 " --> pdb=" O ARG I 248 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'J' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE J 252 " --> pdb=" O ARG J 248 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 Processing helix chain 'K' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE K 252 " --> pdb=" O ARG K 248 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 Processing helix chain 'L' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE L 252 " --> pdb=" O ARG L 248 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 Processing helix chain 'M' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE M 252 " --> pdb=" O ARG M 248 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 Processing helix chain 'N' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE N 252 " --> pdb=" O ARG N 248 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 Processing helix chain 'O' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE O 252 " --> pdb=" O ARG O 248 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 Processing helix chain 'P' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE P 252 " --> pdb=" O ARG P 248 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 Processing helix chain 'Q' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Q 252 " --> pdb=" O ARG Q 248 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 Processing helix chain 'R' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 Processing helix chain 'S' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE S 252 " --> pdb=" O ARG S 248 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 Processing helix chain 'T' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE T 252 " --> pdb=" O ARG T 248 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE U 252 " --> pdb=" O ARG U 248 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 Processing helix chain 'V' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE V 252 " --> pdb=" O ARG V 248 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 Processing helix chain 'W' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 Processing helix chain 'X' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE X 252 " --> pdb=" O ARG X 248 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 Processing helix chain 'Y' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE Y 252 " --> pdb=" O ARG Y 248 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 Processing helix chain 'Z' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Z 252 " --> pdb=" O ARG Z 248 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 Processing helix chain 'a' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE a 252 " --> pdb=" O ARG a 248 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 Processing helix chain 'b' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE b 252 " --> pdb=" O ARG b 248 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 Processing helix chain 'c' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE c 252 " --> pdb=" O ARG c 248 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 Processing helix chain 'd' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE d 252 " --> pdb=" O ARG d 248 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 Processing helix chain 'e' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE e 252 " --> pdb=" O ARG e 248 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 Processing helix chain 'f' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE f 252 " --> pdb=" O ARG f 248 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 Processing helix chain 'g' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE g 252 " --> pdb=" O ARG g 248 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 Processing helix chain 'h' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE h 252 " --> pdb=" O ARG h 248 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 303 removed outlier: 5.370A pdb=" N LEU A 293 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU A 367 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 293 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU B 367 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 293 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU C 367 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU D 293 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU D 367 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU E 293 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU E 367 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU F 293 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU F 367 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU G 293 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU G 367 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 293 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU H 367 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU I 293 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU I 367 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU J 293 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU J 367 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU K 293 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU K 367 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU L 293 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU L 367 " --> pdb=" O LEU L 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU M 293 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU M 367 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU N 293 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU N 367 " --> pdb=" O LEU N 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU O 293 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU O 367 " --> pdb=" O LEU O 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU P 293 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU P 367 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Q 293 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Q 367 " --> pdb=" O LEU Q 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU R 293 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU R 367 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 293 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU S 367 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU T 293 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU T 367 " --> pdb=" O LEU T 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU U 293 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU U 367 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU V 293 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU V 367 " --> pdb=" O LEU V 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU W 293 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU W 367 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU X 293 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU X 367 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Y 293 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Y 367 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Z 293 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU Z 367 " --> pdb=" O LEU Z 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU a 293 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU a 367 " --> pdb=" O LEU a 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU b 293 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU b 367 " --> pdb=" O LEU b 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU c 293 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU c 367 " --> pdb=" O LEU c 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU d 293 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU d 367 " --> pdb=" O LEU d 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU e 293 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU e 367 " --> pdb=" O LEU e 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU f 293 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU f 367 " --> pdb=" O LEU f 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU g 293 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU g 367 " --> pdb=" O LEU g 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU h 293 " --> pdb=" O GLU h 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU h 367 " --> pdb=" O LEU h 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 394 through 395 Processing sheet with id=AB4, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 394 through 395 Processing sheet with id=AB6, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 394 through 395 Processing sheet with id=AB8, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 394 through 395 Processing sheet with id=AC1, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 394 through 395 Processing sheet with id=AC3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 394 through 395 Processing sheet with id=AC5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 394 through 395 Processing sheet with id=AC7, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 394 through 395 Processing sheet with id=AC9, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 394 through 395 Processing sheet with id=AD2, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 394 through 395 Processing sheet with id=AD4, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 394 through 395 Processing sheet with id=AD6, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 394 through 395 Processing sheet with id=AD8, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 394 through 395 Processing sheet with id=AE1, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 394 through 395 Processing sheet with id=AE3, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 394 through 395 Processing sheet with id=AE5, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 394 through 395 Processing sheet with id=AE7, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 394 through 395 Processing sheet with id=AE9, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 394 through 395 Processing sheet with id=AF2, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 394 through 395 Processing sheet with id=AF4, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 394 through 395 Processing sheet with id=AF6, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 394 through 395 Processing sheet with id=AF8, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 394 through 395 Processing sheet with id=AG1, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AG3, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AG5, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 394 through 395 Processing sheet with id=AG7, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 394 through 395 Processing sheet with id=AG9, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 394 through 395 Processing sheet with id=AH2, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 394 through 395 Processing sheet with id=AH4, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 394 through 395 Processing sheet with id=AH6, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 394 through 395 2619 hydrogen bonds defined for protein. 7245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.45 Time building geometry restraints manager: 12.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12392 1.33 - 1.45: 6070 1.45 - 1.57: 25160 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 43826 Sorted by residual: bond pdb=" N VAL a 257 " pdb=" CA VAL a 257 " ideal model delta sigma weight residual 1.459 1.505 -0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" N VAL J 257 " pdb=" CA VAL J 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.19e+01 bond pdb=" N VAL V 257 " pdb=" CA VAL V 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" N VAL E 257 " pdb=" CA VAL E 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" N VAL R 257 " pdb=" CA VAL R 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.17e+01 ... (remaining 43821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 57110 1.53 - 3.06: 1447 3.06 - 4.59: 467 4.59 - 6.12: 102 6.12 - 7.65: 68 Bond angle restraints: 59194 Sorted by residual: angle pdb=" N ASN Q 261 " pdb=" CA ASN Q 261 " pdb=" C ASN Q 261 " ideal model delta sigma weight residual 113.02 106.55 6.47 1.20e+00 6.94e-01 2.91e+01 angle pdb=" N ASN h 261 " pdb=" CA ASN h 261 " pdb=" C ASN h 261 " ideal model delta sigma weight residual 113.02 106.55 6.47 1.20e+00 6.94e-01 2.91e+01 angle pdb=" N ASN g 261 " pdb=" CA ASN g 261 " pdb=" C ASN g 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.90e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" C ASN E 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.89e+01 angle pdb=" N ASN V 261 " pdb=" CA ASN V 261 " pdb=" C ASN V 261 " ideal model delta sigma weight residual 113.02 106.56 6.46 1.20e+00 6.94e-01 2.89e+01 ... (remaining 59189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 22981 16.79 - 33.59: 2859 33.59 - 50.38: 1122 50.38 - 67.18: 238 67.18 - 83.97: 102 Dihedral angle restraints: 27302 sinusoidal: 11152 harmonic: 16150 Sorted by residual: dihedral pdb=" CA ARG c 294 " pdb=" CB ARG c 294 " pdb=" CG ARG c 294 " pdb=" CD ARG c 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.99 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG L 294 " pdb=" CB ARG L 294 " pdb=" CG ARG L 294 " pdb=" CD ARG L 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.99 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG H 294 " pdb=" CB ARG H 294 " pdb=" CG ARG H 294 " pdb=" CD ARG H 294 " ideal model delta sinusoidal sigma weight residual 180.00 121.00 59.00 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 27299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3981 0.027 - 0.053: 1853 0.053 - 0.080: 488 0.080 - 0.107: 222 0.107 - 0.134: 222 Chirality restraints: 6766 Sorted by residual: chirality pdb=" CA VAL a 257 " pdb=" N VAL a 257 " pdb=" C VAL a 257 " pdb=" CB VAL a 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL K 257 " pdb=" N VAL K 257 " pdb=" C VAL K 257 " pdb=" CB VAL K 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL b 257 " pdb=" N VAL b 257 " pdb=" C VAL b 257 " pdb=" CB VAL b 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 6763 not shown) Planarity restraints: 8024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE Q 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE Q 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL Q 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE h 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE h 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE h 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL h 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 256 " -0.017 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE E 256 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE E 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL E 257 " -0.019 2.00e-02 2.50e+03 ... (remaining 8021 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 15168 2.87 - 3.38: 36374 3.38 - 3.88: 72097 3.88 - 4.39: 81332 4.39 - 4.90: 142880 Nonbonded interactions: 347851 Sorted by model distance: nonbonded pdb=" OG1 THR d 429 " pdb=" OE1 GLU e 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR M 429 " pdb=" OE1 GLU N 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR a 429 " pdb=" OE1 GLU b 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR G 429 " pdb=" OE1 GLU H 418 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR X 429 " pdb=" OE1 GLU Y 418 " model vdw 2.362 3.040 ... (remaining 347846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 13.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.970 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 82.200 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43826 Z= 0.229 Angle : 0.707 7.653 59194 Z= 0.443 Chirality : 0.040 0.134 6766 Planarity : 0.004 0.032 8024 Dihedral : 18.035 83.972 16762 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.71 % Allowed : 32.62 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.12), residues: 5440 helix: 4.05 (0.12), residues: 1428 sheet: 0.82 (0.11), residues: 2482 loop : -0.97 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS e 263 PHE 0.007 0.001 PHE J 237 TYR 0.004 0.001 TYR a 366 ARG 0.007 0.000 ARG J 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 978 time to evaluate : 5.004 Fit side-chains REVERT: A 244 ARG cc_start: 0.7049 (mtt90) cc_final: 0.6787 (ptm160) REVERT: A 290 LYS cc_start: 0.8246 (mtmt) cc_final: 0.8034 (mtmm) REVERT: A 376 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8301 (mtpp) REVERT: A 383 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 394 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6348 (mtpp) REVERT: B 296 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7553 (ttm-80) REVERT: B 376 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8388 (mtpp) REVERT: B 394 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6158 (mtmm) REVERT: C 275 LYS cc_start: 0.8268 (mtmp) cc_final: 0.7968 (mttm) REVERT: C 290 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8089 (mtmm) REVERT: C 356 ARG cc_start: 0.6095 (mtp180) cc_final: 0.5792 (ttp-170) REVERT: C 383 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 394 LYS cc_start: 0.7254 (mmmt) cc_final: 0.6404 (mtpp) REVERT: D 246 GLN cc_start: 0.7779 (tt0) cc_final: 0.7300 (tt0) REVERT: D 373 ARG cc_start: 0.8322 (ttt90) cc_final: 0.8026 (tpp-160) REVERT: D 394 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6598 (mtpp) REVERT: D 409 MET cc_start: 0.7068 (mmp) cc_final: 0.6843 (mmm) REVERT: E 244 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6853 (ptm160) REVERT: E 269 GLN cc_start: 0.7541 (mp10) cc_final: 0.7258 (mp-120) REVERT: E 279 GLU cc_start: 0.7687 (tt0) cc_final: 0.7487 (mt-10) REVERT: E 302 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7197 (mt-10) REVERT: E 356 ARG cc_start: 0.6430 (mtp180) cc_final: 0.6192 (ttp-170) REVERT: E 394 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6378 (mtpp) REVERT: E 420 MET cc_start: 0.8382 (ptm) cc_final: 0.8150 (ptp) REVERT: F 244 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6821 (ptm160) REVERT: F 247 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7116 (mtp180) REVERT: F 275 LYS cc_start: 0.8488 (mtmp) cc_final: 0.8220 (mttt) REVERT: F 356 ARG cc_start: 0.6751 (mtp180) cc_final: 0.6550 (ttp-170) REVERT: F 373 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7750 (tpp80) REVERT: G 244 ARG cc_start: 0.6842 (mtt90) cc_final: 0.6612 (ptm160) REVERT: G 290 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7943 (mtmm) REVERT: G 356 ARG cc_start: 0.6670 (mtp180) cc_final: 0.6416 (ttp-170) REVERT: G 373 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7887 (tpp80) REVERT: G 376 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8173 (mtpp) REVERT: G 394 LYS cc_start: 0.7377 (mmmt) cc_final: 0.6358 (mtpm) REVERT: H 244 ARG cc_start: 0.7261 (mtt90) cc_final: 0.7010 (ptm160) REVERT: H 356 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6419 (mtp85) REVERT: H 376 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8346 (mtpp) REVERT: H 383 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7324 (mt-10) REVERT: H 386 SER cc_start: 0.8995 (p) cc_final: 0.8630 (p) REVERT: H 394 LYS cc_start: 0.7301 (mmmt) cc_final: 0.6318 (mtpp) REVERT: I 244 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6666 (ptm160) REVERT: I 290 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8069 (mtmm) REVERT: I 356 ARG cc_start: 0.6499 (mtp180) cc_final: 0.6184 (ttp-170) REVERT: I 376 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8201 (mtpp) REVERT: I 394 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6472 (mmmm) REVERT: I 420 MET cc_start: 0.8167 (ptm) cc_final: 0.7815 (ptp) REVERT: J 244 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6794 (ptm160) REVERT: J 356 ARG cc_start: 0.6444 (mtp180) cc_final: 0.6158 (ttp-170) REVERT: J 376 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8346 (mtpp) REVERT: J 394 LYS cc_start: 0.6981 (mmmt) cc_final: 0.5992 (mtpp) REVERT: K 244 ARG cc_start: 0.6885 (mtt90) cc_final: 0.6673 (ptm160) REVERT: K 271 ASP cc_start: 0.7784 (t0) cc_final: 0.7562 (t0) REVERT: K 275 LYS cc_start: 0.8268 (mtmp) cc_final: 0.8049 (mttm) REVERT: K 361 ASN cc_start: 0.8778 (m-40) cc_final: 0.8562 (m-40) REVERT: K 376 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8294 (mtpp) REVERT: K 394 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6242 (mtpp) REVERT: L 244 ARG cc_start: 0.7228 (mtt90) cc_final: 0.6966 (ptm160) REVERT: L 376 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8416 (mtpp) REVERT: L 394 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6089 (ttmm) REVERT: M 373 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7897 (ttm-80) REVERT: M 383 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7558 (mt-10) REVERT: M 394 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6441 (mmmm) REVERT: N 271 ASP cc_start: 0.7651 (t0) cc_final: 0.7422 (t0) REVERT: N 275 LYS cc_start: 0.8270 (mtmp) cc_final: 0.8044 (mttm) REVERT: N 295 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8904 (p) REVERT: N 376 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8245 (mtpp) REVERT: N 383 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7058 (mm-30) REVERT: N 394 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6166 (mtpp) REVERT: N 416 THR cc_start: 0.7861 (m) cc_final: 0.7475 (p) REVERT: N 420 MET cc_start: 0.8200 (ptm) cc_final: 0.7806 (ptm) REVERT: O 244 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6819 (ptm160) REVERT: O 294 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8110 (ttm170) REVERT: O 303 GLN cc_start: 0.7466 (mt0) cc_final: 0.7265 (mt0) REVERT: O 370 ARG cc_start: 0.8297 (tmm-80) cc_final: 0.7978 (ttm170) REVERT: O 376 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8178 (OUTLIER) REVERT: O 417 ARG cc_start: 0.7250 (mtt90) cc_final: 0.6840 (mtp85) REVERT: O 420 MET cc_start: 0.8259 (ptm) cc_final: 0.7916 (ptp) REVERT: P 244 ARG cc_start: 0.6976 (mtt90) cc_final: 0.6748 (ptm160) REVERT: P 394 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6338 (mtpp) REVERT: P 416 THR cc_start: 0.8457 (m) cc_final: 0.8011 (p) REVERT: Q 271 ASP cc_start: 0.7656 (t0) cc_final: 0.7387 (t0) REVERT: Q 275 LYS cc_start: 0.8259 (mtmp) cc_final: 0.8054 (mttm) REVERT: Q 290 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8186 (mtmm) REVERT: Q 303 GLN cc_start: 0.7809 (mt0) cc_final: 0.7469 (mt0) REVERT: Q 383 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7640 (mt-10) REVERT: Q 420 MET cc_start: 0.8223 (ptm) cc_final: 0.7974 (ptp) REVERT: R 244 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6784 (ptm160) REVERT: R 290 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8034 (mtmm) REVERT: R 376 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8306 (mtpp) REVERT: R 383 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7227 (mt-10) REVERT: R 394 LYS cc_start: 0.7366 (mmmt) cc_final: 0.6348 (mtpp) REVERT: S 296 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7554 (ttm-80) REVERT: S 376 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8389 (mtpp) REVERT: S 394 LYS cc_start: 0.7241 (mmmt) cc_final: 0.6152 (mtmm) REVERT: T 275 LYS cc_start: 0.8269 (mtmp) cc_final: 0.7970 (mttm) REVERT: T 290 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8085 (mtmm) REVERT: T 356 ARG cc_start: 0.6094 (mtp180) cc_final: 0.5791 (ttp-170) REVERT: T 383 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7504 (mt-10) REVERT: T 394 LYS cc_start: 0.7253 (mmmt) cc_final: 0.6402 (mtpp) REVERT: U 246 GLN cc_start: 0.7782 (tt0) cc_final: 0.7304 (tt0) REVERT: U 373 ARG cc_start: 0.8326 (ttt90) cc_final: 0.8032 (tpp-160) REVERT: U 394 LYS cc_start: 0.7447 (mmmt) cc_final: 0.6597 (mtpp) REVERT: U 409 MET cc_start: 0.7071 (mmp) cc_final: 0.6845 (mmm) REVERT: V 244 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6855 (ptm160) REVERT: V 269 GLN cc_start: 0.7540 (mp10) cc_final: 0.7256 (mp-120) REVERT: V 279 GLU cc_start: 0.7687 (tt0) cc_final: 0.7485 (mt-10) REVERT: V 302 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7190 (mt-10) REVERT: V 356 ARG cc_start: 0.6427 (mtp180) cc_final: 0.6023 (ttp-170) REVERT: V 394 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6375 (mtpp) REVERT: V 420 MET cc_start: 0.8383 (ptm) cc_final: 0.8150 (ptp) REVERT: W 244 ARG cc_start: 0.7218 (mtt90) cc_final: 0.6818 (ptm160) REVERT: W 247 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7114 (mtp180) REVERT: W 275 LYS cc_start: 0.8489 (mtmp) cc_final: 0.8222 (mttt) REVERT: W 373 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7756 (tpp80) REVERT: X 244 ARG cc_start: 0.6843 (mtt90) cc_final: 0.6612 (ptm160) REVERT: X 290 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7945 (mtmm) REVERT: X 356 ARG cc_start: 0.6671 (mtp180) cc_final: 0.6417 (ttp-170) REVERT: X 373 ARG cc_start: 0.8229 (ttt90) cc_final: 0.7896 (tpp80) REVERT: X 376 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8171 (mtpp) REVERT: X 394 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6356 (mtpm) REVERT: Y 244 ARG cc_start: 0.7257 (mtt90) cc_final: 0.7008 (ptm160) REVERT: Y 356 ARG cc_start: 0.6734 (mtp180) cc_final: 0.6418 (mtp85) REVERT: Y 376 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8347 (mtpp) REVERT: Y 383 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7327 (mt-10) REVERT: Y 386 SER cc_start: 0.8991 (p) cc_final: 0.8626 (p) REVERT: Y 394 LYS cc_start: 0.7305 (mmmt) cc_final: 0.6322 (mtpp) REVERT: Z 244 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6666 (ptm160) REVERT: Z 290 LYS cc_start: 0.8275 (mtmt) cc_final: 0.8069 (mtmm) REVERT: Z 356 ARG cc_start: 0.6505 (mtp180) cc_final: 0.6188 (ttp-170) REVERT: Z 376 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8203 (mtpp) REVERT: Z 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6468 (mmmm) REVERT: Z 420 MET cc_start: 0.8172 (ptm) cc_final: 0.7821 (ptp) REVERT: a 244 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6794 (ptm160) REVERT: a 356 ARG cc_start: 0.6443 (mtp180) cc_final: 0.6157 (ttp-170) REVERT: a 376 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8351 (mtpp) REVERT: a 394 LYS cc_start: 0.6980 (mmmt) cc_final: 0.5993 (mtpp) REVERT: b 244 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6674 (ptm160) REVERT: b 271 ASP cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: b 275 LYS cc_start: 0.8267 (mtmp) cc_final: 0.8049 (mttm) REVERT: b 361 ASN cc_start: 0.8783 (m-40) cc_final: 0.8564 (m-40) REVERT: b 376 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8297 (mtpp) REVERT: b 394 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6243 (mtpp) REVERT: c 244 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6967 (ptm160) REVERT: c 376 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8418 (mtpp) REVERT: c 394 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6091 (ttmm) REVERT: d 373 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7896 (ttm-80) REVERT: d 383 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7560 (mt-10) REVERT: d 394 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6444 (mmmm) REVERT: e 271 ASP cc_start: 0.7652 (t0) cc_final: 0.7422 (t0) REVERT: e 275 LYS cc_start: 0.8270 (mtmp) cc_final: 0.8044 (mttm) REVERT: e 295 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8903 (p) REVERT: e 376 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8244 (mtpp) REVERT: e 383 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7054 (mm-30) REVERT: e 394 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6174 (mtpp) REVERT: e 416 THR cc_start: 0.7859 (m) cc_final: 0.7476 (p) REVERT: e 420 MET cc_start: 0.8202 (ptm) cc_final: 0.7807 (ptm) REVERT: f 244 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6818 (ptm160) REVERT: f 294 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8113 (ttm170) REVERT: f 370 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.7980 (ttm170) REVERT: f 376 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8178 (OUTLIER) REVERT: f 417 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6846 (mtp85) REVERT: f 420 MET cc_start: 0.8262 (ptm) cc_final: 0.7916 (ptp) REVERT: g 244 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6748 (ptm160) REVERT: g 394 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6340 (mtpp) REVERT: g 416 THR cc_start: 0.8459 (m) cc_final: 0.8011 (p) REVERT: h 244 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6792 (ptm160) REVERT: h 271 ASP cc_start: 0.7657 (t0) cc_final: 0.7388 (t0) REVERT: h 275 LYS cc_start: 0.8258 (mtmp) cc_final: 0.8052 (mttm) REVERT: h 290 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8186 (mtmm) REVERT: h 303 GLN cc_start: 0.7807 (mt0) cc_final: 0.7467 (mt0) REVERT: h 383 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7642 (mt-10) REVERT: h 420 MET cc_start: 0.8222 (ptm) cc_final: 0.7973 (ptp) outliers start: 34 outliers final: 30 residues processed: 984 average time/residue: 2.1423 time to fit residues: 2465.1396 Evaluate side-chains 854 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 824 time to evaluate : 5.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 295 SER Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain O residue 295 SER Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain U residue 295 SER Chi-restraints excluded: chain V residue 295 SER Chi-restraints excluded: chain W residue 295 SER Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain a residue 295 SER Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain c residue 295 SER Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain e residue 295 SER Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain h residue 295 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 459 optimal weight: 2.9990 chunk 412 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 426 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 494 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 303 GLN A 374 HIS A 431 ASN A 434 ASN B 231 ASN B 269 GLN B 303 GLN B 374 HIS B 434 ASN C 231 ASN C 303 GLN C 374 HIS C 434 ASN D 231 ASN D 303 GLN D 374 HIS D 434 ASN E 231 ASN E 303 GLN E 374 HIS E 431 ASN E 434 ASN F 231 ASN F 303 GLN F 374 HIS F 431 ASN F 434 ASN G 303 GLN G 374 HIS G 434 ASN H 231 ASN H 303 GLN H 374 HIS H 431 ASN H 434 ASN I 303 GLN I 361 ASN I 374 HIS I 431 ASN I 434 ASN J 303 GLN J 374 HIS J 434 ASN K 303 GLN K 374 HIS K 434 ASN L 231 ASN L 269 GLN L 303 GLN L 374 HIS L 434 ASN M 231 ASN M 303 GLN M 374 HIS M 431 ASN M 434 ASN N 231 ASN N 269 GLN N 303 GLN N 374 HIS N 434 ASN O 231 ASN O 269 GLN O 303 GLN O 374 HIS O 431 ASN O 434 ASN P 231 ASN P 269 GLN P 303 GLN P 361 ASN P 374 HIS P 434 ASN Q 303 GLN Q 374 HIS Q 431 ASN Q 434 ASN R 303 GLN R 374 HIS R 431 ASN R 434 ASN S 231 ASN S 269 GLN S 303 GLN S 374 HIS S 434 ASN T 231 ASN ** T 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 303 GLN T 374 HIS T 434 ASN U 231 ASN U 303 GLN U 374 HIS U 434 ASN V 303 GLN V 374 HIS V 431 ASN V 434 ASN W 231 ASN W 303 GLN W 374 HIS W 431 ASN W 434 ASN X 303 GLN X 374 HIS X 434 ASN Y 231 ASN Y 303 GLN Y 374 HIS Y 431 ASN Y 434 ASN Z 303 GLN Z 361 ASN Z 374 HIS Z 431 ASN Z 434 ASN a 303 GLN a 374 HIS a 434 ASN b 303 GLN b 374 HIS b 434 ASN c 231 ASN c 269 GLN c 303 GLN c 374 HIS c 431 ASN c 434 ASN d 231 ASN d 303 GLN d 374 HIS d 431 ASN d 434 ASN e 231 ASN e 269 GLN e 303 GLN e 374 HIS e 434 ASN f 231 ASN f 269 GLN f 374 HIS f 431 ASN f 434 ASN g 231 ASN g 269 GLN g 303 GLN g 361 ASN g 374 HIS g 434 ASN h 303 GLN h 374 HIS h 431 ASN h 434 ASN Total number of N/Q/H flips: 154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 43826 Z= 0.314 Angle : 0.596 6.132 59194 Z= 0.318 Chirality : 0.044 0.169 6766 Planarity : 0.004 0.061 8024 Dihedral : 4.170 15.275 6048 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.92 % Allowed : 30.23 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.12), residues: 5440 helix: 4.16 (0.12), residues: 1428 sheet: 0.82 (0.11), residues: 2618 loop : -0.47 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS W 263 PHE 0.013 0.002 PHE D 422 TYR 0.012 0.002 TYR V 282 ARG 0.008 0.001 ARG b 296 *********************** 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 984 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 844 time to evaluate : 5.621 Fit side-chains REVERT: A 244 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6915 (mtm110) REVERT: A 294 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8939 (tpp-160) REVERT: A 394 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6443 (mtpp) REVERT: B 244 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.6886 (mtm110) REVERT: B 275 LYS cc_start: 0.8599 (mttp) cc_final: 0.8331 (mtmp) REVERT: B 303 GLN cc_start: 0.7610 (mt0) cc_final: 0.7357 (mt0) REVERT: B 377 MET cc_start: 0.8455 (mpt) cc_final: 0.7942 (mpt) REVERT: B 394 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6501 (ttpp) REVERT: C 244 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6839 (mtp85) REVERT: C 394 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6497 (ttpp) REVERT: D 394 LYS cc_start: 0.7463 (mmmt) cc_final: 0.6708 (ttpp) REVERT: E 244 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6651 (ptm160) REVERT: E 269 GLN cc_start: 0.7707 (mp10) cc_final: 0.7452 (mp-120) REVERT: E 294 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8273 (tpm170) REVERT: E 356 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6667 (mtp-110) REVERT: F 244 ARG cc_start: 0.7223 (mtt90) cc_final: 0.6972 (mtm110) REVERT: F 246 GLN cc_start: 0.8071 (tt0) cc_final: 0.7720 (tt0) REVERT: F 247 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7159 (mtp180) REVERT: F 275 LYS cc_start: 0.8578 (mtmp) cc_final: 0.8088 (mttt) REVERT: F 287 ASP cc_start: 0.7354 (t0) cc_final: 0.6694 (p0) REVERT: F 290 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8002 (mtpt) REVERT: F 376 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8260 (mtpp) REVERT: F 431 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7941 (t0) REVERT: G 244 ARG cc_start: 0.7234 (mtt90) cc_final: 0.6638 (ptm160) REVERT: G 247 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7462 (mtm180) REVERT: G 290 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8042 (mtmm) REVERT: G 394 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6619 (mtpp) REVERT: H 244 ARG cc_start: 0.7318 (mtt90) cc_final: 0.6925 (mtm110) REVERT: H 290 LYS cc_start: 0.8230 (mtmm) cc_final: 0.8002 (mtmm) REVERT: H 376 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8227 (mtpp) REVERT: H 383 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7408 (mt-10) REVERT: H 386 SER cc_start: 0.8976 (p) cc_final: 0.8642 (p) REVERT: H 394 LYS cc_start: 0.7495 (mmmt) cc_final: 0.6631 (mtpp) REVERT: I 244 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6671 (ptm160) REVERT: I 294 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8643 (tpp-160) REVERT: I 356 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6534 (ttp-170) REVERT: I 394 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6466 (mmmm) REVERT: I 416 THR cc_start: 0.7914 (m) cc_final: 0.7649 (p) REVERT: J 242 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8107 (mt-10) REVERT: J 244 ARG cc_start: 0.7368 (mtt90) cc_final: 0.6775 (ptm160) REVERT: J 276 GLU cc_start: 0.8312 (tt0) cc_final: 0.8047 (mt-10) REVERT: K 244 ARG cc_start: 0.7348 (mtt90) cc_final: 0.6771 (ptm160) REVERT: K 246 GLN cc_start: 0.7956 (tt0) cc_final: 0.7603 (tt0) REVERT: K 247 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7122 (mtm110) REVERT: K 294 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8755 (tpp80) REVERT: K 394 LYS cc_start: 0.7396 (mmmt) cc_final: 0.6525 (mtpp) REVERT: K 416 THR cc_start: 0.8027 (m) cc_final: 0.7742 (p) REVERT: L 244 ARG cc_start: 0.7476 (mtt90) cc_final: 0.6962 (ptm160) REVERT: L 394 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6302 (ttpp) REVERT: M 244 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6720 (mtm110) REVERT: M 279 GLU cc_start: 0.7854 (tt0) cc_final: 0.7615 (mt-10) REVERT: M 294 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8284 (tpm170) REVERT: M 376 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8081 (mtpp) REVERT: M 394 LYS cc_start: 0.7391 (mmmt) cc_final: 0.6499 (mtpp) REVERT: N 244 ARG cc_start: 0.7266 (ptm160) cc_final: 0.6600 (mtt-85) REVERT: N 246 GLN cc_start: 0.8035 (tt0) cc_final: 0.7753 (tt0) REVERT: N 367 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8723 (mm-30) REVERT: N 394 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6365 (tttp) REVERT: O 244 ARG cc_start: 0.7389 (mtt90) cc_final: 0.7017 (mtm110) REVERT: O 376 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8308 (mtpp) REVERT: P 244 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6768 (mtp85) REVERT: P 246 GLN cc_start: 0.7844 (tt0) cc_final: 0.7528 (tt0) REVERT: P 247 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7338 (mtm110) REVERT: P 394 LYS cc_start: 0.7045 (mmmt) cc_final: 0.6293 (mtpp) REVERT: P 416 THR cc_start: 0.8145 (m) cc_final: 0.7900 (p) REVERT: Q 275 LYS cc_start: 0.8320 (mtmp) cc_final: 0.8052 (mttm) REVERT: Q 290 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: Q 383 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7582 (mt-10) REVERT: Q 420 MET cc_start: 0.8391 (ptm) cc_final: 0.8173 (ptp) REVERT: R 244 ARG cc_start: 0.7277 (mtt90) cc_final: 0.6909 (mtm110) REVERT: R 294 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8938 (tpp-160) REVERT: R 394 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6443 (mtpp) REVERT: S 244 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.6886 (mtm110) REVERT: S 275 LYS cc_start: 0.8600 (mttp) cc_final: 0.8332 (mtmp) REVERT: S 303 GLN cc_start: 0.7604 (mt0) cc_final: 0.7353 (mt0) REVERT: S 377 MET cc_start: 0.8458 (mpt) cc_final: 0.7942 (mpt) REVERT: S 394 LYS cc_start: 0.7078 (mmmt) cc_final: 0.6496 (ttpp) REVERT: T 244 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6839 (mtp85) REVERT: T 394 LYS cc_start: 0.7426 (mmmt) cc_final: 0.6493 (ttpp) REVERT: U 394 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6704 (ttpp) REVERT: V 244 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6652 (ptm160) REVERT: V 269 GLN cc_start: 0.7708 (mp10) cc_final: 0.7449 (mp-120) REVERT: V 294 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8274 (tpm170) REVERT: V 356 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6665 (mtp-110) REVERT: W 244 ARG cc_start: 0.7220 (mtt90) cc_final: 0.6971 (mtm110) REVERT: W 246 GLN cc_start: 0.8066 (tt0) cc_final: 0.7715 (tt0) REVERT: W 247 ARG cc_start: 0.7499 (mtp180) cc_final: 0.7162 (mtp180) REVERT: W 275 LYS cc_start: 0.8584 (mtmp) cc_final: 0.8094 (mttt) REVERT: W 287 ASP cc_start: 0.7353 (t0) cc_final: 0.6695 (p0) REVERT: W 290 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8000 (mtpt) REVERT: W 376 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8260 (mtpp) REVERT: W 431 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7942 (t0) REVERT: X 244 ARG cc_start: 0.7229 (mtt90) cc_final: 0.6632 (ptm160) REVERT: X 247 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7460 (mtm180) REVERT: X 290 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (mtmm) REVERT: X 394 LYS cc_start: 0.7331 (mmmt) cc_final: 0.6611 (mtpp) REVERT: Y 244 ARG cc_start: 0.7318 (mtt90) cc_final: 0.6913 (mtm110) REVERT: Y 290 LYS cc_start: 0.8229 (mtmm) cc_final: 0.8000 (mtmm) REVERT: Y 376 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8227 (mtpp) REVERT: Y 383 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7408 (mt-10) REVERT: Y 386 SER cc_start: 0.8977 (p) cc_final: 0.8642 (p) REVERT: Y 394 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6631 (mtpp) REVERT: Z 244 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6675 (ptm160) REVERT: Z 294 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8642 (tpp-160) REVERT: Z 356 ARG cc_start: 0.6792 (mtp180) cc_final: 0.6539 (ttp-170) REVERT: Z 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6463 (mmmm) REVERT: Z 416 THR cc_start: 0.7915 (m) cc_final: 0.7648 (p) REVERT: a 242 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8110 (mt-10) REVERT: a 244 ARG cc_start: 0.7369 (mtt90) cc_final: 0.6774 (ptm160) REVERT: a 276 GLU cc_start: 0.8310 (tt0) cc_final: 0.8046 (mt-10) REVERT: b 244 ARG cc_start: 0.7348 (mtt90) cc_final: 0.6770 (ptm160) REVERT: b 246 GLN cc_start: 0.7958 (tt0) cc_final: 0.7604 (tt0) REVERT: b 247 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7119 (mtm110) REVERT: b 294 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8755 (tpp80) REVERT: b 394 LYS cc_start: 0.7396 (mmmt) cc_final: 0.6526 (mtpp) REVERT: b 416 THR cc_start: 0.8026 (m) cc_final: 0.7743 (p) REVERT: c 244 ARG cc_start: 0.7472 (mtt90) cc_final: 0.6962 (ptm160) REVERT: c 394 LYS cc_start: 0.7114 (mmmt) cc_final: 0.6299 (ttpp) REVERT: d 244 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6721 (mtm110) REVERT: d 279 GLU cc_start: 0.7855 (tt0) cc_final: 0.7614 (mt-10) REVERT: d 294 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8286 (tpm170) REVERT: d 376 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8074 (mtpp) REVERT: d 394 LYS cc_start: 0.7392 (mmmt) cc_final: 0.6500 (mtpp) REVERT: e 244 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6596 (mtt-85) REVERT: e 246 GLN cc_start: 0.8031 (tt0) cc_final: 0.7747 (tt0) REVERT: e 367 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8723 (mm-30) REVERT: e 394 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6368 (tttp) REVERT: f 244 ARG cc_start: 0.7383 (mtt90) cc_final: 0.7010 (mtm110) REVERT: f 376 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8311 (mtpp) REVERT: g 244 ARG cc_start: 0.7278 (mtt90) cc_final: 0.6780 (mtp85) REVERT: g 246 GLN cc_start: 0.7879 (tt0) cc_final: 0.7562 (tt0) REVERT: g 247 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7337 (mtm110) REVERT: g 394 LYS cc_start: 0.7045 (mmmt) cc_final: 0.6296 (mtpp) REVERT: g 416 THR cc_start: 0.8147 (m) cc_final: 0.7904 (p) REVERT: h 244 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6715 (ptm160) REVERT: h 275 LYS cc_start: 0.8318 (mtmp) cc_final: 0.8051 (mttm) REVERT: h 290 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7928 (mtmt) REVERT: h 383 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7581 (mt-10) REVERT: h 420 MET cc_start: 0.8394 (ptm) cc_final: 0.8171 (ptp) outliers start: 140 outliers final: 48 residues processed: 922 average time/residue: 2.2206 time to fit residues: 2379.8695 Evaluate side-chains 845 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 777 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 294 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 294 ARG Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 423 SER Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain R residue 294 ARG Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 294 ARG Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 431 ASN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 294 ARG Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 294 ARG Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 423 SER Chi-restraints excluded: chain g residue 289 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 274 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 411 optimal weight: 0.0980 chunk 336 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 494 optimal weight: 1.9990 chunk 534 optimal weight: 4.9990 chunk 440 optimal weight: 3.9990 chunk 490 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 397 optimal weight: 6.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN F 303 GLN G 269 GLN G 303 GLN H 303 GLN I 274 ASN J 231 ASN K 231 ASN K 303 GLN M 431 ASN N 269 GLN N 303 GLN O 269 GLN O 431 ASN P 269 GLN P 303 GLN R 231 ASN R 274 ASN S 274 ASN V 231 ASN W 303 GLN X 269 GLN X 303 GLN Y 303 GLN Z 231 ASN Z 274 ASN a 231 ASN b 231 ASN b 303 GLN d 431 ASN e 269 GLN e 303 GLN f 269 GLN f 431 ASN g 269 GLN g 303 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 43826 Z= 0.260 Angle : 0.541 5.839 59194 Z= 0.288 Chirality : 0.042 0.154 6766 Planarity : 0.004 0.047 8024 Dihedral : 4.023 14.870 6018 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.71 % Allowed : 26.89 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.12), residues: 5440 helix: 4.07 (0.12), residues: 1428 sheet: 0.82 (0.11), residues: 2618 loop : -0.30 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS c 263 PHE 0.010 0.002 PHE L 422 TYR 0.008 0.002 TYR N 282 ARG 0.006 0.001 ARG C 296 *********************** 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 911 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 781 time to evaluate : 4.905 Fit side-chains REVERT: A 244 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6859 (mtm110) REVERT: A 373 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7654 (ttp-170) REVERT: A 394 LYS cc_start: 0.7363 (mmmt) cc_final: 0.6515 (mtpp) REVERT: B 244 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7205 (mtt-85) REVERT: B 279 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 394 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6494 (ttpp) REVERT: C 244 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6897 (mtp85) REVERT: C 246 GLN cc_start: 0.7878 (tt0) cc_final: 0.7664 (tt0) REVERT: C 394 LYS cc_start: 0.7478 (mmmt) cc_final: 0.6698 (ttmt) REVERT: D 377 MET cc_start: 0.8612 (mpt) cc_final: 0.8338 (mpt) REVERT: D 394 LYS cc_start: 0.7452 (mmmt) cc_final: 0.6730 (ttpp) REVERT: E 244 ARG cc_start: 0.7362 (mtt90) cc_final: 0.6721 (ptm160) REVERT: E 269 GLN cc_start: 0.7816 (mp10) cc_final: 0.7468 (mp-120) REVERT: E 275 LYS cc_start: 0.8578 (mttt) cc_final: 0.8330 (mtmp) REVERT: E 356 ARG cc_start: 0.6782 (mtp180) cc_final: 0.6489 (ttp-170) REVERT: E 394 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6672 (ttpp) REVERT: F 244 ARG cc_start: 0.7373 (mtt90) cc_final: 0.7019 (mtm110) REVERT: F 246 GLN cc_start: 0.7902 (tt0) cc_final: 0.7528 (tt0) REVERT: F 247 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7106 (mtp180) REVERT: F 275 LYS cc_start: 0.8612 (mtmp) cc_final: 0.8070 (mttt) REVERT: F 287 ASP cc_start: 0.7412 (t0) cc_final: 0.6595 (p0) REVERT: F 290 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8055 (mtpt) REVERT: F 370 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7218 (ttm-80) REVERT: F 431 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7709 (t0) REVERT: G 244 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6661 (mtp85) REVERT: G 290 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: G 376 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8112 (mtpp) REVERT: G 394 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6639 (ttpp) REVERT: H 244 ARG cc_start: 0.7311 (mtt90) cc_final: 0.6907 (mtp85) REVERT: H 253 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7265 (mp) REVERT: H 290 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7942 (mtmm) REVERT: H 376 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8275 (mtpp) REVERT: H 394 LYS cc_start: 0.7471 (mmmt) cc_final: 0.6618 (mtpp) REVERT: I 244 ARG cc_start: 0.7387 (mtt90) cc_final: 0.6823 (mtp85) REVERT: I 294 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8711 (tpp-160) REVERT: I 356 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6415 (ttp-170) REVERT: I 394 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6284 (mtpp) REVERT: I 416 THR cc_start: 0.7968 (m) cc_final: 0.7517 (p) REVERT: J 244 ARG cc_start: 0.7229 (mtt90) cc_final: 0.6635 (ptm160) REVERT: J 246 GLN cc_start: 0.7897 (tt0) cc_final: 0.7538 (tt0) REVERT: J 290 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8277 (mtmm) REVERT: K 244 ARG cc_start: 0.7294 (mtt90) cc_final: 0.6994 (mtp85) REVERT: K 246 GLN cc_start: 0.7966 (tt0) cc_final: 0.7606 (tt0) REVERT: K 361 ASN cc_start: 0.8746 (m-40) cc_final: 0.8441 (m-40) REVERT: K 394 LYS cc_start: 0.7086 (mmmt) cc_final: 0.6062 (mtpp) REVERT: K 416 THR cc_start: 0.8002 (m) cc_final: 0.7689 (p) REVERT: L 394 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6392 (ttpp) REVERT: M 244 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6749 (mtm110) REVERT: M 246 GLN cc_start: 0.7946 (tt0) cc_final: 0.7697 (tt0) REVERT: M 294 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8322 (tpm170) REVERT: M 376 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8059 (mtpp) REVERT: M 394 LYS cc_start: 0.7258 (mmmt) cc_final: 0.6483 (mtpt) REVERT: M 431 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7982 (t0) REVERT: N 244 ARG cc_start: 0.7241 (ptm160) cc_final: 0.6607 (mtt-85) REVERT: N 275 LYS cc_start: 0.8428 (mtmp) cc_final: 0.8051 (mttm) REVERT: N 367 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8754 (mm-30) REVERT: N 394 LYS cc_start: 0.7261 (mmmt) cc_final: 0.6443 (ttpp) REVERT: N 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8190 (mm-30) REVERT: O 244 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7053 (mtm110) REVERT: O 376 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8315 (mtpp) REVERT: P 244 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6826 (mtp85) REVERT: P 246 GLN cc_start: 0.7969 (tt0) cc_final: 0.7607 (tt0) REVERT: P 275 LYS cc_start: 0.8552 (mttp) cc_final: 0.8349 (mttp) REVERT: P 376 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8287 (mtpp) REVERT: P 394 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6297 (mtpp) REVERT: P 416 THR cc_start: 0.8119 (m) cc_final: 0.7854 (p) REVERT: Q 246 GLN cc_start: 0.7735 (tt0) cc_final: 0.7439 (tt0) REVERT: Q 275 LYS cc_start: 0.8477 (mtmp) cc_final: 0.8176 (mttm) REVERT: Q 303 GLN cc_start: 0.7447 (mt0) cc_final: 0.7235 (mt0) REVERT: Q 394 LYS cc_start: 0.7094 (mmmt) cc_final: 0.6450 (ttpp) REVERT: Q 420 MET cc_start: 0.8402 (ptm) cc_final: 0.8189 (ptp) REVERT: R 244 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6875 (mtm110) REVERT: R 373 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: R 394 LYS cc_start: 0.7363 (mmmt) cc_final: 0.6515 (mtpp) REVERT: S 244 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7205 (mtt-85) REVERT: S 279 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: S 394 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6488 (ttpp) REVERT: T 244 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6896 (mtp85) REVERT: T 246 GLN cc_start: 0.7874 (tt0) cc_final: 0.7662 (tt0) REVERT: T 394 LYS cc_start: 0.7475 (mmmt) cc_final: 0.6695 (ttmt) REVERT: U 377 MET cc_start: 0.8611 (mpt) cc_final: 0.8338 (mpt) REVERT: U 394 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6728 (ttpp) REVERT: V 244 ARG cc_start: 0.7364 (mtt90) cc_final: 0.6722 (ptm160) REVERT: V 269 GLN cc_start: 0.7814 (mp10) cc_final: 0.7463 (mp-120) REVERT: V 275 LYS cc_start: 0.8584 (mttt) cc_final: 0.8336 (mtmp) REVERT: V 356 ARG cc_start: 0.6782 (mtp180) cc_final: 0.6490 (ttp-170) REVERT: V 394 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6670 (ttpp) REVERT: W 244 ARG cc_start: 0.7373 (mtt90) cc_final: 0.7017 (mtm110) REVERT: W 246 GLN cc_start: 0.7896 (tt0) cc_final: 0.7525 (tt0) REVERT: W 247 ARG cc_start: 0.7462 (mtp180) cc_final: 0.7105 (mtp180) REVERT: W 275 LYS cc_start: 0.8616 (mtmp) cc_final: 0.8073 (mttt) REVERT: W 287 ASP cc_start: 0.7407 (t0) cc_final: 0.6594 (p0) REVERT: W 290 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8056 (mtpt) REVERT: W 370 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7217 (ttm-80) REVERT: W 431 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7709 (t0) REVERT: X 244 ARG cc_start: 0.7151 (mtt90) cc_final: 0.6656 (mtp85) REVERT: X 290 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (mtmm) REVERT: X 376 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: X 394 LYS cc_start: 0.7280 (mmmt) cc_final: 0.6633 (ttpp) REVERT: Y 244 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6904 (mtp85) REVERT: Y 253 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7267 (mp) REVERT: Y 290 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7939 (mtmm) REVERT: Y 376 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8274 (mtpp) REVERT: Y 394 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6618 (mtpp) REVERT: Z 244 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6821 (mtp85) REVERT: Z 290 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7897 (mtmt) REVERT: Z 294 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8714 (tpp-160) REVERT: Z 356 ARG cc_start: 0.6678 (mtp180) cc_final: 0.6418 (ttp-170) REVERT: Z 394 LYS cc_start: 0.7141 (mmmt) cc_final: 0.6284 (mtpp) REVERT: Z 416 THR cc_start: 0.7970 (m) cc_final: 0.7518 (p) REVERT: a 244 ARG cc_start: 0.7231 (mtt90) cc_final: 0.6635 (ptm160) REVERT: a 246 GLN cc_start: 0.7898 (tt0) cc_final: 0.7538 (tt0) REVERT: a 290 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: b 244 ARG cc_start: 0.7292 (mtt90) cc_final: 0.6994 (mtp85) REVERT: b 246 GLN cc_start: 0.7969 (tt0) cc_final: 0.7607 (tt0) REVERT: b 361 ASN cc_start: 0.8747 (m-40) cc_final: 0.8441 (m-40) REVERT: b 394 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6065 (mtpp) REVERT: b 416 THR cc_start: 0.8002 (m) cc_final: 0.7692 (p) REVERT: c 394 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6388 (ttpp) REVERT: d 244 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6748 (mtm110) REVERT: d 246 GLN cc_start: 0.7946 (tt0) cc_final: 0.7695 (tt0) REVERT: d 294 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8324 (tpm170) REVERT: d 376 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8054 (mtpp) REVERT: d 394 LYS cc_start: 0.7260 (mmmt) cc_final: 0.6487 (mtpt) REVERT: d 431 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7983 (t0) REVERT: e 244 ARG cc_start: 0.7222 (ptm160) cc_final: 0.6590 (mtt-85) REVERT: e 275 LYS cc_start: 0.8430 (mtmp) cc_final: 0.8054 (mttm) REVERT: e 367 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8750 (mm-30) REVERT: e 394 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6448 (ttpp) REVERT: e 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8189 (mm-30) REVERT: f 244 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7047 (mtm110) REVERT: f 376 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8320 (mtpp) REVERT: g 244 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6789 (mtp85) REVERT: g 246 GLN cc_start: 0.7972 (tt0) cc_final: 0.7608 (tt0) REVERT: g 275 LYS cc_start: 0.8556 (mttp) cc_final: 0.8295 (mttt) REVERT: g 376 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (mtpp) REVERT: g 394 LYS cc_start: 0.6955 (mmmt) cc_final: 0.6302 (mtpp) REVERT: g 416 THR cc_start: 0.8122 (m) cc_final: 0.7855 (p) REVERT: h 244 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6683 (ptm160) REVERT: h 275 LYS cc_start: 0.8475 (mtmp) cc_final: 0.8165 (mttm) REVERT: h 303 GLN cc_start: 0.7444 (mt0) cc_final: 0.7235 (mt0) REVERT: h 394 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6453 (ttpp) REVERT: h 420 MET cc_start: 0.8402 (ptm) cc_final: 0.8189 (ptp) outliers start: 130 outliers final: 68 residues processed: 864 average time/residue: 2.2059 time to fit residues: 2218.8344 Evaluate side-chains 852 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 755 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 376 LYS Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 356 ARG Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 279 GLU Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 431 ASN Chi-restraints excluded: chain W residue 370 ARG Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 431 ASN Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 376 LYS Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 290 LYS Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 356 ARG Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 294 ARG Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 488 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 332 optimal weight: 0.0270 chunk 496 optimal weight: 2.9990 chunk 525 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 470 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN F 303 GLN F 431 ASN G 231 ASN H 303 GLN I 231 ASN J 303 GLN K 303 GLN L 303 GLN M 431 ASN O 269 GLN O 431 ASN P 269 GLN P 303 GLN R 277 GLN W 303 GLN W 431 ASN X 231 ASN Y 303 GLN a 303 GLN b 303 GLN c 303 GLN d 431 ASN f 269 GLN f 431 ASN g 269 GLN g 303 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 43826 Z= 0.309 Angle : 0.559 5.813 59194 Z= 0.299 Chirality : 0.043 0.180 6766 Planarity : 0.004 0.043 8024 Dihedral : 4.142 14.998 6018 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 4.17 % Allowed : 24.51 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.12), residues: 5440 helix: 3.94 (0.13), residues: 1428 sheet: 0.77 (0.11), residues: 2618 loop : -0.23 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 263 PHE 0.013 0.002 PHE U 422 TYR 0.007 0.002 TYR N 282 ARG 0.009 0.001 ARG T 356 *********************** 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 994 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 794 time to evaluate : 5.302 Fit side-chains REVERT: A 244 ARG cc_start: 0.7568 (mtt90) cc_final: 0.6943 (mtm110) REVERT: A 279 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: A 280 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 373 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7652 (ttp-170) REVERT: A 376 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: A 394 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6559 (ttpp) REVERT: B 244 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7193 (mtt-85) REVERT: B 275 LYS cc_start: 0.8556 (mtmp) cc_final: 0.8302 (mtmp) REVERT: B 394 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6619 (ttpp) REVERT: C 244 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6870 (mtp85) REVERT: C 246 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: C 394 LYS cc_start: 0.7496 (mmmt) cc_final: 0.6610 (ttpp) REVERT: C 424 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: D 244 ARG cc_start: 0.7192 (mtp85) cc_final: 0.6465 (mtt-85) REVERT: D 373 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8184 (ttt90) REVERT: D 377 MET cc_start: 0.8559 (mpt) cc_final: 0.8294 (mpt) REVERT: D 394 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6721 (ttpp) REVERT: E 244 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6551 (ptm160) REVERT: E 252 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8316 (tp) REVERT: E 275 LYS cc_start: 0.8545 (mttt) cc_final: 0.8285 (mtmp) REVERT: E 394 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6524 (ttpp) REVERT: F 244 ARG cc_start: 0.7403 (mtt90) cc_final: 0.6908 (mtm110) REVERT: F 246 GLN cc_start: 0.7965 (tt0) cc_final: 0.7665 (tt0) REVERT: F 247 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6818 (mpp-170) REVERT: F 275 LYS cc_start: 0.8722 (mtmp) cc_final: 0.8147 (mttt) REVERT: F 290 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (ptmt) REVERT: F 373 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7950 (tpp80) REVERT: F 394 LYS cc_start: 0.7514 (mmmt) cc_final: 0.6690 (ttpp) REVERT: G 244 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6631 (mtp85) REVERT: G 290 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8051 (mtmm) REVERT: G 367 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8718 (mm-30) REVERT: G 394 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6472 (ttpp) REVERT: H 244 ARG cc_start: 0.7437 (mtt90) cc_final: 0.6924 (mtp85) REVERT: H 373 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8241 (ttt180) REVERT: H 376 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8361 (mtpp) REVERT: H 394 LYS cc_start: 0.7393 (mmmt) cc_final: 0.6577 (mtpp) REVERT: I 244 ARG cc_start: 0.7240 (mtt90) cc_final: 0.6799 (mtp85) REVERT: I 290 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8040 (ptmt) REVERT: I 294 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8808 (tpp-160) REVERT: I 394 LYS cc_start: 0.7143 (mmmt) cc_final: 0.6288 (mtpp) REVERT: I 416 THR cc_start: 0.8083 (m) cc_final: 0.7599 (p) REVERT: J 244 ARG cc_start: 0.7381 (mtt90) cc_final: 0.6686 (ptm160) REVERT: J 246 GLN cc_start: 0.7933 (tt0) cc_final: 0.7579 (tt0) REVERT: J 267 THR cc_start: 0.8680 (t) cc_final: 0.8470 (t) REVERT: J 290 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8247 (mtmm) REVERT: J 394 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6490 (ttpp) REVERT: K 244 ARG cc_start: 0.7473 (mtt90) cc_final: 0.7093 (mtm110) REVERT: K 246 GLN cc_start: 0.8049 (tt0) cc_final: 0.7538 (tt0) REVERT: K 383 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7483 (mt-10) REVERT: K 394 LYS cc_start: 0.7044 (mmmt) cc_final: 0.6206 (ttpp) REVERT: K 416 THR cc_start: 0.7990 (m) cc_final: 0.7642 (p) REVERT: L 244 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7096 (mtp85) REVERT: L 373 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (ttt180) REVERT: L 394 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6238 (ttpp) REVERT: L 416 THR cc_start: 0.7890 (m) cc_final: 0.7537 (p) REVERT: M 244 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6787 (mtm110) REVERT: M 246 GLN cc_start: 0.8093 (tt0) cc_final: 0.7802 (tt0) REVERT: M 376 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: M 394 LYS cc_start: 0.7247 (mmmt) cc_final: 0.6584 (ttpt) REVERT: M 431 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7775 (m-40) REVERT: N 244 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6636 (mtt-85) REVERT: N 275 LYS cc_start: 0.8552 (mtmp) cc_final: 0.8176 (mttm) REVERT: N 394 LYS cc_start: 0.7171 (mmmt) cc_final: 0.6470 (ttpp) REVERT: O 244 ARG cc_start: 0.7440 (mtt90) cc_final: 0.6967 (mtm110) REVERT: O 376 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8319 (mtpp) REVERT: O 394 LYS cc_start: 0.7099 (mmmt) cc_final: 0.6292 (ttpp) REVERT: P 244 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6769 (mtp85) REVERT: P 246 GLN cc_start: 0.7934 (tt0) cc_final: 0.7655 (tt0) REVERT: P 376 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: P 394 LYS cc_start: 0.6948 (mmmt) cc_final: 0.6396 (ttpp) REVERT: P 416 THR cc_start: 0.8113 (m) cc_final: 0.7801 (p) REVERT: Q 246 GLN cc_start: 0.7806 (tt0) cc_final: 0.7429 (tt0) REVERT: Q 275 LYS cc_start: 0.8593 (mtmp) cc_final: 0.8259 (mttm) REVERT: Q 290 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: Q 383 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7718 (mt-10) REVERT: Q 394 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6536 (ttpp) REVERT: R 244 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6940 (mtm110) REVERT: R 279 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: R 280 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: R 373 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7603 (ttp-170) REVERT: R 376 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: R 394 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6558 (ttpp) REVERT: S 244 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7190 (mtt-85) REVERT: S 275 LYS cc_start: 0.8556 (mtmp) cc_final: 0.8304 (mtmp) REVERT: S 394 LYS cc_start: 0.7333 (mmmt) cc_final: 0.6614 (ttpp) REVERT: T 244 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6868 (mtp85) REVERT: T 246 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: T 394 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6607 (ttpp) REVERT: T 424 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: U 244 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6468 (mtt-85) REVERT: U 373 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8189 (ttt90) REVERT: U 377 MET cc_start: 0.8561 (mpt) cc_final: 0.8297 (mpt) REVERT: U 394 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6718 (ttpp) REVERT: V 244 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6553 (ptm160) REVERT: V 252 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8315 (tp) REVERT: V 275 LYS cc_start: 0.8550 (mttt) cc_final: 0.8293 (mtmp) REVERT: V 394 LYS cc_start: 0.7490 (mmmt) cc_final: 0.6518 (ttpp) REVERT: W 244 ARG cc_start: 0.7407 (mtt90) cc_final: 0.6909 (mtm110) REVERT: W 246 GLN cc_start: 0.7961 (tt0) cc_final: 0.7664 (tt0) REVERT: W 247 ARG cc_start: 0.7448 (mtp180) cc_final: 0.6820 (mpp-170) REVERT: W 275 LYS cc_start: 0.8728 (mtmp) cc_final: 0.8153 (mttt) REVERT: W 290 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8279 (ptmt) REVERT: W 373 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7958 (tpp80) REVERT: W 394 LYS cc_start: 0.7514 (mmmt) cc_final: 0.6687 (ttpp) REVERT: X 244 ARG cc_start: 0.7246 (mtt90) cc_final: 0.6624 (mtp85) REVERT: X 290 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8052 (mtmm) REVERT: X 367 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8723 (mm-30) REVERT: X 394 LYS cc_start: 0.7121 (mmmt) cc_final: 0.6467 (ttpp) REVERT: Y 244 ARG cc_start: 0.7435 (mtt90) cc_final: 0.6923 (mtp85) REVERT: Y 373 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8242 (ttt180) REVERT: Y 376 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: Y 394 LYS cc_start: 0.7394 (mmmt) cc_final: 0.6577 (mtpp) REVERT: Z 244 ARG cc_start: 0.7240 (mtt90) cc_final: 0.6800 (mtp85) REVERT: Z 290 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: Z 294 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8818 (tpp-160) REVERT: Z 394 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6291 (mtpp) REVERT: Z 416 THR cc_start: 0.8081 (m) cc_final: 0.7597 (p) REVERT: a 244 ARG cc_start: 0.7381 (mtt90) cc_final: 0.6685 (ptm160) REVERT: a 246 GLN cc_start: 0.7935 (tt0) cc_final: 0.7580 (tt0) REVERT: a 267 THR cc_start: 0.8682 (t) cc_final: 0.8469 (t) REVERT: a 290 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8243 (mtmm) REVERT: a 394 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6491 (ttpp) REVERT: b 244 ARG cc_start: 0.7471 (mtt90) cc_final: 0.7092 (mtm110) REVERT: b 246 GLN cc_start: 0.8051 (tt0) cc_final: 0.7541 (tt0) REVERT: b 383 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7490 (mt-10) REVERT: b 394 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6206 (ttpp) REVERT: b 416 THR cc_start: 0.7991 (m) cc_final: 0.7644 (p) REVERT: c 244 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7094 (mtp85) REVERT: c 373 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8053 (ttt180) REVERT: c 394 LYS cc_start: 0.7009 (mmmt) cc_final: 0.6237 (ttpp) REVERT: c 416 THR cc_start: 0.7885 (m) cc_final: 0.7531 (p) REVERT: d 244 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6789 (mtm110) REVERT: d 246 GLN cc_start: 0.8094 (tt0) cc_final: 0.7803 (tt0) REVERT: d 376 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8152 (mtpp) REVERT: d 394 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6586 (ttpt) REVERT: d 431 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: e 244 ARG cc_start: 0.7313 (ptm160) cc_final: 0.6636 (mtt-85) REVERT: e 275 LYS cc_start: 0.8553 (mtmp) cc_final: 0.8179 (mttm) REVERT: e 394 LYS cc_start: 0.7177 (mmmt) cc_final: 0.6475 (ttpp) REVERT: f 244 ARG cc_start: 0.7438 (mtt90) cc_final: 0.6957 (mtm110) REVERT: f 376 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8321 (mtpp) REVERT: f 394 LYS cc_start: 0.7103 (mmmt) cc_final: 0.6292 (ttpp) REVERT: g 244 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6767 (mtp85) REVERT: g 246 GLN cc_start: 0.7938 (tt0) cc_final: 0.7660 (tt0) REVERT: g 376 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8333 (mtpp) REVERT: g 394 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6399 (ttpp) REVERT: g 416 THR cc_start: 0.8114 (m) cc_final: 0.7801 (p) REVERT: h 244 ARG cc_start: 0.7473 (mtt90) cc_final: 0.6737 (ptm160) REVERT: h 275 LYS cc_start: 0.8591 (mtmp) cc_final: 0.8265 (mttm) REVERT: h 290 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: h 383 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7720 (mt-10) REVERT: h 394 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6538 (ttpp) outliers start: 200 outliers final: 72 residues processed: 916 average time/residue: 2.2246 time to fit residues: 2373.1493 Evaluate side-chains 884 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 767 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 290 LYS Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 373 ARG Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 373 ARG Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 280 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 290 LYS Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 246 GLN Chi-restraints excluded: chain T residue 247 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 252 ILE Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 431 ASN Chi-restraints excluded: chain W residue 290 LYS Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 356 ARG Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Z residue 290 LYS Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 373 ARG Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain g residue 289 SER Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 437 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 391 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 448 optimal weight: 0.9980 chunk 363 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 471 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN J 303 GLN K 297 GLN K 303 GLN M 303 GLN M 431 ASN O 431 ASN P 269 GLN P 303 GLN V 303 GLN a 303 GLN b 297 GLN b 303 GLN d 303 GLN d 431 ASN f 431 ASN g 269 GLN g 303 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43826 Z= 0.237 Angle : 0.503 5.516 59194 Z= 0.268 Chirality : 0.041 0.142 6766 Planarity : 0.003 0.040 8024 Dihedral : 3.984 14.366 6018 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 3.75 % Allowed : 24.34 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.12), residues: 5440 helix: 4.07 (0.13), residues: 1428 sheet: 0.81 (0.10), residues: 2618 loop : -0.14 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 263 PHE 0.010 0.002 PHE U 422 TYR 0.005 0.001 TYR E 282 ARG 0.011 0.001 ARG T 356 *********************** 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 969 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 789 time to evaluate : 5.379 Fit side-chains REVERT: A 244 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6963 (mtm110) REVERT: A 279 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: A 280 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: A 373 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: A 376 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (mtpp) REVERT: A 394 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6532 (ttpp) REVERT: B 244 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7290 (mtt-85) REVERT: B 246 GLN cc_start: 0.7994 (tt0) cc_final: 0.7623 (tt0) REVERT: B 275 LYS cc_start: 0.8717 (mtmp) cc_final: 0.8345 (mtmp) REVERT: B 359 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: B 376 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8263 (mtpp) REVERT: B 377 MET cc_start: 0.8530 (mpt) cc_final: 0.8107 (mpt) REVERT: B 394 LYS cc_start: 0.7323 (mmmt) cc_final: 0.6671 (ttpp) REVERT: C 244 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6876 (mtp85) REVERT: C 246 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: C 394 LYS cc_start: 0.7531 (mmmt) cc_final: 0.6740 (ttpp) REVERT: C 424 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: D 244 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6495 (mtt-85) REVERT: D 370 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8435 (ttm170) REVERT: D 373 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8175 (ttt90) REVERT: D 394 LYS cc_start: 0.7541 (mmmt) cc_final: 0.6743 (ttpp) REVERT: E 244 ARG cc_start: 0.7345 (mtt90) cc_final: 0.6826 (mtp85) REVERT: E 275 LYS cc_start: 0.8540 (mttt) cc_final: 0.8260 (mtmp) REVERT: E 394 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6379 (ttpp) REVERT: F 244 ARG cc_start: 0.7465 (mtt90) cc_final: 0.6950 (mtm110) REVERT: F 246 GLN cc_start: 0.7870 (tt0) cc_final: 0.7552 (tt0) REVERT: F 275 LYS cc_start: 0.8717 (mtmp) cc_final: 0.8240 (mttt) REVERT: F 373 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7959 (tpp80) REVERT: F 376 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8208 (mtpt) REVERT: F 394 LYS cc_start: 0.7431 (mmmt) cc_final: 0.6671 (ttpp) REVERT: G 244 ARG cc_start: 0.7380 (mtt90) cc_final: 0.6694 (mtp85) REVERT: G 290 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8007 (mtmm) REVERT: G 394 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6561 (ttpp) REVERT: H 244 ARG cc_start: 0.7475 (mtt90) cc_final: 0.6943 (mtp85) REVERT: H 376 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8347 (mtpp) REVERT: H 394 LYS cc_start: 0.7467 (mmmt) cc_final: 0.6644 (mtpp) REVERT: I 244 ARG cc_start: 0.7289 (mtt90) cc_final: 0.6786 (mtp85) REVERT: I 279 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: I 290 LYS cc_start: 0.8519 (mtmm) cc_final: 0.7995 (ptmt) REVERT: I 294 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8625 (tpp-160) REVERT: I 394 LYS cc_start: 0.7150 (mmmt) cc_final: 0.6323 (mtpp) REVERT: I 416 THR cc_start: 0.8066 (m) cc_final: 0.7575 (p) REVERT: J 244 ARG cc_start: 0.7370 (mtt90) cc_final: 0.6989 (mtp85) REVERT: J 246 GLN cc_start: 0.7934 (tt0) cc_final: 0.7593 (tt0) REVERT: J 290 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8144 (mtmm) REVERT: J 376 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: J 394 LYS cc_start: 0.7102 (mmmt) cc_final: 0.6485 (ttpp) REVERT: K 244 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6952 (mtp85) REVERT: K 246 GLN cc_start: 0.8018 (tt0) cc_final: 0.7509 (tt0) REVERT: K 361 ASN cc_start: 0.8682 (m-40) cc_final: 0.8386 (m-40) REVERT: K 383 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: K 394 LYS cc_start: 0.6972 (mmmt) cc_final: 0.6107 (ttpp) REVERT: K 404 LEU cc_start: 0.7144 (mp) cc_final: 0.6928 (mt) REVERT: K 415 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6709 (mt) REVERT: K 416 THR cc_start: 0.7995 (m) cc_final: 0.7656 (p) REVERT: L 244 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.6955 (mtp85) REVERT: L 394 LYS cc_start: 0.7108 (mmmt) cc_final: 0.6453 (ttpp) REVERT: L 415 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7113 (mt) REVERT: M 244 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6735 (mtm110) REVERT: M 376 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8067 (mtpp) REVERT: M 377 MET cc_start: 0.8552 (mpt) cc_final: 0.8335 (mpt) REVERT: M 394 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6643 (ttpt) REVERT: M 431 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7971 (m-40) REVERT: N 244 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6631 (mtt-85) REVERT: N 275 LYS cc_start: 0.8628 (mtmp) cc_final: 0.8225 (mttm) REVERT: N 370 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7712 (ttm-80) REVERT: N 394 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6560 (ttpp) REVERT: O 244 ARG cc_start: 0.7496 (mtt90) cc_final: 0.6962 (mtm110) REVERT: O 367 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8747 (mm-30) REVERT: O 376 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: O 384 ARG cc_start: 0.8794 (ttm170) cc_final: 0.8579 (ttp80) REVERT: O 394 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6445 (ttpp) REVERT: P 244 ARG cc_start: 0.7390 (mtt90) cc_final: 0.6832 (mtp85) REVERT: P 246 GLN cc_start: 0.7963 (tt0) cc_final: 0.7664 (tt0) REVERT: P 376 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: P 394 LYS cc_start: 0.6933 (mmmt) cc_final: 0.6424 (ttpp) REVERT: Q 246 GLN cc_start: 0.7732 (tt0) cc_final: 0.7404 (tt0) REVERT: Q 275 LYS cc_start: 0.8613 (mtmp) cc_final: 0.8304 (mttm) REVERT: Q 290 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: Q 394 LYS cc_start: 0.7250 (mmmt) cc_final: 0.6613 (ttpp) REVERT: R 244 ARG cc_start: 0.7564 (mtt90) cc_final: 0.6957 (mtm110) REVERT: R 279 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: R 280 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: R 290 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7920 (pttm) REVERT: R 373 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7576 (ttp-170) REVERT: R 376 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8159 (mtpp) REVERT: R 394 LYS cc_start: 0.7156 (mmmt) cc_final: 0.6534 (ttpp) REVERT: S 244 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7287 (mtt-85) REVERT: S 246 GLN cc_start: 0.7996 (tt0) cc_final: 0.7626 (tt0) REVERT: S 275 LYS cc_start: 0.8715 (mtmp) cc_final: 0.8343 (mtmp) REVERT: S 359 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: S 376 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8264 (mtpp) REVERT: S 377 MET cc_start: 0.8538 (mpt) cc_final: 0.8118 (mpt) REVERT: S 394 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6667 (ttpp) REVERT: T 244 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6872 (mtp85) REVERT: T 246 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: T 394 LYS cc_start: 0.7528 (mmmt) cc_final: 0.6739 (ttpp) REVERT: T 424 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: U 244 ARG cc_start: 0.7223 (mtp85) cc_final: 0.6492 (mtt-85) REVERT: U 370 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8439 (ttm170) REVERT: U 373 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8181 (ttt90) REVERT: U 394 LYS cc_start: 0.7545 (mmmt) cc_final: 0.6744 (ttpp) REVERT: V 244 ARG cc_start: 0.7348 (mtt90) cc_final: 0.6825 (mtp85) REVERT: V 275 LYS cc_start: 0.8546 (mttt) cc_final: 0.8263 (mtmp) REVERT: V 394 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6377 (ttpp) REVERT: W 244 ARG cc_start: 0.7464 (mtt90) cc_final: 0.6950 (mtm110) REVERT: W 246 GLN cc_start: 0.7865 (tt0) cc_final: 0.7548 (tt0) REVERT: W 275 LYS cc_start: 0.8717 (mtmp) cc_final: 0.8241 (mttt) REVERT: W 373 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7967 (tpp80) REVERT: W 376 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8213 (mtpt) REVERT: W 394 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6672 (ttpp) REVERT: X 244 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6686 (mtp85) REVERT: X 290 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8006 (mtmm) REVERT: X 394 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6557 (ttpp) REVERT: Y 244 ARG cc_start: 0.7470 (mtt90) cc_final: 0.6941 (mtp85) REVERT: Y 376 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: Y 394 LYS cc_start: 0.7467 (mmmt) cc_final: 0.6644 (mtpp) REVERT: Z 244 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6786 (mtp85) REVERT: Z 279 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: Z 290 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: Z 294 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8690 (tpp-160) REVERT: Z 394 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6326 (mtpp) REVERT: Z 416 THR cc_start: 0.8068 (m) cc_final: 0.7575 (p) REVERT: a 244 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6988 (mtp85) REVERT: a 246 GLN cc_start: 0.7935 (tt0) cc_final: 0.7593 (tt0) REVERT: a 290 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8138 (mtmm) REVERT: a 376 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8063 (mtpp) REVERT: a 394 LYS cc_start: 0.7105 (mmmt) cc_final: 0.6487 (ttpp) REVERT: b 244 ARG cc_start: 0.7387 (mtt90) cc_final: 0.6951 (mtp85) REVERT: b 246 GLN cc_start: 0.8018 (tt0) cc_final: 0.7509 (tt0) REVERT: b 361 ASN cc_start: 0.8681 (m-40) cc_final: 0.8385 (m-40) REVERT: b 383 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: b 394 LYS cc_start: 0.6969 (mmmt) cc_final: 0.6107 (ttpp) REVERT: b 404 LEU cc_start: 0.7141 (mp) cc_final: 0.6925 (mt) REVERT: b 415 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6708 (mt) REVERT: b 416 THR cc_start: 0.7996 (m) cc_final: 0.7656 (p) REVERT: c 244 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.6955 (mtp85) REVERT: c 394 LYS cc_start: 0.7068 (mmmt) cc_final: 0.6389 (ttpp) REVERT: c 415 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7113 (mt) REVERT: d 244 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6735 (mtm110) REVERT: d 376 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8069 (mtpp) REVERT: d 394 LYS cc_start: 0.7322 (mmmt) cc_final: 0.6646 (ttpt) REVERT: d 431 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7970 (m-40) REVERT: e 244 ARG cc_start: 0.7307 (ptm160) cc_final: 0.6631 (mtt-85) REVERT: e 275 LYS cc_start: 0.8627 (mtmp) cc_final: 0.8225 (mttm) REVERT: e 370 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7726 (ttm-80) REVERT: e 394 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6566 (ttpp) REVERT: f 244 ARG cc_start: 0.7490 (mtt90) cc_final: 0.6953 (mtm110) REVERT: f 376 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8302 (mtpp) REVERT: f 384 ARG cc_start: 0.8794 (ttm170) cc_final: 0.8577 (ttp80) REVERT: f 394 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6446 (ttpp) REVERT: g 244 ARG cc_start: 0.7382 (mtt90) cc_final: 0.6830 (mtp85) REVERT: g 246 GLN cc_start: 0.7969 (tt0) cc_final: 0.7668 (tt0) REVERT: g 376 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: g 394 LYS cc_start: 0.6941 (mmmt) cc_final: 0.6429 (ttpp) REVERT: h 244 ARG cc_start: 0.7529 (mtt90) cc_final: 0.6886 (mtm110) REVERT: h 246 GLN cc_start: 0.7774 (tt0) cc_final: 0.7382 (tt0) REVERT: h 275 LYS cc_start: 0.8613 (mtmp) cc_final: 0.8297 (mttm) REVERT: h 290 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8077 (mtmm) REVERT: h 296 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7715 (ttm-80) REVERT: h 394 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6606 (ttpp) outliers start: 180 outliers final: 75 residues processed: 900 average time/residue: 2.2494 time to fit residues: 2352.2321 Evaluate side-chains 900 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 768 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 356 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 280 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 246 GLN Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 247 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 431 ASN Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 356 ARG Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 290 LYS Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain Z residue 356 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 176 optimal weight: 0.9980 chunk 473 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 526 optimal weight: 0.3980 chunk 436 optimal weight: 2.9990 chunk 243 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN J 303 GLN K 277 GLN K 297 GLN K 303 GLN M 303 GLN N 269 GLN O 431 ASN P 269 GLN V 303 GLN a 303 GLN b 277 GLN b 297 GLN b 303 GLN d 303 GLN e 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43826 Z= 0.212 Angle : 0.487 5.434 59194 Z= 0.259 Chirality : 0.040 0.134 6766 Planarity : 0.003 0.041 8024 Dihedral : 3.924 15.492 6018 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.61 % Allowed : 24.68 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.12), residues: 5440 helix: 4.12 (0.13), residues: 1428 sheet: 0.86 (0.10), residues: 2618 loop : -0.10 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 263 PHE 0.009 0.002 PHE D 422 TYR 0.005 0.001 TYR f 366 ARG 0.012 0.001 ARG T 356 *********************** 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 962 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 789 time to evaluate : 4.876 Fit side-chains REVERT: A 244 ARG cc_start: 0.7560 (mtt90) cc_final: 0.6954 (mtm110) REVERT: A 279 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 373 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7594 (ttp-170) REVERT: A 394 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6577 (ttpp) REVERT: B 244 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7290 (mtt-85) REVERT: B 246 GLN cc_start: 0.8005 (tt0) cc_final: 0.7616 (tt0) REVERT: B 275 LYS cc_start: 0.8721 (mtmp) cc_final: 0.8350 (mtmp) REVERT: B 359 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: B 376 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8244 (mtpp) REVERT: B 377 MET cc_start: 0.8562 (mpt) cc_final: 0.8124 (mpt) REVERT: B 394 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6752 (ttpp) REVERT: C 244 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6863 (mtp85) REVERT: C 394 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6626 (ttpp) REVERT: C 416 THR cc_start: 0.7921 (m) cc_final: 0.7485 (p) REVERT: C 424 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: D 244 ARG cc_start: 0.7184 (mtp85) cc_final: 0.6472 (mtt-85) REVERT: D 246 GLN cc_start: 0.7901 (tt0) cc_final: 0.7407 (tt0) REVERT: D 370 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8444 (ttm170) REVERT: D 373 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: D 394 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6724 (ttpp) REVERT: E 244 ARG cc_start: 0.7603 (mtt90) cc_final: 0.7063 (mtp85) REVERT: E 275 LYS cc_start: 0.8527 (mttt) cc_final: 0.8263 (mttp) REVERT: E 394 LYS cc_start: 0.7341 (mmmt) cc_final: 0.6492 (ttpp) REVERT: F 244 ARG cc_start: 0.7474 (mtt90) cc_final: 0.6955 (mtm110) REVERT: F 246 GLN cc_start: 0.7821 (tt0) cc_final: 0.7491 (tt0) REVERT: F 247 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6555 (mpp-170) REVERT: F 275 LYS cc_start: 0.8725 (mtmp) cc_final: 0.8213 (mttt) REVERT: F 373 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7965 (tpp80) REVERT: F 394 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6615 (ttpp) REVERT: G 244 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6582 (mtp85) REVERT: G 246 GLN cc_start: 0.7602 (tt0) cc_final: 0.7142 (tt0) REVERT: G 290 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: G 367 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8782 (mm-30) REVERT: G 394 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6549 (ttpp) REVERT: H 244 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7035 (mtm110) REVERT: H 376 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: H 394 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6519 (mtpp) REVERT: I 244 ARG cc_start: 0.7369 (mtt90) cc_final: 0.6851 (mtp85) REVERT: I 279 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: I 290 LYS cc_start: 0.8509 (mtmm) cc_final: 0.7994 (ptmt) REVERT: I 294 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8662 (tpp-160) REVERT: I 394 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6387 (mtpp) REVERT: I 416 THR cc_start: 0.8036 (m) cc_final: 0.7539 (p) REVERT: J 244 ARG cc_start: 0.7311 (mtt90) cc_final: 0.6960 (mtp85) REVERT: J 246 GLN cc_start: 0.7947 (tt0) cc_final: 0.7581 (tt0) REVERT: J 281 HIS cc_start: 0.7724 (m90) cc_final: 0.7414 (m90) REVERT: J 290 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: J 376 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8056 (mtpp) REVERT: J 394 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6638 (ttpp) REVERT: K 244 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7014 (mtp85) REVERT: K 246 GLN cc_start: 0.7844 (tt0) cc_final: 0.7347 (tt0) REVERT: K 361 ASN cc_start: 0.8676 (m-40) cc_final: 0.8380 (m-40) REVERT: K 376 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8184 (mtpp) REVERT: K 383 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: K 394 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6318 (ttpp) REVERT: K 404 LEU cc_start: 0.7148 (mp) cc_final: 0.6937 (mt) REVERT: K 415 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6755 (mt) REVERT: L 244 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.6956 (mtp85) REVERT: L 279 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: L 394 LYS cc_start: 0.7392 (mmmt) cc_final: 0.6683 (ttpp) REVERT: L 415 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7109 (mt) REVERT: M 244 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6720 (mtm110) REVERT: M 279 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: M 376 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: M 377 MET cc_start: 0.8622 (mpt) cc_final: 0.8388 (mpt) REVERT: M 394 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6645 (ttpt) REVERT: N 244 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6634 (mtt-85) REVERT: N 275 LYS cc_start: 0.8610 (mtmp) cc_final: 0.8229 (mttm) REVERT: N 370 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7707 (ttm-80) REVERT: N 394 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6516 (ttpp) REVERT: O 244 ARG cc_start: 0.7553 (mtt90) cc_final: 0.7019 (mtm110) REVERT: O 376 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8297 (mtpp) REVERT: O 384 ARG cc_start: 0.8795 (ttm170) cc_final: 0.8590 (ttp80) REVERT: O 394 LYS cc_start: 0.7211 (mmmt) cc_final: 0.6496 (ttpp) REVERT: P 244 ARG cc_start: 0.7351 (mtt90) cc_final: 0.6810 (mtp85) REVERT: P 246 GLN cc_start: 0.7969 (tt0) cc_final: 0.7649 (tt0) REVERT: P 359 GLN cc_start: 0.7658 (tt0) cc_final: 0.7356 (tm-30) REVERT: P 376 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8328 (mtpp) REVERT: P 383 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7467 (mt-10) REVERT: P 394 LYS cc_start: 0.6930 (mmmt) cc_final: 0.6425 (ttpp) REVERT: Q 246 GLN cc_start: 0.7737 (tt0) cc_final: 0.7339 (tt0) REVERT: Q 275 LYS cc_start: 0.8602 (mtmp) cc_final: 0.8258 (mttm) REVERT: Q 290 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: Q 367 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8746 (mm-30) REVERT: Q 394 LYS cc_start: 0.7294 (mmmt) cc_final: 0.6700 (ttpp) REVERT: R 244 ARG cc_start: 0.7558 (mtt90) cc_final: 0.6964 (mtm110) REVERT: R 279 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: R 280 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: R 290 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7958 (pttm) REVERT: R 373 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7597 (ttp-170) REVERT: R 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6581 (ttpp) REVERT: S 244 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7286 (mtt-85) REVERT: S 246 GLN cc_start: 0.8006 (tt0) cc_final: 0.7619 (tt0) REVERT: S 275 LYS cc_start: 0.8719 (mtmp) cc_final: 0.8358 (mtmp) REVERT: S 359 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: S 376 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: S 377 MET cc_start: 0.8572 (mpt) cc_final: 0.8192 (mpt) REVERT: S 394 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6751 (ttpp) REVERT: T 244 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6862 (mtp85) REVERT: T 394 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6627 (ttpp) REVERT: T 416 THR cc_start: 0.7918 (m) cc_final: 0.7487 (p) REVERT: T 424 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: U 244 ARG cc_start: 0.7183 (mtp85) cc_final: 0.6469 (mtt-85) REVERT: U 246 GLN cc_start: 0.7905 (tt0) cc_final: 0.7412 (tt0) REVERT: U 370 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8448 (ttm170) REVERT: U 373 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (ttt90) REVERT: U 394 LYS cc_start: 0.7441 (mmmt) cc_final: 0.6748 (ttpp) REVERT: V 244 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7061 (mtp85) REVERT: V 275 LYS cc_start: 0.8534 (mttt) cc_final: 0.8266 (mttp) REVERT: V 394 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6490 (ttpp) REVERT: W 244 ARG cc_start: 0.7474 (mtt90) cc_final: 0.6955 (mtm110) REVERT: W 246 GLN cc_start: 0.7818 (tt0) cc_final: 0.7487 (tt0) REVERT: W 247 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6556 (mpp-170) REVERT: W 275 LYS cc_start: 0.8732 (mtmp) cc_final: 0.8219 (mttt) REVERT: W 373 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (tpp80) REVERT: W 394 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6614 (ttpp) REVERT: X 244 ARG cc_start: 0.7277 (mtt90) cc_final: 0.6573 (mtp85) REVERT: X 246 GLN cc_start: 0.7598 (tt0) cc_final: 0.7137 (tt0) REVERT: X 290 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: X 367 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8779 (mm-30) REVERT: X 394 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6543 (ttpp) REVERT: Y 244 ARG cc_start: 0.7568 (mtt90) cc_final: 0.7035 (mtm110) REVERT: Y 376 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8332 (mtpp) REVERT: Y 394 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6519 (mtpp) REVERT: Z 244 ARG cc_start: 0.7368 (mtt90) cc_final: 0.6850 (mtp85) REVERT: Z 279 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: Z 294 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8658 (tpp-160) REVERT: Z 394 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6390 (mtpp) REVERT: Z 416 THR cc_start: 0.8038 (m) cc_final: 0.7540 (p) REVERT: a 244 ARG cc_start: 0.7313 (mtt90) cc_final: 0.6959 (mtp85) REVERT: a 246 GLN cc_start: 0.7947 (tt0) cc_final: 0.7582 (tt0) REVERT: a 281 HIS cc_start: 0.7726 (m90) cc_final: 0.7413 (m90) REVERT: a 290 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: a 376 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: a 394 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6641 (ttpp) REVERT: b 244 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7012 (mtp85) REVERT: b 246 GLN cc_start: 0.7844 (tt0) cc_final: 0.7348 (tt0) REVERT: b 361 ASN cc_start: 0.8676 (m-40) cc_final: 0.8378 (m-40) REVERT: b 376 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: b 383 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: b 394 LYS cc_start: 0.7164 (mmmt) cc_final: 0.6318 (ttpp) REVERT: b 404 LEU cc_start: 0.7146 (mp) cc_final: 0.6933 (mt) REVERT: b 415 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6756 (mt) REVERT: c 244 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.6955 (mtp85) REVERT: c 279 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: c 394 LYS cc_start: 0.7390 (mmmt) cc_final: 0.6685 (ttpp) REVERT: c 415 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7108 (mt) REVERT: d 244 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6718 (mtm110) REVERT: d 279 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: d 376 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8067 (mtpp) REVERT: d 394 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6648 (ttpt) REVERT: e 244 ARG cc_start: 0.7298 (ptm160) cc_final: 0.6632 (mtt-85) REVERT: e 275 LYS cc_start: 0.8612 (mtmp) cc_final: 0.8229 (mttm) REVERT: e 370 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7709 (ttm-80) REVERT: e 394 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6521 (ttpp) REVERT: f 244 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7016 (mtm110) REVERT: f 376 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8301 (mtpp) REVERT: f 384 ARG cc_start: 0.8794 (ttm170) cc_final: 0.8590 (ttp80) REVERT: f 394 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6496 (ttpp) REVERT: g 244 ARG cc_start: 0.7346 (mtt90) cc_final: 0.6814 (mtp85) REVERT: g 246 GLN cc_start: 0.7972 (tt0) cc_final: 0.7651 (tt0) REVERT: g 359 GLN cc_start: 0.7655 (tt0) cc_final: 0.7353 (tm-30) REVERT: g 376 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: g 394 LYS cc_start: 0.6931 (mmmt) cc_final: 0.6424 (ttpp) REVERT: h 244 ARG cc_start: 0.7527 (mtt90) cc_final: 0.6867 (mtm110) REVERT: h 246 GLN cc_start: 0.7760 (tt0) cc_final: 0.7436 (tt0) REVERT: h 275 LYS cc_start: 0.8604 (mtmp) cc_final: 0.8251 (mttm) REVERT: h 290 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8084 (mtmm) REVERT: h 296 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7706 (ttm-80) REVERT: h 367 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8742 (mm-30) REVERT: h 394 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6700 (ttpp) outliers start: 173 outliers final: 82 residues processed: 904 average time/residue: 2.2092 time to fit residues: 2322.3602 Evaluate side-chains 898 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 759 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 356 ARG Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 290 LYS Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 280 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 247 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 431 ASN Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 290 LYS Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain Z residue 356 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 383 GLU Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 507 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 384 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 443 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 524 optimal weight: 20.0000 chunk 328 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN E 303 GLN J 303 GLN K 303 GLN M 303 GLN M 431 ASN N 269 GLN O 431 ASN P 269 GLN T 246 GLN V 303 GLN a 303 GLN b 303 GLN d 303 GLN d 431 ASN e 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 43826 Z= 0.304 Angle : 0.530 5.714 59194 Z= 0.283 Chirality : 0.042 0.148 6766 Planarity : 0.004 0.042 8024 Dihedral : 4.118 16.926 6018 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.23 % Allowed : 23.97 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.12), residues: 5440 helix: 3.91 (0.13), residues: 1428 sheet: 0.80 (0.10), residues: 2618 loop : -0.07 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 263 PHE 0.012 0.002 PHE D 422 TYR 0.007 0.002 TYR T 282 ARG 0.013 0.001 ARG C 356 *********************** 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 994 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 791 time to evaluate : 5.037 Fit side-chains REVERT: A 244 ARG cc_start: 0.7515 (mtt90) cc_final: 0.6942 (mtm110) REVERT: A 279 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: A 373 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7670 (ttp-170) REVERT: A 376 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8171 (mtpp) REVERT: A 394 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6545 (ttpp) REVERT: B 244 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7189 (mtt-85) REVERT: B 246 GLN cc_start: 0.8091 (tt0) cc_final: 0.7728 (tt0) REVERT: B 275 LYS cc_start: 0.8762 (mtmp) cc_final: 0.8399 (mtmp) REVERT: B 359 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: B 376 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: B 377 MET cc_start: 0.8558 (mpt) cc_final: 0.8265 (mpt) REVERT: B 394 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6783 (ttpp) REVERT: C 235 LEU cc_start: 0.8236 (mt) cc_final: 0.8007 (mm) REVERT: C 244 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6867 (mtp85) REVERT: C 394 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6542 (ttpp) REVERT: D 244 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6269 (mtt-85) REVERT: D 370 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7799 (ttm-80) REVERT: D 373 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (ttt90) REVERT: D 394 LYS cc_start: 0.7515 (mmmt) cc_final: 0.6745 (ttpp) REVERT: D 415 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7159 (mt) REVERT: E 244 ARG cc_start: 0.7456 (mtt90) cc_final: 0.6837 (mtp85) REVERT: E 275 LYS cc_start: 0.8551 (mttt) cc_final: 0.8207 (mtmp) REVERT: E 394 LYS cc_start: 0.7353 (mmmt) cc_final: 0.6415 (ttpp) REVERT: E 416 THR cc_start: 0.8128 (m) cc_final: 0.7872 (p) REVERT: F 244 ARG cc_start: 0.7485 (mtt90) cc_final: 0.6951 (mtm110) REVERT: F 246 GLN cc_start: 0.7960 (tt0) cc_final: 0.7668 (tt0) REVERT: F 247 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6520 (mpp-170) REVERT: F 275 LYS cc_start: 0.8780 (mtmp) cc_final: 0.8323 (mttm) REVERT: F 373 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8002 (tpp80) REVERT: F 376 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8214 (mtpt) REVERT: F 394 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6896 (mmtp) REVERT: G 244 ARG cc_start: 0.7353 (mtt90) cc_final: 0.6599 (mtp85) REVERT: G 290 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8034 (mtmm) REVERT: G 394 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6617 (ttpp) REVERT: H 244 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7002 (mtp85) REVERT: H 356 ARG cc_start: 0.6641 (ttp-170) cc_final: 0.6369 (ttp-170) REVERT: H 373 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8274 (ttt180) REVERT: H 376 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8372 (mtpp) REVERT: H 394 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6595 (ttpp) REVERT: I 244 ARG cc_start: 0.7319 (mtt90) cc_final: 0.6798 (mtp85) REVERT: I 279 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: I 290 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8082 (ptmt) REVERT: I 294 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (tpp-160) REVERT: I 394 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6336 (mtpp) REVERT: I 416 THR cc_start: 0.8068 (m) cc_final: 0.7569 (p) REVERT: J 244 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6757 (mtp85) REVERT: J 246 GLN cc_start: 0.7976 (tt0) cc_final: 0.7660 (tt0) REVERT: J 281 HIS cc_start: 0.7720 (m90) cc_final: 0.7409 (m90) REVERT: J 290 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: J 376 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8104 (mtpp) REVERT: J 394 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6627 (ttpp) REVERT: K 244 ARG cc_start: 0.7547 (mtt90) cc_final: 0.7046 (mtp85) REVERT: K 246 GLN cc_start: 0.7887 (tt0) cc_final: 0.7526 (tt0) REVERT: K 376 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (mtpp) REVERT: K 394 LYS cc_start: 0.7130 (mmmt) cc_final: 0.6288 (ttpp) REVERT: K 404 LEU cc_start: 0.7194 (mp) cc_final: 0.6972 (mt) REVERT: K 415 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6989 (mt) REVERT: K 416 THR cc_start: 0.7998 (m) cc_final: 0.7647 (p) REVERT: L 244 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.6952 (mtp85) REVERT: L 279 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: L 373 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (ttt180) REVERT: L 394 LYS cc_start: 0.7346 (mmmt) cc_final: 0.6645 (ttpp) REVERT: L 416 THR cc_start: 0.7892 (m) cc_final: 0.7510 (p) REVERT: M 244 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6742 (mtm110) REVERT: M 246 GLN cc_start: 0.7741 (tt0) cc_final: 0.7527 (tt0) REVERT: M 279 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: M 376 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: M 377 MET cc_start: 0.8657 (mpt) cc_final: 0.8395 (mpt) REVERT: M 394 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6673 (ttpt) REVERT: M 416 THR cc_start: 0.8152 (m) cc_final: 0.7679 (p) REVERT: M 431 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7813 (t0) REVERT: N 244 ARG cc_start: 0.7316 (ptm160) cc_final: 0.6649 (mtt-85) REVERT: N 275 LYS cc_start: 0.8689 (mtmp) cc_final: 0.8292 (mttm) REVERT: N 280 GLU cc_start: 0.8142 (tt0) cc_final: 0.7921 (tt0) REVERT: N 356 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6623 (ttp-170) REVERT: N 370 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7771 (ttm-80) REVERT: N 394 LYS cc_start: 0.7172 (mmmt) cc_final: 0.6479 (ttpp) REVERT: O 244 ARG cc_start: 0.7490 (mtt90) cc_final: 0.6891 (mtm110) REVERT: O 376 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8338 (mtpp) REVERT: O 417 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6746 (mtt90) REVERT: P 244 ARG cc_start: 0.7413 (mtt90) cc_final: 0.6838 (mtp85) REVERT: P 246 GLN cc_start: 0.7943 (tt0) cc_final: 0.7592 (tt0) REVERT: P 279 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: P 359 GLN cc_start: 0.7631 (tt0) cc_final: 0.7348 (tm-30) REVERT: P 376 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: P 383 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7444 (mt-10) REVERT: P 394 LYS cc_start: 0.6912 (mmmt) cc_final: 0.6387 (ttpp) REVERT: P 415 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7255 (mt) REVERT: P 416 THR cc_start: 0.8032 (m) cc_final: 0.7666 (p) REVERT: Q 246 GLN cc_start: 0.7810 (tt0) cc_final: 0.7381 (tt0) REVERT: Q 275 LYS cc_start: 0.8632 (mtmp) cc_final: 0.8292 (mttm) REVERT: Q 276 GLU cc_start: 0.8194 (tt0) cc_final: 0.7912 (mt-10) REVERT: Q 279 GLU cc_start: 0.7934 (tt0) cc_final: 0.7608 (mt-10) REVERT: Q 280 GLU cc_start: 0.8281 (tt0) cc_final: 0.7968 (tt0) REVERT: Q 290 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8111 (mtmm) REVERT: Q 373 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8039 (tpt-90) REVERT: Q 394 LYS cc_start: 0.7298 (mmmt) cc_final: 0.6685 (ttpp) REVERT: Q 415 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7222 (mt) REVERT: R 244 ARG cc_start: 0.7518 (mtt90) cc_final: 0.6945 (mtm110) REVERT: R 279 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: R 290 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7816 (ptmt) REVERT: R 373 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7638 (ttp-170) REVERT: R 376 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8176 (mtpp) REVERT: R 394 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6550 (ttpp) REVERT: S 244 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7289 (mtt-85) REVERT: S 246 GLN cc_start: 0.8092 (tt0) cc_final: 0.7728 (tt0) REVERT: S 275 LYS cc_start: 0.8762 (mtmp) cc_final: 0.8404 (mtmp) REVERT: S 359 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: S 376 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8328 (mtpp) REVERT: S 377 MET cc_start: 0.8531 (mpt) cc_final: 0.8236 (mpt) REVERT: S 394 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6784 (ttpp) REVERT: T 235 LEU cc_start: 0.8236 (mt) cc_final: 0.8007 (mm) REVERT: T 244 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: T 394 LYS cc_start: 0.7448 (mmmt) cc_final: 0.6541 (ttpp) REVERT: U 244 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6268 (mtt-85) REVERT: U 370 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7800 (ttm-80) REVERT: U 373 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: U 394 LYS cc_start: 0.7539 (mmmt) cc_final: 0.6740 (ttpp) REVERT: U 415 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (mt) REVERT: V 244 ARG cc_start: 0.7459 (mtt90) cc_final: 0.6838 (mtp85) REVERT: V 275 LYS cc_start: 0.8554 (mttt) cc_final: 0.8212 (mtmp) REVERT: V 394 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6414 (ttpp) REVERT: V 416 THR cc_start: 0.8132 (m) cc_final: 0.7873 (p) REVERT: W 244 ARG cc_start: 0.7486 (mtt90) cc_final: 0.6952 (mtm110) REVERT: W 246 GLN cc_start: 0.7881 (tt0) cc_final: 0.7579 (tt0) REVERT: W 247 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6518 (mpp-170) REVERT: W 275 LYS cc_start: 0.8786 (mtmp) cc_final: 0.8327 (mttm) REVERT: W 373 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8009 (tpp80) REVERT: W 376 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8221 (mtpt) REVERT: W 394 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6897 (mmtp) REVERT: X 244 ARG cc_start: 0.7348 (mtt90) cc_final: 0.6590 (mtp85) REVERT: X 290 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8036 (mtmm) REVERT: X 394 LYS cc_start: 0.7209 (mmmt) cc_final: 0.6617 (ttpp) REVERT: Y 244 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7001 (mtp85) REVERT: Y 373 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (ttt180) REVERT: Y 376 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8374 (mtpp) REVERT: Y 394 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6599 (ttpp) REVERT: Z 244 ARG cc_start: 0.7320 (mtt90) cc_final: 0.6800 (mtp85) REVERT: Z 279 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: Z 290 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8094 (mtmm) REVERT: Z 294 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8889 (tpp-160) REVERT: Z 394 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6338 (mtpp) REVERT: Z 416 THR cc_start: 0.8070 (m) cc_final: 0.7571 (p) REVERT: a 244 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6758 (mtp85) REVERT: a 246 GLN cc_start: 0.7977 (tt0) cc_final: 0.7661 (tt0) REVERT: a 281 HIS cc_start: 0.7719 (m90) cc_final: 0.7407 (m90) REVERT: a 290 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8123 (mtmm) REVERT: a 376 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: a 394 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6629 (ttpp) REVERT: b 244 ARG cc_start: 0.7547 (mtt90) cc_final: 0.7045 (mtp85) REVERT: b 246 GLN cc_start: 0.7887 (tt0) cc_final: 0.7526 (tt0) REVERT: b 376 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (mtpp) REVERT: b 394 LYS cc_start: 0.7131 (mmmt) cc_final: 0.6293 (ttpp) REVERT: b 404 LEU cc_start: 0.7190 (mp) cc_final: 0.6967 (mt) REVERT: b 415 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6991 (mt) REVERT: b 416 THR cc_start: 0.7996 (m) cc_final: 0.7646 (p) REVERT: c 244 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.6951 (mtp85) REVERT: c 279 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: c 373 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: c 394 LYS cc_start: 0.7346 (mmmt) cc_final: 0.6646 (ttpp) REVERT: c 415 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7236 (mt) REVERT: c 416 THR cc_start: 0.7894 (m) cc_final: 0.7511 (p) REVERT: d 244 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6742 (mtm110) REVERT: d 246 GLN cc_start: 0.7743 (tt0) cc_final: 0.7526 (tt0) REVERT: d 279 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: d 376 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8118 (mtpp) REVERT: d 394 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6673 (ttpt) REVERT: d 416 THR cc_start: 0.8157 (m) cc_final: 0.7684 (p) REVERT: d 431 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7814 (t0) REVERT: e 244 ARG cc_start: 0.7313 (ptm160) cc_final: 0.6645 (mtt-85) REVERT: e 275 LYS cc_start: 0.8689 (mtmp) cc_final: 0.8291 (mttm) REVERT: e 280 GLU cc_start: 0.8145 (tt0) cc_final: 0.7920 (tt0) REVERT: e 356 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6628 (ttp-170) REVERT: e 370 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7755 (ttm-80) REVERT: e 394 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6487 (ttpp) REVERT: f 244 ARG cc_start: 0.7487 (mtt90) cc_final: 0.6884 (mtm110) REVERT: f 376 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8342 (mtpp) REVERT: f 417 ARG cc_start: 0.7061 (mtt90) cc_final: 0.6745 (mtt90) REVERT: g 244 ARG cc_start: 0.7410 (mtt90) cc_final: 0.6843 (mtp85) REVERT: g 246 GLN cc_start: 0.7946 (tt0) cc_final: 0.7640 (tt0) REVERT: g 279 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: g 359 GLN cc_start: 0.7631 (tt0) cc_final: 0.7348 (tm-30) REVERT: g 376 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: g 383 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7365 (mt-10) REVERT: g 394 LYS cc_start: 0.6915 (mmmt) cc_final: 0.6389 (ttpp) REVERT: g 415 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7255 (mt) REVERT: g 416 THR cc_start: 0.8038 (m) cc_final: 0.7693 (p) REVERT: h 244 ARG cc_start: 0.7633 (mtt90) cc_final: 0.6906 (mtm110) REVERT: h 246 GLN cc_start: 0.7842 (tt0) cc_final: 0.7422 (tt0) REVERT: h 275 LYS cc_start: 0.8630 (mtmp) cc_final: 0.8258 (mttm) REVERT: h 276 GLU cc_start: 0.8196 (tt0) cc_final: 0.7911 (mt-10) REVERT: h 280 GLU cc_start: 0.8281 (tt0) cc_final: 0.7975 (tt0) REVERT: h 290 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8089 (mtmm) REVERT: h 373 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8148 (tpt-90) REVERT: h 394 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6684 (ttpp) REVERT: h 415 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7226 (mt) outliers start: 203 outliers final: 71 residues processed: 920 average time/residue: 2.1837 time to fit residues: 2338.1015 Evaluate side-chains 939 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 798 time to evaluate : 4.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 373 ARG Chi-restraints excluded: chain H residue 376 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 373 ARG Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 279 GLU Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 356 ARG Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain P residue 415 LEU Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 295 SER Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain S residue 373 ARG Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 247 ARG Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 373 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain V residue 431 ASN Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 376 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 279 GLU Chi-restraints excluded: chain Z residue 290 LYS Chi-restraints excluded: chain Z residue 294 ARG Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 295 SER Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 373 ARG Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain d residue 431 ASN Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain g residue 415 LEU Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 415 LEU Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 324 optimal weight: 0.6980 chunk 209 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 357 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 412 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN E 303 GLN J 303 GLN K 303 GLN M 303 GLN N 269 GLN O 431 ASN P 269 GLN V 303 GLN a 303 GLN b 303 GLN d 303 GLN e 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43826 Z= 0.170 Angle : 0.467 6.889 59194 Z= 0.247 Chirality : 0.039 0.127 6766 Planarity : 0.003 0.053 8024 Dihedral : 3.835 18.058 6018 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 2.77 % Allowed : 25.82 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.12), residues: 5440 helix: 4.13 (0.13), residues: 1428 sheet: 0.92 (0.10), residues: 2618 loop : -0.05 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 263 PHE 0.007 0.001 PHE c 422 TYR 0.006 0.001 TYR f 366 ARG 0.013 0.000 ARG C 356 *********************** 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 945 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 812 time to evaluate : 5.412 Fit side-chains REVERT: A 244 ARG cc_start: 0.7587 (mtt90) cc_final: 0.6980 (mtm110) REVERT: A 246 GLN cc_start: 0.7832 (tt0) cc_final: 0.7500 (tt0) REVERT: A 279 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: A 373 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7592 (ttp-170) REVERT: A 394 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6733 (ttpp) REVERT: B 244 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7240 (mtt-85) REVERT: B 246 GLN cc_start: 0.8005 (tt0) cc_final: 0.7677 (tt0) REVERT: B 275 LYS cc_start: 0.8742 (mtmp) cc_final: 0.8367 (mtmp) REVERT: B 359 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: B 377 MET cc_start: 0.8572 (mpt) cc_final: 0.8171 (mpt) REVERT: B 394 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6679 (ttpp) REVERT: C 235 LEU cc_start: 0.8157 (mt) cc_final: 0.7954 (mm) REVERT: C 244 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6839 (mtp85) REVERT: C 246 GLN cc_start: 0.7712 (tt0) cc_final: 0.7204 (tt0) REVERT: C 290 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8066 (mtmm) REVERT: C 394 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6609 (ttpp) REVERT: C 424 ASP cc_start: 0.8223 (m-30) cc_final: 0.7977 (m-30) REVERT: D 244 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6488 (mtt-85) REVERT: D 370 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: D 394 LYS cc_start: 0.7403 (mmmt) cc_final: 0.6745 (ttpp) REVERT: E 244 ARG cc_start: 0.7558 (mtt90) cc_final: 0.7035 (mtp85) REVERT: E 275 LYS cc_start: 0.8554 (mttt) cc_final: 0.8276 (mtmp) REVERT: E 394 LYS cc_start: 0.7340 (mmmt) cc_final: 0.6489 (ttpp) REVERT: F 244 ARG cc_start: 0.7464 (mtt90) cc_final: 0.6991 (mtm110) REVERT: F 246 GLN cc_start: 0.7782 (tt0) cc_final: 0.7416 (tt0) REVERT: F 275 LYS cc_start: 0.8730 (mtmp) cc_final: 0.8185 (mttt) REVERT: F 376 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8215 (mtpt) REVERT: F 394 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6581 (ttpp) REVERT: G 244 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6600 (mtp85) REVERT: G 246 GLN cc_start: 0.7718 (tt0) cc_final: 0.7258 (tt0) REVERT: G 290 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: G 394 LYS cc_start: 0.7230 (mmmt) cc_final: 0.6578 (ttpp) REVERT: H 244 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7030 (mtp85) REVERT: H 246 GLN cc_start: 0.7855 (tt0) cc_final: 0.7490 (tt0) REVERT: H 376 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8332 (mtpp) REVERT: H 394 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6624 (ttpp) REVERT: I 244 ARG cc_start: 0.7172 (mtt90) cc_final: 0.6687 (mtp85) REVERT: I 279 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: I 290 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8020 (ptmt) REVERT: I 294 ARG cc_start: 0.8984 (ttm170) cc_final: 0.8703 (tpp-160) REVERT: I 295 SER cc_start: 0.8650 (p) cc_final: 0.8446 (t) REVERT: I 394 LYS cc_start: 0.7180 (mmmt) cc_final: 0.6368 (mtpp) REVERT: J 244 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6788 (mtp85) REVERT: J 246 GLN cc_start: 0.7848 (tt0) cc_final: 0.7458 (tt0) REVERT: J 281 HIS cc_start: 0.7720 (m90) cc_final: 0.7418 (m90) REVERT: J 290 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8112 (mtmm) REVERT: J 376 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: J 394 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6711 (ttpp) REVERT: K 244 ARG cc_start: 0.7516 (mtt90) cc_final: 0.7046 (mtp85) REVERT: K 246 GLN cc_start: 0.7877 (tt0) cc_final: 0.7350 (tt0) REVERT: K 361 ASN cc_start: 0.8693 (m-40) cc_final: 0.8461 (m-40) REVERT: K 376 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8198 (mtpp) REVERT: K 394 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6336 (ttpp) REVERT: K 404 LEU cc_start: 0.7165 (mp) cc_final: 0.6960 (mt) REVERT: K 415 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6720 (mt) REVERT: L 244 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.6926 (mtp85) REVERT: L 279 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: L 394 LYS cc_start: 0.7346 (mmmt) cc_final: 0.6658 (ttpp) REVERT: M 244 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6636 (ttp-110) REVERT: M 246 GLN cc_start: 0.7724 (tt0) cc_final: 0.7415 (tt0) REVERT: M 376 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8080 (mtpp) REVERT: M 383 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: M 394 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6683 (ttpt) REVERT: N 244 ARG cc_start: 0.7291 (ptm160) cc_final: 0.6638 (mtt-85) REVERT: N 246 GLN cc_start: 0.8017 (tt0) cc_final: 0.7697 (tt0) REVERT: N 275 LYS cc_start: 0.8611 (mtmp) cc_final: 0.8295 (mttm) REVERT: N 356 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6440 (ttp-170) REVERT: N 370 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7746 (ttm-80) REVERT: N 394 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6540 (ttpp) REVERT: O 244 ARG cc_start: 0.7500 (mtt90) cc_final: 0.6978 (mtm110) REVERT: O 376 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: O 377 MET cc_start: 0.8562 (mpt) cc_final: 0.8073 (mpt) REVERT: O 417 ARG cc_start: 0.7071 (mtt90) cc_final: 0.6768 (mtt90) REVERT: P 244 ARG cc_start: 0.7367 (mtt90) cc_final: 0.6825 (mtp85) REVERT: P 246 GLN cc_start: 0.7948 (tt0) cc_final: 0.7618 (tt0) REVERT: P 279 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: P 295 SER cc_start: 0.8881 (p) cc_final: 0.8609 (t) REVERT: P 297 GLN cc_start: 0.8327 (tt0) cc_final: 0.8111 (tt0) REVERT: P 376 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: P 383 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7389 (mt-10) REVERT: P 394 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6404 (ttpp) REVERT: Q 246 GLN cc_start: 0.7702 (tt0) cc_final: 0.7289 (tt0) REVERT: Q 275 LYS cc_start: 0.8612 (mtmp) cc_final: 0.8256 (mttm) REVERT: Q 276 GLU cc_start: 0.8134 (tt0) cc_final: 0.7899 (mt-10) REVERT: Q 279 GLU cc_start: 0.7901 (tt0) cc_final: 0.7631 (mt-10) REVERT: Q 290 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7983 (mtmm) REVERT: Q 373 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7981 (tpt-90) REVERT: Q 394 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6606 (ttpp) REVERT: R 244 ARG cc_start: 0.7587 (mtt90) cc_final: 0.6976 (mtm110) REVERT: R 279 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: R 290 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7983 (pttm) REVERT: R 373 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: R 394 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6738 (ttpp) REVERT: S 244 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7236 (mtt-85) REVERT: S 246 GLN cc_start: 0.8007 (tt0) cc_final: 0.7680 (tt0) REVERT: S 275 LYS cc_start: 0.8743 (mtmp) cc_final: 0.8368 (mtmp) REVERT: S 359 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: S 377 MET cc_start: 0.8569 (mpt) cc_final: 0.8174 (mpt) REVERT: S 394 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6680 (ttpp) REVERT: T 235 LEU cc_start: 0.8159 (mt) cc_final: 0.7957 (mm) REVERT: T 244 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6837 (mtp85) REVERT: T 246 GLN cc_start: 0.7705 (tt0) cc_final: 0.7271 (tt0) REVERT: T 290 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8042 (mtmm) REVERT: T 394 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6614 (ttpp) REVERT: T 424 ASP cc_start: 0.8315 (m-30) cc_final: 0.8023 (m-30) REVERT: U 244 ARG cc_start: 0.7198 (mtp85) cc_final: 0.6488 (mtt-85) REVERT: U 370 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: U 394 LYS cc_start: 0.7426 (mmmt) cc_final: 0.6739 (ttpp) REVERT: V 244 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7033 (mtp85) REVERT: V 275 LYS cc_start: 0.8557 (mttt) cc_final: 0.8279 (mtmp) REVERT: V 394 LYS cc_start: 0.7340 (mmmt) cc_final: 0.6510 (ttpp) REVERT: W 244 ARG cc_start: 0.7462 (mtt90) cc_final: 0.6989 (mtm110) REVERT: W 246 GLN cc_start: 0.7779 (tt0) cc_final: 0.7414 (tt0) REVERT: W 275 LYS cc_start: 0.8739 (mtmp) cc_final: 0.8192 (mttt) REVERT: W 376 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8219 (mtpt) REVERT: W 394 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6579 (ttpp) REVERT: X 244 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6593 (mtp85) REVERT: X 246 GLN cc_start: 0.7712 (tt0) cc_final: 0.7251 (tt0) REVERT: X 290 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8004 (mtmm) REVERT: X 394 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6559 (ttpp) REVERT: Y 244 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7028 (mtp85) REVERT: Y 246 GLN cc_start: 0.7855 (tt0) cc_final: 0.7494 (tt0) REVERT: Y 376 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8332 (mtpp) REVERT: Y 394 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6628 (ttpp) REVERT: Z 244 ARG cc_start: 0.7158 (mtt90) cc_final: 0.6668 (mtp85) REVERT: Z 294 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8704 (tpp-160) REVERT: Z 394 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6372 (mtpp) REVERT: a 244 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6786 (mtp85) REVERT: a 246 GLN cc_start: 0.7850 (tt0) cc_final: 0.7459 (tt0) REVERT: a 281 HIS cc_start: 0.7719 (m90) cc_final: 0.7409 (m90) REVERT: a 290 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (mtmm) REVERT: a 376 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: a 394 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6714 (ttpp) REVERT: b 244 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7058 (mtp85) REVERT: b 246 GLN cc_start: 0.7881 (tt0) cc_final: 0.7356 (tt0) REVERT: b 361 ASN cc_start: 0.8694 (m-40) cc_final: 0.8462 (m-40) REVERT: b 376 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8196 (mtpp) REVERT: b 394 LYS cc_start: 0.7167 (mmmt) cc_final: 0.6339 (ttpp) REVERT: b 404 LEU cc_start: 0.7152 (mp) cc_final: 0.6947 (mt) REVERT: b 415 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6721 (mt) REVERT: c 244 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.6925 (mtp85) REVERT: c 279 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: c 394 LYS cc_start: 0.7342 (mmmt) cc_final: 0.6660 (ttpp) REVERT: d 244 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6639 (ttp-110) REVERT: d 246 GLN cc_start: 0.7724 (tt0) cc_final: 0.7413 (tt0) REVERT: d 376 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: d 383 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: d 394 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6685 (ttpt) REVERT: e 244 ARG cc_start: 0.7289 (ptm160) cc_final: 0.6633 (mtt-85) REVERT: e 246 GLN cc_start: 0.8015 (tt0) cc_final: 0.7692 (tt0) REVERT: e 275 LYS cc_start: 0.8612 (mtmp) cc_final: 0.8297 (mttm) REVERT: e 356 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6447 (ttp-170) REVERT: e 370 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: e 394 LYS cc_start: 0.7225 (mmmt) cc_final: 0.6547 (ttpp) REVERT: f 244 ARG cc_start: 0.7497 (mtt90) cc_final: 0.6972 (mtm110) REVERT: f 376 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (mtpp) REVERT: f 377 MET cc_start: 0.8560 (mpt) cc_final: 0.8072 (mpt) REVERT: f 417 ARG cc_start: 0.7073 (mtt90) cc_final: 0.6764 (mtt90) REVERT: g 244 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6821 (mtp85) REVERT: g 246 GLN cc_start: 0.7953 (tt0) cc_final: 0.7621 (tt0) REVERT: g 279 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: g 295 SER cc_start: 0.8886 (p) cc_final: 0.8614 (t) REVERT: g 297 GLN cc_start: 0.8321 (tt0) cc_final: 0.8099 (tt0) REVERT: g 376 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8312 (mtpp) REVERT: g 383 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7319 (mt-10) REVERT: g 394 LYS cc_start: 0.6888 (mmmt) cc_final: 0.6377 (ttpp) REVERT: h 244 ARG cc_start: 0.7591 (mtt90) cc_final: 0.6897 (mtm110) REVERT: h 246 GLN cc_start: 0.7755 (tt0) cc_final: 0.7397 (tt0) REVERT: h 275 LYS cc_start: 0.8611 (mtmp) cc_final: 0.8253 (mttm) REVERT: h 276 GLU cc_start: 0.8130 (tt0) cc_final: 0.7896 (mt-10) REVERT: h 279 GLU cc_start: 0.7902 (tt0) cc_final: 0.7633 (mt-10) REVERT: h 290 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7983 (mtmm) REVERT: h 296 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7735 (ttm-80) REVERT: h 373 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.8146 (tpp-160) REVERT: h 394 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6608 (ttpp) outliers start: 133 outliers final: 51 residues processed: 892 average time/residue: 2.2176 time to fit residues: 2304.3131 Evaluate side-chains 863 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 771 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 356 ARG Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain S residue 359 GLN Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 290 LYS Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain a residue 391 VAL Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 383 GLU Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain f residue 394 LYS Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 280 GLU Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 476 optimal weight: 0.2980 chunk 502 optimal weight: 1.9990 chunk 458 optimal weight: 2.9990 chunk 488 optimal weight: 3.9990 chunk 294 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 441 optimal weight: 5.9990 chunk 462 optimal weight: 0.9980 chunk 486 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN E 303 GLN G 269 GLN J 303 GLN K 277 GLN K 303 GLN M 303 GLN N 269 GLN O 269 GLN O 431 ASN P 269 GLN R 274 ASN V 303 GLN a 303 GLN b 277 GLN b 303 GLN d 303 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43826 Z= 0.176 Angle : 0.467 7.431 59194 Z= 0.247 Chirality : 0.039 0.122 6766 Planarity : 0.003 0.058 8024 Dihedral : 3.812 18.850 6018 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 2.54 % Allowed : 26.18 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.12), residues: 5440 helix: 4.17 (0.13), residues: 1428 sheet: 0.97 (0.10), residues: 2618 loop : -0.05 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 263 PHE 0.007 0.001 PHE D 422 TYR 0.006 0.001 TYR f 366 ARG 0.015 0.000 ARG T 356 *********************** 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 925 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 803 time to evaluate : 5.449 Fit side-chains REVERT: A 244 ARG cc_start: 0.7595 (mtt90) cc_final: 0.6989 (mtm110) REVERT: A 279 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: A 373 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7577 (ttp-170) REVERT: A 394 LYS cc_start: 0.7412 (mmmt) cc_final: 0.6870 (ttpp) REVERT: B 244 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7309 (mtt-85) REVERT: B 246 GLN cc_start: 0.8015 (tt0) cc_final: 0.7674 (tt0) REVERT: B 275 LYS cc_start: 0.8784 (mtmp) cc_final: 0.8413 (mtmp) REVERT: B 377 MET cc_start: 0.8563 (mpt) cc_final: 0.8202 (mpt) REVERT: B 394 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6740 (ttpp) REVERT: C 235 LEU cc_start: 0.8194 (mt) cc_final: 0.7970 (mm) REVERT: C 244 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6835 (mtp85) REVERT: C 246 GLN cc_start: 0.7708 (tt0) cc_final: 0.7204 (tt0) REVERT: C 394 LYS cc_start: 0.7391 (mmmt) cc_final: 0.6575 (ttpp) REVERT: C 416 THR cc_start: 0.7834 (m) cc_final: 0.7389 (p) REVERT: C 424 ASP cc_start: 0.8333 (m-30) cc_final: 0.8079 (m-30) REVERT: D 244 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6485 (mtt-85) REVERT: D 370 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7830 (ttm-80) REVERT: D 394 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6847 (ttpp) REVERT: E 244 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7050 (mtp85) REVERT: E 275 LYS cc_start: 0.8564 (mttt) cc_final: 0.8282 (mtmp) REVERT: E 303 GLN cc_start: 0.7556 (mt0) cc_final: 0.7349 (mt0) REVERT: E 394 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6504 (ttpp) REVERT: F 244 ARG cc_start: 0.7482 (mtt90) cc_final: 0.6994 (mtm110) REVERT: F 246 GLN cc_start: 0.7857 (tt0) cc_final: 0.7490 (tt0) REVERT: F 275 LYS cc_start: 0.8733 (mtmp) cc_final: 0.8216 (mttt) REVERT: F 394 LYS cc_start: 0.7185 (mmmt) cc_final: 0.6552 (ttpp) REVERT: G 244 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6591 (mtp85) REVERT: G 246 GLN cc_start: 0.7711 (tt0) cc_final: 0.7195 (tt0) REVERT: G 290 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7980 (mtmm) REVERT: G 394 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6573 (ttpp) REVERT: H 244 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7036 (mtp85) REVERT: H 246 GLN cc_start: 0.7859 (tt0) cc_final: 0.7507 (tt0) REVERT: H 376 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8351 (mtpp) REVERT: H 394 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6669 (ttpp) REVERT: I 244 ARG cc_start: 0.7180 (mtt90) cc_final: 0.6761 (mtp85) REVERT: I 290 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8029 (ptmt) REVERT: I 294 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8561 (tpp-160) REVERT: I 296 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7894 (tpp80) REVERT: I 394 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6385 (mtpp) REVERT: I 416 THR cc_start: 0.8032 (m) cc_final: 0.7525 (p) REVERT: J 244 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6814 (mtp85) REVERT: J 246 GLN cc_start: 0.7851 (tt0) cc_final: 0.7465 (tt0) REVERT: J 279 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: J 281 HIS cc_start: 0.7730 (m90) cc_final: 0.7402 (m90) REVERT: J 376 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7961 (mtpp) REVERT: J 394 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6709 (ttpp) REVERT: K 244 ARG cc_start: 0.7540 (mtt90) cc_final: 0.7066 (mtp85) REVERT: K 246 GLN cc_start: 0.7904 (tt0) cc_final: 0.7367 (tt0) REVERT: K 361 ASN cc_start: 0.8706 (m-40) cc_final: 0.8421 (m-40) REVERT: K 376 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: K 394 LYS cc_start: 0.7180 (mmmt) cc_final: 0.6391 (ttpp) REVERT: K 415 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6734 (mt) REVERT: L 244 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.6931 (mtp85) REVERT: L 246 GLN cc_start: 0.8144 (tt0) cc_final: 0.7631 (pt0) REVERT: L 394 LYS cc_start: 0.7459 (mmmt) cc_final: 0.6811 (ttpp) REVERT: M 376 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: M 394 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6683 (ttpt) REVERT: M 416 THR cc_start: 0.8074 (m) cc_final: 0.7654 (p) REVERT: N 244 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6639 (mtt-85) REVERT: N 275 LYS cc_start: 0.8683 (mtmp) cc_final: 0.8292 (mttm) REVERT: N 356 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6452 (ttp-170) REVERT: N 370 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7790 (ttm-80) REVERT: N 394 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6570 (ttpp) REVERT: O 244 ARG cc_start: 0.7520 (mtt90) cc_final: 0.6989 (mtm110) REVERT: O 246 GLN cc_start: 0.7804 (tt0) cc_final: 0.7349 (tt0) REVERT: O 376 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: O 417 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6703 (mtt90) REVERT: P 244 ARG cc_start: 0.7378 (mtt90) cc_final: 0.6826 (mtp85) REVERT: P 246 GLN cc_start: 0.7964 (tt0) cc_final: 0.7637 (tt0) REVERT: P 279 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: P 295 SER cc_start: 0.8878 (p) cc_final: 0.8598 (t) REVERT: P 297 GLN cc_start: 0.8291 (tt0) cc_final: 0.8088 (tt0) REVERT: P 376 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8317 (mtpp) REVERT: P 394 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6386 (ttpp) REVERT: Q 246 GLN cc_start: 0.7700 (tt0) cc_final: 0.7275 (tt0) REVERT: Q 275 LYS cc_start: 0.8599 (mtmp) cc_final: 0.8238 (mttm) REVERT: Q 276 GLU cc_start: 0.8192 (tt0) cc_final: 0.7912 (mt-10) REVERT: Q 279 GLU cc_start: 0.7892 (tt0) cc_final: 0.7667 (mt-10) REVERT: Q 290 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: Q 373 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8043 (tpt-90) REVERT: Q 394 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6620 (ttpp) REVERT: R 244 ARG cc_start: 0.7596 (mtt90) cc_final: 0.6981 (mtm110) REVERT: R 279 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: R 290 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7998 (pttm) REVERT: R 373 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7559 (ttp-170) REVERT: R 394 LYS cc_start: 0.7416 (mmmt) cc_final: 0.6875 (ttpp) REVERT: S 244 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7304 (mtt-85) REVERT: S 246 GLN cc_start: 0.8014 (tt0) cc_final: 0.7675 (tt0) REVERT: S 275 LYS cc_start: 0.8832 (mtmp) cc_final: 0.8475 (mtmp) REVERT: S 276 GLU cc_start: 0.8112 (tt0) cc_final: 0.7881 (mt-10) REVERT: S 377 MET cc_start: 0.8562 (mpt) cc_final: 0.8201 (mpt) REVERT: S 394 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6741 (ttpp) REVERT: T 235 LEU cc_start: 0.8196 (mt) cc_final: 0.7973 (mm) REVERT: T 244 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6835 (mtp85) REVERT: T 246 GLN cc_start: 0.7700 (tt0) cc_final: 0.7205 (tt0) REVERT: T 394 LYS cc_start: 0.7393 (mmmt) cc_final: 0.6576 (ttpp) REVERT: T 416 THR cc_start: 0.7833 (m) cc_final: 0.7393 (p) REVERT: T 424 ASP cc_start: 0.8273 (m-30) cc_final: 0.8003 (m-30) REVERT: U 244 ARG cc_start: 0.7198 (mtp85) cc_final: 0.6486 (mtt-85) REVERT: U 370 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7836 (ttm-80) REVERT: U 377 MET cc_start: 0.8435 (mpt) cc_final: 0.8189 (mpt) REVERT: U 394 LYS cc_start: 0.7498 (mmmt) cc_final: 0.6841 (ttpp) REVERT: V 244 ARG cc_start: 0.7596 (mtt90) cc_final: 0.7077 (mtp85) REVERT: V 275 LYS cc_start: 0.8568 (mttt) cc_final: 0.8285 (mtmp) REVERT: V 303 GLN cc_start: 0.7555 (mt0) cc_final: 0.7349 (mt0) REVERT: V 391 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6463 (t) REVERT: V 394 LYS cc_start: 0.7383 (mmmt) cc_final: 0.6509 (ttpp) REVERT: W 244 ARG cc_start: 0.7477 (mtt90) cc_final: 0.6992 (mtm110) REVERT: W 246 GLN cc_start: 0.7857 (tt0) cc_final: 0.7490 (tt0) REVERT: W 275 LYS cc_start: 0.8747 (mtmp) cc_final: 0.8232 (mttt) REVERT: W 376 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8229 (mtpt) REVERT: W 394 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6551 (ttpp) REVERT: X 244 ARG cc_start: 0.7296 (mtt90) cc_final: 0.6581 (mtp85) REVERT: X 246 GLN cc_start: 0.7707 (tt0) cc_final: 0.7188 (tt0) REVERT: X 290 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7982 (mtmm) REVERT: X 394 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6551 (ttpp) REVERT: Y 244 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7033 (mtp85) REVERT: Y 246 GLN cc_start: 0.7860 (tt0) cc_final: 0.7510 (tt0) REVERT: Y 376 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8352 (mtpp) REVERT: Y 394 LYS cc_start: 0.7282 (mmmt) cc_final: 0.6673 (ttpp) REVERT: Z 244 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6760 (mtp85) REVERT: Z 294 ARG cc_start: 0.8981 (ttm170) cc_final: 0.8552 (tpp-160) REVERT: Z 296 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7913 (tpp80) REVERT: Z 394 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6387 (mtpp) REVERT: Z 416 THR cc_start: 0.8029 (m) cc_final: 0.7524 (p) REVERT: a 244 ARG cc_start: 0.7229 (mtt90) cc_final: 0.6811 (mtp85) REVERT: a 246 GLN cc_start: 0.7854 (tt0) cc_final: 0.7470 (tt0) REVERT: a 279 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: a 281 HIS cc_start: 0.7729 (m90) cc_final: 0.7408 (m90) REVERT: a 376 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7986 (mtpp) REVERT: a 394 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6714 (ttpp) REVERT: b 244 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7065 (mtp85) REVERT: b 246 GLN cc_start: 0.7906 (tt0) cc_final: 0.7365 (tt0) REVERT: b 361 ASN cc_start: 0.8724 (m-40) cc_final: 0.8431 (m-40) REVERT: b 376 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: b 394 LYS cc_start: 0.7177 (mmmt) cc_final: 0.6373 (ttpp) REVERT: b 404 LEU cc_start: 0.7169 (mp) cc_final: 0.6922 (mt) REVERT: b 415 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6736 (mt) REVERT: c 244 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.6931 (mtp85) REVERT: c 246 GLN cc_start: 0.8147 (tt0) cc_final: 0.7634 (pt0) REVERT: c 394 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6698 (ttpp) REVERT: d 376 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8201 (mtpp) REVERT: d 394 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6687 (ttpt) REVERT: e 244 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6638 (mtt-85) REVERT: e 275 LYS cc_start: 0.8684 (mtmp) cc_final: 0.8290 (mttm) REVERT: e 356 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6454 (ttp-170) REVERT: e 370 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7798 (ttm-80) REVERT: e 394 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6576 (ttpp) REVERT: f 244 ARG cc_start: 0.7519 (mtt90) cc_final: 0.6985 (mtm110) REVERT: f 246 GLN cc_start: 0.7803 (tt0) cc_final: 0.7338 (tt0) REVERT: f 376 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: f 417 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6702 (mtt90) REVERT: g 244 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6826 (mtp85) REVERT: g 246 GLN cc_start: 0.8006 (tt0) cc_final: 0.7676 (tt0) REVERT: g 279 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: g 295 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8607 (t) REVERT: g 297 GLN cc_start: 0.8282 (tt0) cc_final: 0.8074 (tt0) REVERT: g 376 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (mtpp) REVERT: g 394 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6382 (ttpp) REVERT: h 244 ARG cc_start: 0.7607 (mtt90) cc_final: 0.6906 (mtm110) REVERT: h 246 GLN cc_start: 0.7758 (tt0) cc_final: 0.7401 (tt0) REVERT: h 275 LYS cc_start: 0.8591 (mtmp) cc_final: 0.8228 (mttm) REVERT: h 276 GLU cc_start: 0.8131 (tt0) cc_final: 0.7908 (mt-10) REVERT: h 279 GLU cc_start: 0.7893 (tt0) cc_final: 0.7663 (mt-10) REVERT: h 290 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7991 (mtmm) REVERT: h 296 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7643 (ttm-80) REVERT: h 394 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6622 (ttpp) outliers start: 122 outliers final: 56 residues processed: 874 average time/residue: 2.2607 time to fit residues: 2295.0156 Evaluate side-chains 890 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 799 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 356 ARG Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 381 ASP Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 381 ASP Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain f residue 394 LYS Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 320 optimal weight: 3.9990 chunk 516 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 chunk 245 optimal weight: 0.4980 chunk 359 optimal weight: 1.9990 chunk 541 optimal weight: 6.9990 chunk 498 optimal weight: 1.9990 chunk 431 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 333 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 269 GLN J 303 GLN K 303 GLN N 246 GLN N 269 GLN O 269 GLN O 431 ASN P 269 GLN W 303 GLN a 303 GLN b 303 GLN e 246 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43826 Z= 0.216 Angle : 0.488 8.118 59194 Z= 0.258 Chirality : 0.040 0.124 6766 Planarity : 0.003 0.059 8024 Dihedral : 3.898 18.974 6018 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.29 % Allowed : 26.53 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.12), residues: 5440 helix: 4.06 (0.13), residues: 1428 sheet: 0.93 (0.10), residues: 2618 loop : -0.03 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 263 PHE 0.009 0.002 PHE D 422 TYR 0.006 0.001 TYR f 366 ARG 0.015 0.001 ARG C 356 ********************** 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 925 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 815 time to evaluate : 5.066 Fit side-chains REVERT: A 244 ARG cc_start: 0.7549 (mtt90) cc_final: 0.6993 (mtm110) REVERT: A 279 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: A 373 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: A 394 LYS cc_start: 0.7394 (mmmt) cc_final: 0.6862 (ttpp) REVERT: B 244 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7314 (mtt-85) REVERT: B 246 GLN cc_start: 0.8015 (tt0) cc_final: 0.7632 (tt0) REVERT: B 275 LYS cc_start: 0.8734 (mtmp) cc_final: 0.8392 (mtmp) REVERT: B 377 MET cc_start: 0.8553 (mpt) cc_final: 0.8286 (mpt) REVERT: B 394 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6746 (ttpp) REVERT: C 235 LEU cc_start: 0.8204 (mt) cc_final: 0.7969 (mm) REVERT: C 244 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6843 (mtp85) REVERT: C 394 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6494 (ttpp) REVERT: C 416 THR cc_start: 0.7832 (m) cc_final: 0.7379 (p) REVERT: C 424 ASP cc_start: 0.8294 (m-30) cc_final: 0.8000 (m-30) REVERT: D 244 ARG cc_start: 0.7185 (mtp85) cc_final: 0.6465 (mtt-85) REVERT: D 370 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7807 (ttm-80) REVERT: D 394 LYS cc_start: 0.7423 (mmmt) cc_final: 0.6757 (ttpp) REVERT: E 244 ARG cc_start: 0.7465 (mtt90) cc_final: 0.6883 (mtp85) REVERT: E 275 LYS cc_start: 0.8569 (mttt) cc_final: 0.8193 (mtmp) REVERT: E 394 LYS cc_start: 0.7364 (mmmt) cc_final: 0.6479 (ttpp) REVERT: F 244 ARG cc_start: 0.7474 (mtt90) cc_final: 0.6962 (mtm110) REVERT: F 246 GLN cc_start: 0.7873 (tt0) cc_final: 0.7582 (tt0) REVERT: F 247 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6542 (mpp-170) REVERT: F 275 LYS cc_start: 0.8812 (mtmp) cc_final: 0.8310 (mttt) REVERT: F 373 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7990 (tpp80) REVERT: F 376 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8257 (mtpt) REVERT: F 394 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6560 (ttpp) REVERT: G 244 ARG cc_start: 0.7336 (mtt90) cc_final: 0.6622 (mtp85) REVERT: G 246 GLN cc_start: 0.7736 (tt0) cc_final: 0.7169 (tt0) REVERT: G 247 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7541 (mtm180) REVERT: G 290 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: G 394 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6578 (ttpp) REVERT: H 244 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7035 (mtp85) REVERT: H 246 GLN cc_start: 0.7867 (tt0) cc_final: 0.7498 (tt0) REVERT: H 376 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8360 (mtpp) REVERT: H 394 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6646 (ttpp) REVERT: H 416 THR cc_start: 0.8038 (m) cc_final: 0.7661 (p) REVERT: I 244 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6681 (mtp85) REVERT: I 280 GLU cc_start: 0.8160 (tt0) cc_final: 0.7934 (tt0) REVERT: I 290 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8085 (ptmt) REVERT: I 294 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8570 (tpp-160) REVERT: I 296 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7912 (tpp80) REVERT: I 394 LYS cc_start: 0.7139 (mmmt) cc_final: 0.6328 (mtpp) REVERT: I 416 THR cc_start: 0.8033 (m) cc_final: 0.7540 (p) REVERT: J 244 ARG cc_start: 0.7265 (mtt90) cc_final: 0.6832 (mtp85) REVERT: J 246 GLN cc_start: 0.7867 (tt0) cc_final: 0.7542 (tt0) REVERT: J 279 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: J 281 HIS cc_start: 0.7726 (m90) cc_final: 0.7400 (m90) REVERT: J 376 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: J 394 LYS cc_start: 0.7332 (mmmt) cc_final: 0.6741 (ttpp) REVERT: K 244 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7083 (mtp85) REVERT: K 246 GLN cc_start: 0.7880 (tt0) cc_final: 0.7517 (tt0) REVERT: K 361 ASN cc_start: 0.8725 (m-40) cc_final: 0.8433 (m-40) REVERT: K 376 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8201 (mtpp) REVERT: K 394 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6383 (ttpp) REVERT: K 415 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6764 (mt) REVERT: L 244 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.6938 (mtp85) REVERT: L 246 GLN cc_start: 0.7909 (tt0) cc_final: 0.7396 (pt0) REVERT: L 394 LYS cc_start: 0.7462 (mmmt) cc_final: 0.6817 (ttpp) REVERT: M 246 GLN cc_start: 0.7771 (tt0) cc_final: 0.7243 (tt0) REVERT: M 376 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (mtpp) REVERT: M 383 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: M 394 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6684 (ttpt) REVERT: M 416 THR cc_start: 0.8144 (m) cc_final: 0.7694 (p) REVERT: N 244 ARG cc_start: 0.7306 (ptm160) cc_final: 0.6645 (mtt-85) REVERT: N 246 GLN cc_start: 0.7982 (tt0) cc_final: 0.7644 (tt0) REVERT: N 275 LYS cc_start: 0.8690 (mtmp) cc_final: 0.8300 (mttm) REVERT: N 356 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6513 (ttp-170) REVERT: N 370 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7770 (ttm-80) REVERT: N 394 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6541 (ttpp) REVERT: O 244 ARG cc_start: 0.7548 (mtt90) cc_final: 0.6998 (mtm110) REVERT: O 246 GLN cc_start: 0.7809 (tt0) cc_final: 0.7405 (tt0) REVERT: O 376 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8280 (mtpp) REVERT: P 244 ARG cc_start: 0.7404 (mtt90) cc_final: 0.6840 (mtp85) REVERT: P 246 GLN cc_start: 0.7963 (tt0) cc_final: 0.7633 (tt0) REVERT: P 279 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: P 297 GLN cc_start: 0.8296 (tt0) cc_final: 0.8085 (tt0) REVERT: P 376 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (mtpp) REVERT: P 394 LYS cc_start: 0.6924 (mmmt) cc_final: 0.6411 (ttpp) REVERT: Q 246 GLN cc_start: 0.7741 (tt0) cc_final: 0.7367 (tt0) REVERT: Q 275 LYS cc_start: 0.8593 (mtmp) cc_final: 0.8220 (mttm) REVERT: Q 276 GLU cc_start: 0.8139 (tt0) cc_final: 0.7906 (mt-10) REVERT: Q 279 GLU cc_start: 0.7916 (tt0) cc_final: 0.7712 (mt-10) REVERT: Q 290 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7986 (mtmm) REVERT: Q 373 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8003 (tpt-90) REVERT: Q 394 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6621 (ttpp) REVERT: R 244 ARG cc_start: 0.7550 (mtt90) cc_final: 0.6995 (mtm110) REVERT: R 279 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: R 290 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7922 (ptmt) REVERT: R 373 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7568 (ttp-170) REVERT: R 394 LYS cc_start: 0.7399 (mmmt) cc_final: 0.6867 (ttpp) REVERT: S 244 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7298 (mtt-85) REVERT: S 246 GLN cc_start: 0.8017 (tt0) cc_final: 0.7634 (tt0) REVERT: S 275 LYS cc_start: 0.8740 (mtmp) cc_final: 0.8387 (mtmp) REVERT: S 376 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8280 (mtpp) REVERT: S 377 MET cc_start: 0.8555 (mpt) cc_final: 0.8294 (mpt) REVERT: S 394 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6748 (ttpp) REVERT: T 235 LEU cc_start: 0.8207 (mt) cc_final: 0.7972 (mm) REVERT: T 244 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6845 (mtp85) REVERT: T 394 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6495 (ttpp) REVERT: T 416 THR cc_start: 0.7834 (m) cc_final: 0.7390 (p) REVERT: T 424 ASP cc_start: 0.8273 (m-30) cc_final: 0.7981 (m-30) REVERT: U 244 ARG cc_start: 0.7185 (mtp85) cc_final: 0.6463 (mtt-85) REVERT: U 370 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7808 (ttm-80) REVERT: U 394 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6752 (ttpp) REVERT: V 244 ARG cc_start: 0.7464 (mtt90) cc_final: 0.6882 (mtp85) REVERT: V 275 LYS cc_start: 0.8570 (mttt) cc_final: 0.8274 (mttp) REVERT: V 394 LYS cc_start: 0.7362 (mmmt) cc_final: 0.6478 (ttpp) REVERT: W 244 ARG cc_start: 0.7473 (mtt90) cc_final: 0.6961 (mtm110) REVERT: W 246 GLN cc_start: 0.7872 (tt0) cc_final: 0.7580 (tt0) REVERT: W 247 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6541 (mpp-170) REVERT: W 275 LYS cc_start: 0.8822 (mtmp) cc_final: 0.8314 (mttt) REVERT: W 373 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7995 (tpp80) REVERT: W 394 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6560 (ttpp) REVERT: X 244 ARG cc_start: 0.7331 (mtt90) cc_final: 0.6617 (mtp85) REVERT: X 246 GLN cc_start: 0.7733 (tt0) cc_final: 0.7164 (tt0) REVERT: X 247 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7540 (mtm180) REVERT: X 290 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (mtmm) REVERT: X 394 LYS cc_start: 0.7215 (mmmt) cc_final: 0.6570 (ttpp) REVERT: Y 244 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7034 (mtp85) REVERT: Y 246 GLN cc_start: 0.7868 (tt0) cc_final: 0.7502 (tt0) REVERT: Y 376 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8361 (mtpp) REVERT: Y 394 LYS cc_start: 0.7284 (mmmt) cc_final: 0.6649 (ttpp) REVERT: Y 416 THR cc_start: 0.8042 (m) cc_final: 0.7661 (p) REVERT: Z 244 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6682 (mtp85) REVERT: Z 280 GLU cc_start: 0.8056 (tt0) cc_final: 0.7816 (tt0) REVERT: Z 290 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7973 (pttm) REVERT: Z 294 ARG cc_start: 0.8991 (ttm170) cc_final: 0.8662 (tpp-160) REVERT: Z 296 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7912 (tpp80) REVERT: Z 394 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6330 (mtpp) REVERT: Z 416 THR cc_start: 0.8031 (m) cc_final: 0.7537 (p) REVERT: a 244 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6832 (mtp85) REVERT: a 246 GLN cc_start: 0.7972 (tt0) cc_final: 0.7656 (tt0) REVERT: a 279 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: a 281 HIS cc_start: 0.7725 (m90) cc_final: 0.7397 (m90) REVERT: a 376 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8012 (mtpp) REVERT: a 394 LYS cc_start: 0.7337 (mmmt) cc_final: 0.6746 (ttpp) REVERT: b 244 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7084 (mtp85) REVERT: b 246 GLN cc_start: 0.7879 (tt0) cc_final: 0.7380 (tt0) REVERT: b 361 ASN cc_start: 0.8725 (m-40) cc_final: 0.8430 (m-40) REVERT: b 376 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: b 394 LYS cc_start: 0.7177 (mmmt) cc_final: 0.6385 (ttpp) REVERT: b 415 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6766 (mt) REVERT: c 244 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.6941 (mtp85) REVERT: c 246 GLN cc_start: 0.7909 (tt0) cc_final: 0.7399 (pt0) REVERT: c 394 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6819 (ttpp) REVERT: d 246 GLN cc_start: 0.7772 (tt0) cc_final: 0.7243 (tt0) REVERT: d 376 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: d 383 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: d 394 LYS cc_start: 0.7370 (mmmt) cc_final: 0.6687 (ttpt) REVERT: d 416 THR cc_start: 0.8064 (m) cc_final: 0.7627 (p) REVERT: e 244 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6637 (mtt-85) REVERT: e 246 GLN cc_start: 0.7976 (tt0) cc_final: 0.7636 (tt0) REVERT: e 275 LYS cc_start: 0.8690 (mtmp) cc_final: 0.8292 (mttm) REVERT: e 356 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6519 (ttp-170) REVERT: e 370 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7780 (ttm-80) REVERT: e 394 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6549 (ttpp) REVERT: f 244 ARG cc_start: 0.7545 (mtt90) cc_final: 0.6993 (mtm110) REVERT: f 246 GLN cc_start: 0.7808 (tt0) cc_final: 0.7400 (tt0) REVERT: f 376 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: g 244 ARG cc_start: 0.7397 (mtt90) cc_final: 0.6834 (mtp85) REVERT: g 246 GLN cc_start: 0.7963 (tt0) cc_final: 0.7629 (tt0) REVERT: g 279 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: g 297 GLN cc_start: 0.8287 (tt0) cc_final: 0.8079 (tt0) REVERT: g 376 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: g 394 LYS cc_start: 0.6891 (mmmt) cc_final: 0.6381 (ttpp) REVERT: h 244 ARG cc_start: 0.7669 (mtt90) cc_final: 0.6915 (mtm110) REVERT: h 246 GLN cc_start: 0.7767 (tt0) cc_final: 0.7392 (tt0) REVERT: h 275 LYS cc_start: 0.8589 (mtmp) cc_final: 0.8214 (mttm) REVERT: h 276 GLU cc_start: 0.8140 (tt0) cc_final: 0.7899 (mt-10) REVERT: h 279 GLU cc_start: 0.7884 (tt0) cc_final: 0.7670 (mt-10) REVERT: h 290 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: h 394 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6624 (ttpp) outliers start: 110 outliers final: 58 residues processed: 882 average time/residue: 2.2241 time to fit residues: 2280.8343 Evaluate side-chains 904 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 806 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 431 ASN Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 383 GLU Chi-restraints excluded: chain I residue 294 ARG Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 244 ARG Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain M residue 376 LYS Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 290 LYS Chi-restraints excluded: chain N residue 356 ARG Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 290 LYS Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain Q residue 290 LYS Chi-restraints excluded: chain Q residue 295 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 431 ASN Chi-restraints excluded: chain R residue 279 GLU Chi-restraints excluded: chain R residue 373 ARG Chi-restraints excluded: chain R residue 376 LYS Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 370 ARG Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 431 ASN Chi-restraints excluded: chain V residue 290 LYS Chi-restraints excluded: chain V residue 391 VAL Chi-restraints excluded: chain W residue 247 ARG Chi-restraints excluded: chain W residue 373 ARG Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 290 LYS Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 383 GLU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 289 SER Chi-restraints excluded: chain a residue 376 LYS Chi-restraints excluded: chain b residue 376 LYS Chi-restraints excluded: chain b residue 391 VAL Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain d residue 244 ARG Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 376 LYS Chi-restraints excluded: chain d residue 383 GLU Chi-restraints excluded: chain e residue 290 LYS Chi-restraints excluded: chain e residue 356 ARG Chi-restraints excluded: chain e residue 370 ARG Chi-restraints excluded: chain e residue 381 ASP Chi-restraints excluded: chain e residue 391 VAL Chi-restraints excluded: chain f residue 289 SER Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 376 LYS Chi-restraints excluded: chain f residue 394 LYS Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 295 SER Chi-restraints excluded: chain g residue 376 LYS Chi-restraints excluded: chain g residue 381 ASP Chi-restraints excluded: chain g residue 391 VAL Chi-restraints excluded: chain h residue 290 LYS Chi-restraints excluded: chain h residue 295 SER Chi-restraints excluded: chain h residue 381 ASP Chi-restraints excluded: chain h residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 0.9990 chunk 459 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 397 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 443 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN J 303 GLN K 277 GLN K 303 GLN N 269 GLN O 269 GLN O 431 ASN P 269 GLN V 303 GLN a 303 GLN b 277 GLN b 303 GLN e 269 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122117 restraints weight = 48799.551| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.56 r_work: 0.3281 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3269 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= 0.189 Angle : 0.477 8.023 59194 Z= 0.251 Chirality : 0.039 0.121 6766 Planarity : 0.003 0.061 8024 Dihedral : 3.837 19.386 6018 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 2.23 % Allowed : 26.62 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.12), residues: 5440 helix: 4.08 (0.13), residues: 1428 sheet: 0.95 (0.10), residues: 2618 loop : -0.01 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 263 PHE 0.008 0.001 PHE D 422 TYR 0.010 0.001 TYR O 393 ARG 0.015 0.001 ARG T 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27650.94 seconds wall clock time: 493 minutes 50.29 seconds (29630.29 seconds total)