Starting phenix.real_space_refine on Fri Mar 6 03:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7okn_12962/03_2026/7okn_12962.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 187 5.16 5 C 17442 2.51 5 N 4896 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28067 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e, g, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f, h Time building chain proxies: 2.39, per 1000 atoms: 0.09 Number of scatterers: 28067 At special positions: 0 Unit cell: (184.8, 184.8, 97.9, 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 187 16.00 O 5542 8.00 N 4896 7.00 C 17442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 274 " distance=2.02 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS F 35 " distance=1.36 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 274 " distance=2.02 Simple disulfide: pdb=" SG CYS E 250 " - pdb=" SG CYS E 274 " distance=2.02 Simple disulfide: pdb=" SG CYS G 250 " - pdb=" SG CYS G 274 " distance=2.02 Simple disulfide: pdb=" SG CYS I 250 " - pdb=" SG CYS I 274 " distance=2.02 Simple disulfide: pdb=" SG CYS K 250 " - pdb=" SG CYS K 274 " distance=2.02 Simple disulfide: pdb=" SG CYS M 250 " - pdb=" SG CYS M 274 " distance=2.02 Simple disulfide: pdb=" SG CYS O 250 " - pdb=" SG CYS O 274 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 250 " - pdb=" SG CYS Q 274 " distance=2.02 Simple disulfide: pdb=" SG CYS S 250 " - pdb=" SG CYS S 274 " distance=2.02 Simple disulfide: pdb=" SG CYS U 250 " - pdb=" SG CYS U 274 " distance=2.02 Simple disulfide: pdb=" SG CYS W 250 " - pdb=" SG CYS W 274 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 250 " - pdb=" SG CYS Y 274 " distance=2.02 Simple disulfide: pdb=" SG CYS a 250 " - pdb=" SG CYS a 274 " distance=2.02 Simple disulfide: pdb=" SG CYS c 250 " - pdb=" SG CYS c 274 " distance=2.02 Simple disulfide: pdb=" SG CYS e 250 " - pdb=" SG CYS e 274 " distance=2.02 Simple disulfide: pdb=" SG CYS g 250 " - pdb=" SG CYS g 274 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS J 35 " distance=1.86 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS D 35 " distance=1.86 Simple disulfide: pdb=" SG CYS J 27 " - pdb=" SG CYS h 35 " distance=1.86 Simple disulfide: pdb=" SG CYS L 27 " - pdb=" SG CYS H 35 " distance=1.86 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS L 35 " distance=1.86 Simple disulfide: pdb=" SG CYS P 27 " - pdb=" SG CYS N 35 " distance=1.86 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS P 35 " distance=1.86 Simple disulfide: pdb=" SG CYS T 27 " - pdb=" SG CYS R 35 " distance=1.86 Simple disulfide: pdb=" SG CYS V 27 " - pdb=" SG CYS T 35 " distance=1.86 Simple disulfide: pdb=" SG CYS X 27 " - pdb=" SG CYS V 35 " distance=1.86 Simple disulfide: pdb=" SG CYS Z 27 " - pdb=" SG CYS X 35 " distance=1.86 Simple disulfide: pdb=" SG CYS b 27 " - pdb=" SG CYS Z 35 " distance=1.86 Simple disulfide: pdb=" SG CYS d 27 " - pdb=" SG CYS b 35 " distance=1.86 Simple disulfide: pdb=" SG CYS f 27 " - pdb=" SG CYS d 35 " distance=1.86 Simple disulfide: pdb=" SG CYS h 27 " - pdb=" SG CYS f 35 " distance=1.86 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6698 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 26.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'E' and resid 306 through 325 Processing helix chain 'E' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 Processing helix chain 'G' and resid 306 through 325 Processing helix chain 'G' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR G 365 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN G 372 " --> pdb=" O LYS G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 Processing helix chain 'I' and resid 306 through 325 Processing helix chain 'I' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR I 365 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN I 372 " --> pdb=" O LYS I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA I 407 " --> pdb=" O ALA I 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 53 Processing helix chain 'K' and resid 306 through 325 Processing helix chain 'K' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP K 364 " --> pdb=" O LYS K 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR K 365 " --> pdb=" O THR K 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN K 372 " --> pdb=" O LYS K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA K 407 " --> pdb=" O ALA K 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 53 Processing helix chain 'M' and resid 306 through 325 Processing helix chain 'M' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP M 364 " --> pdb=" O LYS M 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR M 365 " --> pdb=" O THR M 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN M 372 " --> pdb=" O LYS M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 398 through 407 removed outlier: 3.539A pdb=" N ALA M 407 " --> pdb=" O ALA M 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'O' and resid 306 through 325 Processing helix chain 'O' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP O 364 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR O 365 " --> pdb=" O THR O 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN O 372 " --> pdb=" O LYS O 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA O 407 " --> pdb=" O ALA O 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 53 Processing helix chain 'Q' and resid 306 through 325 Processing helix chain 'Q' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP Q 364 " --> pdb=" O LYS Q 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Q 365 " --> pdb=" O THR Q 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN Q 372 " --> pdb=" O LYS Q 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA Q 407 " --> pdb=" O ALA Q 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 53 Processing helix chain 'S' and resid 306 through 325 Processing helix chain 'S' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP S 364 " --> pdb=" O LYS S 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR S 365 " --> pdb=" O THR S 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN S 372 " --> pdb=" O LYS S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA S 407 " --> pdb=" O ALA S 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 53 Processing helix chain 'U' and resid 306 through 325 Processing helix chain 'U' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP U 364 " --> pdb=" O LYS U 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR U 365 " --> pdb=" O THR U 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN U 372 " --> pdb=" O LYS U 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA U 407 " --> pdb=" O ALA U 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 53 Processing helix chain 'W' and resid 306 through 325 Processing helix chain 'W' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP W 364 " --> pdb=" O LYS W 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR W 365 " --> pdb=" O THR W 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN W 372 " --> pdb=" O LYS W 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 398 through 407 removed outlier: 3.539A pdb=" N ALA W 407 " --> pdb=" O ALA W 403 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 53 Processing helix chain 'Y' and resid 306 through 325 Processing helix chain 'Y' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP Y 364 " --> pdb=" O LYS Y 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR Y 365 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN Y 372 " --> pdb=" O LYS Y 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA Y 407 " --> pdb=" O ALA Y 403 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 53 Processing helix chain 'Z' and resid 38 through 53 Processing helix chain 'a' and resid 306 through 325 Processing helix chain 'a' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP a 364 " --> pdb=" O LYS a 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR a 365 " --> pdb=" O THR a 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN a 372 " --> pdb=" O LYS a 368 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA a 407 " --> pdb=" O ALA a 403 " (cutoff:3.500A) Processing helix chain 'c' and resid 306 through 325 Processing helix chain 'c' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP c 364 " --> pdb=" O LYS c 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR c 365 " --> pdb=" O THR c 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN c 372 " --> pdb=" O LYS c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA c 407 " --> pdb=" O ALA c 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'e' and resid 306 through 325 Processing helix chain 'e' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP e 364 " --> pdb=" O LYS e 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR e 365 " --> pdb=" O THR e 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN e 372 " --> pdb=" O LYS e 368 " (cutoff:3.500A) Processing helix chain 'e' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA e 407 " --> pdb=" O ALA e 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 53 Processing helix chain 'g' and resid 306 through 325 Processing helix chain 'g' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP g 364 " --> pdb=" O LYS g 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR g 365 " --> pdb=" O THR g 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN g 372 " --> pdb=" O LYS g 368 " (cutoff:3.500A) Processing helix chain 'g' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA g 407 " --> pdb=" O ALA g 403 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 53 Processing helix chain 'h' and resid 38 through 53 663 hydrogen bonds defined for protein. 1989 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: 3.22 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9571 1.34 - 1.46: 6083 1.46 - 1.58: 12498 1.58 - 1.71: 0 1.71 - 1.83: 289 Bond restraints: 28441 Sorted by residual: bond pdb=" CB ARG I 232 " pdb=" CG ARG I 232 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB ARG S 232 " pdb=" CG ARG S 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB ARG g 232 " pdb=" CG ARG g 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB ARG Y 232 " pdb=" CG ARG Y 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB ARG c 232 " pdb=" CG ARG c 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 ... (remaining 28436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 36128 1.72 - 3.43: 1609 3.43 - 5.15: 346 5.15 - 6.87: 133 6.87 - 8.58: 17 Bond angle restraints: 38233 Sorted by residual: angle pdb=" CB ARG T 46 " pdb=" CG ARG T 46 " pdb=" CD ARG T 46 " ideal model delta sigma weight residual 111.30 102.72 8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG J 46 " pdb=" CG ARG J 46 " pdb=" CD ARG J 46 " ideal model delta sigma weight residual 111.30 102.73 8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG F 46 " pdb=" CG ARG F 46 " pdb=" CD ARG F 46 " ideal model delta sigma weight residual 111.30 102.73 8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG h 46 " pdb=" CG ARG h 46 " pdb=" CD ARG h 46 " ideal model delta sigma weight residual 111.30 102.74 8.56 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CB ARG N 46 " pdb=" CG ARG N 46 " pdb=" CD ARG N 46 " ideal model delta sigma weight residual 111.30 102.76 8.54 2.30e+00 1.89e-01 1.38e+01 ... (remaining 38228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 14783 17.67 - 35.34: 1741 35.34 - 53.02: 459 53.02 - 70.69: 153 70.69 - 88.36: 85 Dihedral angle restraints: 17221 sinusoidal: 6749 harmonic: 10472 Sorted by residual: dihedral pdb=" CB CYS B 27 " pdb=" SG CYS B 27 " pdb=" SG CYS F 35 " pdb=" CB CYS F 35 " ideal model delta sinusoidal sigma weight residual -86.00 -144.57 58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS B 35 " pdb=" SG CYS B 35 " pdb=" SG CYS D 27 " pdb=" CB CYS D 27 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS J 27 " pdb=" SG CYS J 27 " pdb=" SG CYS h 35 " pdb=" CB CYS h 35 " ideal model delta sinusoidal sigma weight residual -86.00 -141.02 55.02 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 17218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2300 0.029 - 0.058: 1236 0.058 - 0.087: 423 0.087 - 0.116: 265 0.116 - 0.145: 43 Chirality restraints: 4267 Sorted by residual: chirality pdb=" CA PRO M 240 " pdb=" N PRO M 240 " pdb=" C PRO M 240 " pdb=" CB PRO M 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA PRO E 240 " pdb=" N PRO E 240 " pdb=" C PRO E 240 " pdb=" CB PRO E 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA PRO S 240 " pdb=" N PRO S 240 " pdb=" C PRO S 240 " pdb=" CB PRO S 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 4264 not shown) Planarity restraints: 5015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 199 " 0.011 2.00e-02 2.50e+03 8.52e-03 1.81e+00 pdb=" CG TRP I 199 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP I 199 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP I 199 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP I 199 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 199 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 199 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 199 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP I 199 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 199 " -0.011 2.00e-02 2.50e+03 8.51e-03 1.81e+00 pdb=" CG TRP Q 199 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 199 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 199 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 199 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 199 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 199 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 199 " -0.011 2.00e-02 2.50e+03 8.49e-03 1.80e+00 pdb=" CG TRP K 199 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP K 199 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 199 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 199 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 199 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 199 " -0.001 2.00e-02 2.50e+03 ... (remaining 5012 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 124 2.50 - 3.10: 20789 3.10 - 3.70: 40469 3.70 - 4.30: 55956 4.30 - 4.90: 99825 Nonbonded interactions: 217163 Sorted by model distance: nonbonded pdb=" OG SER B 23 " pdb=" O MET E 303 " model vdw 1.898 3.040 nonbonded pdb=" O CYS D 18 " pdb=" OH TYR E 366 " model vdw 1.968 3.040 nonbonded pdb=" O CYS B 18 " pdb=" OH TYR I 366 " model vdw 2.104 3.040 nonbonded pdb=" OD1 ASN A 241 " pdb=" N LYS E 275 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR C 366 " pdb=" O CYS L 18 " model vdw 2.220 3.040 ... (remaining 217158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.590 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 17.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 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 : 0.008 0.669 28475 Z= 0.402 Angle : 0.935 8.582 38301 Z= 0.519 Chirality : 0.045 0.145 4267 Planarity : 0.004 0.030 5015 Dihedral : 17.962 88.360 10421 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.03 % Allowed : 36.73 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3655 helix: 1.14 (0.17), residues: 1020 sheet: -2.70 (0.16), residues: 901 loop : -3.39 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG c 232 TYR 0.011 0.002 TYR E 373 PHE 0.012 0.001 PHE e 251 TRP 0.022 0.003 TRP K 199 HIS 0.003 0.001 HIS Q 288 Details of bonding type rmsd covalent geometry : bond 0.00622 (28441) covalent geometry : angle 0.92260 (38233) SS BOND : bond 0.16101 ( 34) SS BOND : angle 3.74713 ( 68) hydrogen bonds : bond 0.13368 ( 663) hydrogen bonds : angle 4.50013 ( 1989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 981 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7649 (p0) cc_final: 0.7360 (p0) REVERT: A 303 MET cc_start: 0.8385 (tpt) cc_final: 0.8004 (tpt) REVERT: A 364 ASP cc_start: 0.8682 (m-30) cc_final: 0.8460 (p0) REVERT: B 43 GLN cc_start: 0.7627 (mt0) cc_final: 0.7216 (mt0) REVERT: C 244 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7742 (mt-10) REVERT: C 303 MET cc_start: 0.8386 (tpt) cc_final: 0.7971 (tpt) REVERT: G 292 MET cc_start: 0.8240 (tpt) cc_final: 0.8018 (tpp) REVERT: H 21 VAL cc_start: 0.8157 (m) cc_final: 0.7898 (p) REVERT: I 242 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6474 (m-30) REVERT: I 255 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 303 MET cc_start: 0.8076 (tpt) cc_final: 0.7782 (tpt) REVERT: J 21 VAL cc_start: 0.7692 (m) cc_final: 0.7466 (p) REVERT: J 38 MET cc_start: 0.7455 (mtt) cc_final: 0.7152 (mtt) REVERT: J 40 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7736 (mmtt) REVERT: J 48 LYS cc_start: 0.8408 (tppt) cc_final: 0.8127 (tppt) REVERT: K 207 GLU cc_start: 0.7496 (tt0) cc_final: 0.7191 (tm-30) REVERT: K 298 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7890 (tttp) REVERT: L 21 VAL cc_start: 0.8040 (m) cc_final: 0.7819 (p) REVERT: M 272 ILE cc_start: 0.8179 (tt) cc_final: 0.7934 (tp) REVERT: M 284 LYS cc_start: 0.6787 (mmmt) cc_final: 0.6586 (mmtm) REVERT: N 21 VAL cc_start: 0.7945 (m) cc_final: 0.7707 (p) REVERT: O 226 THR cc_start: 0.6933 (p) cc_final: 0.6660 (p) REVERT: O 272 ILE cc_start: 0.8314 (tt) cc_final: 0.8013 (tp) REVERT: O 284 LYS cc_start: 0.6752 (mmmt) cc_final: 0.6444 (mmtm) REVERT: O 298 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7076 (tttp) REVERT: P 21 VAL cc_start: 0.7697 (m) cc_final: 0.7336 (p) REVERT: Q 237 VAL cc_start: 0.5383 (t) cc_final: 0.4786 (m) REVERT: Q 272 ILE cc_start: 0.8284 (tt) cc_final: 0.8010 (tp) REVERT: Q 298 LYS cc_start: 0.7060 (ptmt) cc_final: 0.6557 (tttp) REVERT: Q 386 THR cc_start: 0.6863 (p) cc_final: 0.6337 (p) REVERT: S 237 VAL cc_start: 0.5713 (t) cc_final: 0.5303 (m) REVERT: S 272 ILE cc_start: 0.7752 (tt) cc_final: 0.7478 (tp) REVERT: S 298 LYS cc_start: 0.6579 (ptmt) cc_final: 0.6039 (tttp) REVERT: U 237 VAL cc_start: 0.5380 (t) cc_final: 0.4867 (m) REVERT: U 319 ASP cc_start: 0.7021 (m-30) cc_final: 0.6687 (m-30) REVERT: U 377 ILE cc_start: 0.8418 (mt) cc_final: 0.8174 (mp) REVERT: V 43 GLN cc_start: 0.6059 (mt0) cc_final: 0.5800 (mt0) REVERT: W 207 GLU cc_start: 0.7041 (tt0) cc_final: 0.6708 (tm-30) REVERT: W 224 LYS cc_start: 0.8172 (mppt) cc_final: 0.7633 (mtmm) REVERT: W 377 ILE cc_start: 0.8218 (mt) cc_final: 0.7971 (mp) REVERT: W 379 ILE cc_start: 0.7817 (mm) cc_final: 0.7549 (mm) REVERT: Y 272 ILE cc_start: 0.6594 (tt) cc_final: 0.6385 (tp) REVERT: a 272 ILE cc_start: 0.6700 (tt) cc_final: 0.6500 (tp) REVERT: c 268 ARG cc_start: 0.7149 (ttm170) cc_final: 0.6745 (ttp80) REVERT: c 279 ASP cc_start: 0.7155 (p0) cc_final: 0.6896 (t0) REVERT: e 255 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6120 (mt-10) REVERT: e 318 LEU cc_start: 0.8061 (tp) cc_final: 0.7851 (tt) REVERT: e 396 GLU cc_start: 0.7033 (pt0) cc_final: 0.6515 (pp20) REVERT: g 284 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8455 (mmtp) REVERT: g 303 MET cc_start: 0.8170 (tpt) cc_final: 0.7781 (tpt) REVERT: h 38 MET cc_start: 0.7267 (mtt) cc_final: 0.7045 (mtt) outliers start: 30 outliers final: 14 residues processed: 1007 average time/residue: 0.2044 time to fit residues: 308.4026 Evaluate side-chains 642 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 627 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 283 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN E 390 GLN F 43 GLN J 52 GLN K 283 GLN K 390 GLN M 283 GLN N 52 GLN U 295 ASN W 307 GLN W 390 GLN ** a 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN c 390 GLN d 43 GLN g 295 ASN h 52 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103575 restraints weight = 47123.657| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.02 r_work: 0.3226 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28475 Z= 0.158 Angle : 0.665 9.953 38301 Z= 0.340 Chirality : 0.044 0.166 4267 Planarity : 0.004 0.035 5015 Dihedral : 6.876 88.434 3985 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 8.62 % Allowed : 28.63 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3655 helix: 2.01 (0.16), residues: 986 sheet: -2.06 (0.16), residues: 1054 loop : -3.04 (0.13), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 402 TYR 0.015 0.002 TYR g 373 PHE 0.022 0.002 PHE W 205 TRP 0.012 0.001 TRP I 257 HIS 0.004 0.001 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.00354 (28441) covalent geometry : angle 0.65989 (38233) SS BOND : bond 0.02012 ( 34) SS BOND : angle 1.98785 ( 68) hydrogen bonds : bond 0.02719 ( 663) hydrogen bonds : angle 3.12620 ( 1989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 689 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8889 (mtmp) cc_final: 0.8650 (mtmt) REVERT: A 303 MET cc_start: 0.8685 (tpt) cc_final: 0.8459 (tpt) REVERT: B 48 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (ttpt) REVERT: C 199 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.8071 (t-100) REVERT: C 236 LYS cc_start: 0.8750 (mtmp) cc_final: 0.8544 (mtmt) REVERT: C 279 ASP cc_start: 0.7182 (p0) cc_final: 0.6806 (p0) REVERT: E 199 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (t-100) REVERT: E 279 ASP cc_start: 0.7669 (p0) cc_final: 0.7455 (p0) REVERT: E 364 ASP cc_start: 0.8302 (p0) cc_final: 0.7614 (t0) REVERT: G 283 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: I 236 LYS cc_start: 0.8535 (mtmp) cc_final: 0.8296 (mtmt) REVERT: J 48 LYS cc_start: 0.8854 (tppt) cc_final: 0.8647 (ttmm) REVERT: K 303 MET cc_start: 0.8618 (tpt) cc_final: 0.8371 (tpt) REVERT: M 399 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7494 (mp0) REVERT: N 18 CYS cc_start: 0.8167 (t) cc_final: 0.7867 (t) REVERT: N 21 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8023 (p) REVERT: O 268 ARG cc_start: 0.8555 (ptm160) cc_final: 0.8323 (ttp80) REVERT: O 270 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7314 (mtp85) REVERT: O 283 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6453 (mp10) REVERT: P 18 CYS cc_start: 0.7782 (t) cc_final: 0.7454 (t) REVERT: P 21 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8083 (p) REVERT: Q 199 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6581 (t60) REVERT: Q 236 LYS cc_start: 0.7998 (mtmp) cc_final: 0.7798 (mtmt) REVERT: Q 268 ARG cc_start: 0.8437 (ptt180) cc_final: 0.8196 (ttp80) REVERT: Q 311 TYR cc_start: 0.7631 (m-10) cc_final: 0.7141 (m-10) REVERT: Q 368 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7803 (ptpp) REVERT: S 199 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.6550 (t60) REVERT: S 284 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7626 (mmtm) REVERT: T 38 MET cc_start: 0.6595 (mtt) cc_final: 0.6232 (mtt) REVERT: T 43 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: W 246 ASP cc_start: 0.8097 (t0) cc_final: 0.7770 (t70) REVERT: W 255 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8307 (mt-10) REVERT: W 268 ARG cc_start: 0.8792 (ptt180) cc_final: 0.8535 (ttp80) REVERT: W 319 ASP cc_start: 0.6976 (m-30) cc_final: 0.6441 (m-30) REVERT: W 368 LYS cc_start: 0.8074 (ptpp) cc_final: 0.7613 (ptpp) REVERT: Y 199 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.6926 (t60) REVERT: Y 201 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8025 (m) REVERT: Y 319 ASP cc_start: 0.6873 (m-30) cc_final: 0.6433 (m-30) REVERT: Z 43 GLN cc_start: 0.7018 (mt0) cc_final: 0.6779 (mt0) REVERT: a 255 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8537 (mt-10) REVERT: b 43 GLN cc_start: 0.7230 (mt0) cc_final: 0.6831 (mt0) REVERT: b 47 ASP cc_start: 0.8584 (m-30) cc_final: 0.8325 (m-30) REVERT: c 311 TYR cc_start: 0.8268 (m-10) cc_final: 0.7995 (m-10) REVERT: c 368 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8156 (ptpp) REVERT: d 36 MET cc_start: 0.7326 (mtp) cc_final: 0.7026 (ptp) REVERT: d 48 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7921 (mttm) REVERT: e 270 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8370 (mtp85) REVERT: e 303 MET cc_start: 0.8349 (tpt) cc_final: 0.8035 (tpt) REVERT: e 318 LEU cc_start: 0.8221 (tp) cc_final: 0.7976 (tt) REVERT: e 387 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (tp) REVERT: f 47 ASP cc_start: 0.8764 (t70) cc_final: 0.8495 (t0) REVERT: g 284 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8576 (mmtp) REVERT: g 303 MET cc_start: 0.8367 (tpt) cc_final: 0.8129 (tpt) outliers start: 252 outliers final: 91 residues processed: 888 average time/residue: 0.2128 time to fit residues: 280.7370 Evaluate side-chains 656 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 550 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 270 ARG Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 397 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 210 VAL Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 309 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 201 SER Chi-restraints excluded: chain Y residue 221 THR Chi-restraints excluded: chain Y residue 309 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 48 LYS Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 335 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 237 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 350 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 295 ASN F 52 GLN G 390 GLN I 283 GLN I 374 HIS K 283 GLN M 283 GLN O 390 GLN Y 288 HIS a 288 HIS c 394 GLN e 283 GLN e 394 GLN g 283 GLN g 295 ASN g 390 GLN g 394 GLN h 52 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090836 restraints weight = 47235.741| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.01 r_work: 0.3031 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28475 Z= 0.207 Angle : 0.655 7.877 38301 Z= 0.335 Chirality : 0.045 0.163 4267 Planarity : 0.004 0.037 5015 Dihedral : 5.879 75.333 3964 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 7.42 % Allowed : 27.70 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3655 helix: 2.22 (0.17), residues: 1020 sheet: -1.97 (0.16), residues: 1054 loop : -3.17 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 402 TYR 0.021 0.002 TYR Y 373 PHE 0.014 0.002 PHE S 251 TRP 0.010 0.001 TRP C 199 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00486 (28441) covalent geometry : angle 0.64884 (38233) SS BOND : bond 0.00731 ( 34) SS BOND : angle 2.19849 ( 68) hydrogen bonds : bond 0.03060 ( 663) hydrogen bonds : angle 2.92636 ( 1989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 610 time to evaluate : 1.103 Fit side-chains REVERT: A 242 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 282 ASP cc_start: 0.8240 (m-30) cc_final: 0.7629 (m-30) REVERT: A 298 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8615 (tttp) REVERT: B 21 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7977 (p) REVERT: B 51 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8689 (tmmt) REVERT: C 199 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7211 (t60) REVERT: C 387 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8731 (tp) REVERT: E 199 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7995 (t60) REVERT: E 298 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8691 (tttp) REVERT: E 387 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8745 (tp) REVERT: K 280 ASP cc_start: 0.8321 (m-30) cc_final: 0.8081 (m-30) REVERT: K 298 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8685 (tttp) REVERT: K 303 MET cc_start: 0.8874 (tpt) cc_final: 0.8393 (tpt) REVERT: K 408 ARG cc_start: 0.6929 (tpm170) cc_final: 0.6552 (mmp-170) REVERT: O 199 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.7375 (t60) REVERT: O 268 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8337 (ttp80) REVERT: O 282 ASP cc_start: 0.7990 (m-30) cc_final: 0.7439 (m-30) REVERT: O 303 MET cc_start: 0.8913 (tpt) cc_final: 0.8705 (tpt) REVERT: Q 199 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7454 (t60) REVERT: Q 236 LYS cc_start: 0.8718 (mtmp) cc_final: 0.8460 (mtmt) REVERT: Q 268 ARG cc_start: 0.8435 (ptt180) cc_final: 0.8208 (ttp80) REVERT: Q 298 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8657 (tttp) REVERT: S 199 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.7693 (t60) REVERT: S 368 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8199 (ptpp) REVERT: T 43 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: T 47 ASP cc_start: 0.8834 (m-30) cc_final: 0.8607 (m-30) REVERT: U 199 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7576 (t60) REVERT: U 282 ASP cc_start: 0.8102 (m-30) cc_final: 0.7891 (m-30) REVERT: U 319 ASP cc_start: 0.7565 (m-30) cc_final: 0.6946 (m-30) REVERT: U 368 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8363 (ptpp) REVERT: W 199 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7720 (t60) REVERT: W 268 ARG cc_start: 0.8575 (ptt180) cc_final: 0.8372 (ttp80) REVERT: W 368 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8206 (ptpp) REVERT: X 43 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: Y 199 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.7860 (t60) REVERT: Y 368 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8401 (ptpp) REVERT: Z 36 MET cc_start: 0.8588 (mtp) cc_final: 0.8125 (ptp) REVERT: a 368 LYS cc_start: 0.8886 (ptpt) cc_final: 0.8486 (ptpp) REVERT: c 298 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8723 (tttp) REVERT: c 368 LYS cc_start: 0.8801 (ptpp) cc_final: 0.8417 (ptpp) REVERT: e 270 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8400 (mtp85) REVERT: f 47 ASP cc_start: 0.8980 (t70) cc_final: 0.8775 (t0) REVERT: g 196 ARG cc_start: 0.8154 (tmm-80) cc_final: 0.7939 (ptt-90) REVERT: g 279 ASP cc_start: 0.8266 (p0) cc_final: 0.8008 (p0) REVERT: g 294 LYS cc_start: 0.8390 (mttt) cc_final: 0.8183 (mttm) REVERT: g 303 MET cc_start: 0.8762 (tpt) cc_final: 0.8406 (tpt) REVERT: h 21 VAL cc_start: 0.8478 (m) cc_final: 0.8247 (p) REVERT: h 51 LYS cc_start: 0.9117 (tppt) cc_final: 0.8567 (tmmt) outliers start: 217 outliers final: 117 residues processed: 768 average time/residue: 0.2131 time to fit residues: 241.4444 Evaluate side-chains 664 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 527 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 280 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 ILE Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 361 THR Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 242 ASP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 361 THR Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 361 THR Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 43 GLN Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 221 THR Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 21 optimal weight: 0.0010 chunk 47 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN F 52 GLN P 52 GLN V 52 GLN W 374 HIS e 374 HIS f 52 GLN h 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093826 restraints weight = 46562.070| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.97 r_work: 0.3073 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28475 Z= 0.113 Angle : 0.537 8.198 38301 Z= 0.272 Chirality : 0.042 0.172 4267 Planarity : 0.003 0.044 5015 Dihedral : 5.556 82.825 3964 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.92 % Allowed : 29.14 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3655 helix: 2.51 (0.17), residues: 1003 sheet: -1.73 (0.17), residues: 1003 loop : -2.93 (0.13), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 46 TYR 0.013 0.001 TYR M 373 PHE 0.010 0.001 PHE W 205 TRP 0.010 0.001 TRP M 199 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00269 (28441) covalent geometry : angle 0.53570 (38233) SS BOND : bond 0.00515 ( 34) SS BOND : angle 1.09562 ( 68) hydrogen bonds : bond 0.01905 ( 663) hydrogen bonds : angle 2.60068 ( 1989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 557 time to evaluate : 1.051 Fit side-chains REVERT: A 298 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8759 (tttp) REVERT: B 51 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8638 (tmmt) REVERT: C 298 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8859 (tttp) REVERT: E 199 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.7947 (t60) REVERT: G 280 ASP cc_start: 0.8312 (m-30) cc_final: 0.8067 (m-30) REVERT: K 298 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8799 (tttp) REVERT: K 303 MET cc_start: 0.8737 (tpt) cc_final: 0.8477 (tpt) REVERT: K 408 ARG cc_start: 0.6947 (tpm170) cc_final: 0.6719 (mmp-170) REVERT: L 46 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7376 (mtm110) REVERT: N 21 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7803 (p) REVERT: O 268 ARG cc_start: 0.8535 (ptm160) cc_final: 0.8297 (ttp80) REVERT: O 282 ASP cc_start: 0.7909 (m-30) cc_final: 0.7183 (m-30) REVERT: O 408 ARG cc_start: 0.6663 (tpm170) cc_final: 0.6299 (tpm170) REVERT: Q 199 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.7443 (t60) REVERT: Q 268 ARG cc_start: 0.8428 (ptt180) cc_final: 0.8101 (ttp80) REVERT: Q 298 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8748 (tttp) REVERT: Q 379 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8422 (mp) REVERT: S 199 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.7623 (t60) REVERT: S 311 TYR cc_start: 0.7891 (m-10) cc_final: 0.7679 (m-10) REVERT: S 368 LYS cc_start: 0.8442 (ptpp) cc_final: 0.8151 (ptpp) REVERT: T 43 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8018 (mm-40) REVERT: U 298 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8420 (tttp) REVERT: U 303 MET cc_start: 0.8988 (tpt) cc_final: 0.8407 (tpt) REVERT: U 311 TYR cc_start: 0.8045 (m-10) cc_final: 0.7777 (m-10) REVERT: U 368 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8325 (ptpp) REVERT: V 43 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: W 199 TRP cc_start: 0.8275 (OUTLIER) cc_final: 0.7671 (t60) REVERT: W 268 ARG cc_start: 0.8713 (ptt180) cc_final: 0.8451 (ttp80) REVERT: W 368 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8203 (ptpp) REVERT: X 43 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: Y 199 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7567 (t60) REVERT: Y 368 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8302 (ptpp) REVERT: Z 36 MET cc_start: 0.8513 (mtp) cc_final: 0.8277 (ptp) REVERT: a 282 ASP cc_start: 0.8407 (m-30) cc_final: 0.8169 (m-30) REVERT: a 368 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8417 (ptpp) REVERT: c 298 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8661 (tttp) REVERT: c 368 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8348 (ptpp) REVERT: c 402 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7901 (ptp90) REVERT: d 36 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8220 (ptp) REVERT: g 196 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7923 (ptt90) REVERT: g 279 ASP cc_start: 0.8182 (p0) cc_final: 0.7831 (p0) REVERT: g 298 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8893 (tttp) REVERT: g 303 MET cc_start: 0.8661 (tpt) cc_final: 0.8301 (tpt) REVERT: g 408 ARG cc_start: 0.7229 (mmp-170) cc_final: 0.6944 (mmm160) REVERT: h 51 LYS cc_start: 0.9105 (tppt) cc_final: 0.8571 (tmmt) outliers start: 173 outliers final: 110 residues processed: 688 average time/residue: 0.2231 time to fit residues: 224.9218 Evaluate side-chains 644 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 515 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 408 ARG Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 387 LEU Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 242 ASP Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 43 GLN Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 221 THR Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 276 LEU Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 318 LEU Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 383 ASN C 383 ASN E 374 HIS E 383 ASN F 52 GLN G 374 HIS G 383 ASN I 383 ASN I 390 GLN S 374 HIS V 52 GLN X 52 GLN Y 283 GLN Y 374 HIS Y 390 GLN a 374 HIS a 383 ASN a 390 GLN c 374 HIS e 383 ASN f 52 GLN g 374 HIS g 383 ASN h 52 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087679 restraints weight = 47072.062| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.64 r_work: 0.2967 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.8403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.066 28475 Z= 0.428 Angle : 0.824 9.811 38301 Z= 0.418 Chirality : 0.051 0.213 4267 Planarity : 0.005 0.056 5015 Dihedral : 6.376 63.617 3964 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 8.65 % Allowed : 28.35 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 3655 helix: 1.97 (0.17), residues: 1020 sheet: -2.28 (0.16), residues: 901 loop : -3.18 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 402 TYR 0.021 0.002 TYR M 373 PHE 0.014 0.002 PHE S 245 TRP 0.015 0.003 TRP Q 199 HIS 0.007 0.002 HIS e 374 Details of bonding type rmsd covalent geometry : bond 0.01007 (28441) covalent geometry : angle 0.81889 (38233) SS BOND : bond 0.00844 ( 34) SS BOND : angle 2.37640 ( 68) hydrogen bonds : bond 0.04378 ( 663) hydrogen bonds : angle 3.18267 ( 1989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 578 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 282 ASP cc_start: 0.8277 (m-30) cc_final: 0.7790 (m-30) REVERT: A 298 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8723 (tttp) REVERT: B 46 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7475 (ttp-170) REVERT: C 199 TRP cc_start: 0.8531 (OUTLIER) cc_final: 0.7607 (t60) REVERT: C 242 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: C 387 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8814 (tp) REVERT: D 18 CYS cc_start: 0.8290 (t) cc_final: 0.7797 (p) REVERT: E 199 TRP cc_start: 0.8678 (OUTLIER) cc_final: 0.7869 (t60) REVERT: E 298 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8897 (tttp) REVERT: E 303 MET cc_start: 0.8921 (tpt) cc_final: 0.8532 (tpt) REVERT: G 199 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.7850 (t60) REVERT: G 242 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: G 282 ASP cc_start: 0.8206 (m-30) cc_final: 0.7586 (m-30) REVERT: I 303 MET cc_start: 0.8859 (tpt) cc_final: 0.8491 (tpt) REVERT: J 51 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8739 (tmmt) REVERT: K 199 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.7404 (t60) REVERT: K 303 MET cc_start: 0.8852 (tpt) cc_final: 0.8192 (tpt) REVERT: K 408 ARG cc_start: 0.7005 (tpm170) cc_final: 0.6786 (mmp-170) REVERT: M 199 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7494 (t60) REVERT: O 199 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.7802 (t60) REVERT: O 408 ARG cc_start: 0.6818 (tpm170) cc_final: 0.6435 (tpm170) REVERT: P 33 ASP cc_start: 0.7849 (t0) cc_final: 0.7570 (t0) REVERT: Q 199 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.7624 (t60) REVERT: Q 268 ARG cc_start: 0.8564 (ptt180) cc_final: 0.8305 (ttp80) REVERT: Q 280 ASP cc_start: 0.8133 (m-30) cc_final: 0.7930 (m-30) REVERT: Q 298 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8704 (tttp) REVERT: Q 379 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8538 (mp) REVERT: S 199 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.7645 (t60) REVERT: S 303 MET cc_start: 0.8838 (tpt) cc_final: 0.8308 (tpt) REVERT: T 33 ASP cc_start: 0.7503 (t0) cc_final: 0.7112 (t0) REVERT: U 199 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7632 (t60) REVERT: U 239 MET cc_start: 0.7494 (mmt) cc_final: 0.7221 (mmm) REVERT: U 282 ASP cc_start: 0.8183 (m-30) cc_final: 0.7623 (m-30) REVERT: U 298 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8538 (tttp) REVERT: V 43 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: V 47 ASP cc_start: 0.8734 (m-30) cc_final: 0.8489 (t0) REVERT: V 51 LYS cc_start: 0.9136 (mptt) cc_final: 0.8841 (mptt) REVERT: W 199 TRP cc_start: 0.8579 (OUTLIER) cc_final: 0.7933 (t60) REVERT: Y 199 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7699 (t60) REVERT: Y 282 ASP cc_start: 0.8340 (m-30) cc_final: 0.8096 (m-30) REVERT: Z 51 LYS cc_start: 0.8999 (mptt) cc_final: 0.8709 (tmmt) REVERT: a 283 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: b 51 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (tmmt) REVERT: c 233 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8796 (mp) REVERT: c 283 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: c 298 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8803 (tttp) REVERT: d 51 LYS cc_start: 0.9225 (tppt) cc_final: 0.8684 (tmmt) REVERT: e 303 MET cc_start: 0.8706 (tpt) cc_final: 0.8436 (tpt) REVERT: f 51 LYS cc_start: 0.9176 (tppt) cc_final: 0.8846 (tmmt) REVERT: g 196 ARG cc_start: 0.8255 (tmm-80) cc_final: 0.7924 (ptt90) REVERT: g 279 ASP cc_start: 0.8149 (p0) cc_final: 0.7856 (p0) REVERT: g 298 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9003 (tttp) REVERT: h 51 LYS cc_start: 0.9199 (tppt) cc_final: 0.8843 (tmmt) outliers start: 253 outliers final: 148 residues processed: 762 average time/residue: 0.2199 time to fit residues: 247.3176 Evaluate side-chains 723 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 548 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 199 TRP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 297 ILE Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain a residue 383 ASN Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 233 LEU Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain g residue 383 ASN Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 297 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 246 optimal weight: 0.2980 chunk 330 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS D 52 GLN E 383 ASN F 52 GLN I 383 ASN M 374 HIS O 374 HIS P 52 GLN Q 390 GLN S 390 GLN U 374 HIS U 390 GLN V 52 GLN b 52 GLN f 52 GLN h 52 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094863 restraints weight = 46319.110| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.65 r_work: 0.3088 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28475 Z= 0.119 Angle : 0.576 7.785 38301 Z= 0.291 Chirality : 0.042 0.158 4267 Planarity : 0.003 0.053 5015 Dihedral : 5.600 73.186 3964 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.09 % Allowed : 31.16 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3655 helix: 2.48 (0.16), residues: 1020 sheet: -1.97 (0.17), residues: 901 loop : -2.97 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 46 TYR 0.012 0.001 TYR e 373 PHE 0.009 0.001 PHE E 317 TRP 0.012 0.001 TRP S 199 HIS 0.007 0.002 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00284 (28441) covalent geometry : angle 0.57394 (38233) SS BOND : bond 0.00506 ( 34) SS BOND : angle 1.35856 ( 68) hydrogen bonds : bond 0.01969 ( 663) hydrogen bonds : angle 2.55500 ( 1989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 586 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8851 (tttp) REVERT: B 33 ASP cc_start: 0.7532 (t0) cc_final: 0.7321 (t0) REVERT: B 51 LYS cc_start: 0.8559 (tmmt) cc_final: 0.8345 (tmmt) REVERT: C 199 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7671 (t60) REVERT: C 298 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8906 (tttp) REVERT: E 199 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.7986 (t60) REVERT: E 298 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9032 (tttp) REVERT: G 199 TRP cc_start: 0.8340 (OUTLIER) cc_final: 0.7643 (t60) REVERT: G 303 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8293 (tpp) REVERT: K 298 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8853 (tttp) REVERT: K 303 MET cc_start: 0.8684 (tpt) cc_final: 0.8400 (tpt) REVERT: O 408 ARG cc_start: 0.6794 (tpm170) cc_final: 0.6486 (tpm170) REVERT: P 46 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7303 (mtm110) REVERT: Q 268 ARG cc_start: 0.8486 (ptt180) cc_final: 0.8203 (ttp80) REVERT: Q 298 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8787 (tttp) REVERT: Q 379 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8508 (mp) REVERT: R 33 ASP cc_start: 0.7668 (t0) cc_final: 0.7408 (t0) REVERT: S 268 ARG cc_start: 0.8538 (ptt180) cc_final: 0.8311 (ttp80) REVERT: S 282 ASP cc_start: 0.8004 (m-30) cc_final: 0.7637 (m-30) REVERT: U 199 TRP cc_start: 0.8353 (OUTLIER) cc_final: 0.7503 (t60) REVERT: U 298 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8616 (tttp) REVERT: W 199 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.7987 (t60) REVERT: W 408 ARG cc_start: 0.6457 (mmm160) cc_final: 0.6225 (mmm160) REVERT: X 43 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8203 (mp10) REVERT: Z 42 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: a 298 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9084 (tttp) REVERT: b 48 LYS cc_start: 0.8787 (tppt) cc_final: 0.8494 (ttmt) REVERT: c 283 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: c 298 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8860 (tttp) REVERT: d 51 LYS cc_start: 0.9132 (tppt) cc_final: 0.8645 (tmmt) REVERT: e 196 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7844 (ptt90) REVERT: e 303 MET cc_start: 0.8599 (tpt) cc_final: 0.8319 (tpt) REVERT: f 51 LYS cc_start: 0.9024 (tppt) cc_final: 0.8725 (tmmt) REVERT: g 196 ARG cc_start: 0.8206 (tmm-80) cc_final: 0.7864 (ptt90) REVERT: g 279 ASP cc_start: 0.8037 (p0) cc_final: 0.7733 (p0) REVERT: g 298 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8911 (tttp) REVERT: g 303 MET cc_start: 0.8695 (tpt) cc_final: 0.8436 (tpt) REVERT: g 408 ARG cc_start: 0.7326 (mmp-170) cc_final: 0.7095 (mmm160) REVERT: h 51 LYS cc_start: 0.9089 (tppt) cc_final: 0.8799 (tmmt) outliers start: 178 outliers final: 118 residues processed: 708 average time/residue: 0.2211 time to fit residues: 228.5326 Evaluate side-chains 673 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 536 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 27 CYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 276 LEU Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 280 ASP Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain g residue 388 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 104 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 340 optimal weight: 0.0000 chunk 48 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN K 374 HIS V 52 GLN g 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090883 restraints weight = 46437.425| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.63 r_work: 0.3020 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.8620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 28475 Z= 0.235 Angle : 0.670 8.621 38301 Z= 0.335 Chirality : 0.045 0.194 4267 Planarity : 0.004 0.055 5015 Dihedral : 5.790 72.720 3964 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 7.11 % Allowed : 30.20 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3655 helix: 2.41 (0.16), residues: 1020 sheet: -2.01 (0.17), residues: 901 loop : -3.01 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 46 TYR 0.017 0.002 TYR M 373 PHE 0.009 0.001 PHE A 251 TRP 0.013 0.002 TRP Q 199 HIS 0.006 0.002 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00560 (28441) covalent geometry : angle 0.66428 (38233) SS BOND : bond 0.00526 ( 34) SS BOND : angle 2.12023 ( 68) hydrogen bonds : bond 0.02834 ( 663) hydrogen bonds : angle 2.66346 ( 1989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 566 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.8268 (m-30) cc_final: 0.7730 (m-30) REVERT: A 298 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8862 (tttp) REVERT: C 199 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.7521 (t60) REVERT: E 199 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.7929 (t60) REVERT: E 298 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8977 (tttp) REVERT: E 303 MET cc_start: 0.8891 (tpt) cc_final: 0.8495 (tpt) REVERT: G 199 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.7695 (t60) REVERT: K 298 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8765 (tttp) REVERT: K 303 MET cc_start: 0.8833 (tpt) cc_final: 0.8300 (tpt) REVERT: M 199 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7603 (t60) REVERT: O 270 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8333 (mtp85) REVERT: O 408 ARG cc_start: 0.6802 (tpm170) cc_final: 0.6529 (tpm170) REVERT: Q 268 ARG cc_start: 0.8500 (ptt180) cc_final: 0.8220 (ttp80) REVERT: Q 298 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8788 (tttp) REVERT: Q 379 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8543 (mp) REVERT: U 199 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7601 (t60) REVERT: U 239 MET cc_start: 0.7468 (mmt) cc_final: 0.6787 (mmm) REVERT: U 298 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8643 (tttp) REVERT: U 303 MET cc_start: 0.9001 (tpt) cc_final: 0.8740 (tpt) REVERT: U 360 LYS cc_start: 0.4874 (mmtm) cc_final: 0.4666 (mmtm) REVERT: W 199 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7922 (t60) REVERT: X 51 LYS cc_start: 0.8954 (mptt) cc_final: 0.8655 (tmmt) REVERT: Z 32 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8632 (p) REVERT: Z 42 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: a 298 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9091 (tttp) REVERT: b 48 LYS cc_start: 0.8770 (tppt) cc_final: 0.8501 (ttmt) REVERT: c 283 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: c 298 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: d 51 LYS cc_start: 0.9222 (tppt) cc_final: 0.8791 (tmmt) REVERT: e 196 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7811 (ptt90) REVERT: e 292 MET cc_start: 0.8588 (mtp) cc_final: 0.8376 (mtp) REVERT: e 303 MET cc_start: 0.8700 (tpt) cc_final: 0.8378 (tpt) REVERT: f 51 LYS cc_start: 0.9175 (tppt) cc_final: 0.8851 (tmmt) REVERT: g 196 ARG cc_start: 0.8262 (tmm-80) cc_final: 0.7900 (ptt90) REVERT: g 279 ASP cc_start: 0.8039 (p0) cc_final: 0.7675 (p0) REVERT: g 298 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8909 (tttp) REVERT: h 51 LYS cc_start: 0.9093 (tppt) cc_final: 0.8892 (tmmt) outliers start: 208 outliers final: 150 residues processed: 709 average time/residue: 0.2241 time to fit residues: 232.1169 Evaluate side-chains 711 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 542 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 27 CYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 27 CYS Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 27 CYS Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 297 ILE Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain a residue 302 VAL Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 196 ARG Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain e residue 388 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain g residue 388 VAL Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 174 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN V 52 GLN g 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089873 restraints weight = 46973.892| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.92 r_work: 0.3004 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.8713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28475 Z= 0.147 Angle : 0.601 7.868 38301 Z= 0.301 Chirality : 0.043 0.172 4267 Planarity : 0.004 0.055 5015 Dihedral : 5.568 78.299 3964 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.43 % Allowed : 30.92 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3655 helix: 2.64 (0.16), residues: 1020 sheet: -2.24 (0.15), residues: 1071 loop : -2.78 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 46 TYR 0.013 0.001 TYR K 373 PHE 0.009 0.001 PHE O 291 TRP 0.011 0.001 TRP Q 199 HIS 0.006 0.002 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00353 (28441) covalent geometry : angle 0.59740 (38233) SS BOND : bond 0.00388 ( 34) SS BOND : angle 1.68728 ( 68) hydrogen bonds : bond 0.02147 ( 663) hydrogen bonds : angle 2.47232 ( 1989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 542 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8790 (tttp) REVERT: C 199 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7417 (t60) REVERT: C 298 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8859 (tttp) REVERT: E 199 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7775 (t60) REVERT: E 298 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8986 (tttp) REVERT: G 199 TRP cc_start: 0.8343 (OUTLIER) cc_final: 0.7484 (t60) REVERT: G 298 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8973 (tttp) REVERT: K 298 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8734 (tttp) REVERT: K 303 MET cc_start: 0.8766 (tpt) cc_final: 0.8412 (tpt) REVERT: M 280 ASP cc_start: 0.8110 (m-30) cc_final: 0.7799 (m-30) REVERT: O 270 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8333 (mtp85) REVERT: O 280 ASP cc_start: 0.8400 (m-30) cc_final: 0.7871 (m-30) REVERT: O 282 ASP cc_start: 0.7820 (m-30) cc_final: 0.7351 (m-30) REVERT: O 408 ARG cc_start: 0.6839 (tpm170) cc_final: 0.6592 (tpm170) REVERT: Q 199 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7787 (t60) REVERT: Q 255 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8281 (mt-10) REVERT: Q 268 ARG cc_start: 0.8478 (ptt180) cc_final: 0.8098 (ttp80) REVERT: Q 298 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8809 (tttp) REVERT: Q 379 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8478 (mp) REVERT: S 268 ARG cc_start: 0.8479 (ptt180) cc_final: 0.8234 (ttp80) REVERT: U 199 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7491 (t60) REVERT: U 282 ASP cc_start: 0.8231 (m-30) cc_final: 0.7324 (m-30) REVERT: U 298 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8527 (tttp) REVERT: U 303 MET cc_start: 0.9039 (tpt) cc_final: 0.8667 (tpt) REVERT: W 199 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.7685 (t60) REVERT: X 51 LYS cc_start: 0.8922 (mptt) cc_final: 0.8548 (tmmt) REVERT: Z 42 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8429 (m-40) REVERT: a 298 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9071 (tttp) REVERT: c 283 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: c 298 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8874 (tttp) REVERT: d 51 LYS cc_start: 0.9228 (tppt) cc_final: 0.8779 (tmmt) REVERT: e 196 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7983 (ptt90) REVERT: e 303 MET cc_start: 0.8679 (tpt) cc_final: 0.8427 (tpt) REVERT: f 51 LYS cc_start: 0.9109 (tppt) cc_final: 0.8792 (tmmt) REVERT: g 196 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7974 (ptt90) REVERT: g 279 ASP cc_start: 0.8128 (p0) cc_final: 0.7694 (p0) REVERT: g 298 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8895 (tttp) REVERT: g 408 ARG cc_start: 0.7381 (mmp-170) cc_final: 0.7180 (mmm160) REVERT: h 51 LYS cc_start: 0.9068 (tppt) cc_final: 0.8808 (tmmt) outliers start: 188 outliers final: 151 residues processed: 680 average time/residue: 0.2263 time to fit residues: 224.1551 Evaluate side-chains 694 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 523 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 27 CYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 387 LEU Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 27 CYS Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 276 LEU Chi-restraints excluded: chain W residue 280 ASP Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 196 ARG Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 298 LYS Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain e residue 388 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain g residue 388 VAL Chi-restraints excluded: chain h residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 383 ASN K 383 ASN P 52 GLN S 383 ASN U 383 ASN V 52 GLN W 383 ASN Y 383 ASN a 383 ASN b 52 GLN c 383 ASN g 295 ASN g 383 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086200 restraints weight = 47350.546| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.91 r_work: 0.2938 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 28475 Z= 0.300 Angle : 0.733 9.267 38301 Z= 0.366 Chirality : 0.047 0.208 4267 Planarity : 0.004 0.067 5015 Dihedral : 5.996 69.767 3964 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 7.46 % Allowed : 30.92 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.14), residues: 3655 helix: 2.38 (0.16), residues: 1020 sheet: -2.46 (0.15), residues: 1071 loop : -2.87 (0.13), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 46 TYR 0.019 0.002 TYR M 373 PHE 0.012 0.002 PHE e 251 TRP 0.012 0.002 TRP Q 199 HIS 0.006 0.002 HIS a 374 Details of bonding type rmsd covalent geometry : bond 0.00715 (28441) covalent geometry : angle 0.72822 (38233) SS BOND : bond 0.00598 ( 34) SS BOND : angle 2.02618 ( 68) hydrogen bonds : bond 0.03309 ( 663) hydrogen bonds : angle 2.71271 ( 1989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 560 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8812 (tttp) REVERT: C 199 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.7438 (t60) REVERT: D 18 CYS cc_start: 0.8184 (t) cc_final: 0.7756 (p) REVERT: E 199 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.7771 (t60) REVERT: E 298 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8960 (tttp) REVERT: E 303 MET cc_start: 0.8955 (tpt) cc_final: 0.8524 (tpt) REVERT: F 51 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8675 (tmmt) REVERT: G 199 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7795 (t60) REVERT: I 282 ASP cc_start: 0.8277 (m-30) cc_final: 0.7824 (m-30) REVERT: J 51 LYS cc_start: 0.9050 (tppt) cc_final: 0.8741 (tmmt) REVERT: K 298 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8638 (tttp) REVERT: K 303 MET cc_start: 0.8853 (tpt) cc_final: 0.8222 (tpt) REVERT: M 199 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7421 (t60) REVERT: M 280 ASP cc_start: 0.8190 (m-30) cc_final: 0.7981 (m-30) REVERT: O 408 ARG cc_start: 0.6675 (tpm170) cc_final: 0.6416 (tpm170) REVERT: P 51 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8609 (tmmt) REVERT: Q 268 ARG cc_start: 0.8523 (ptt180) cc_final: 0.8222 (ttp80) REVERT: Q 298 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: Q 379 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8503 (mp) REVERT: S 199 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7658 (t60) REVERT: U 199 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7528 (t60) REVERT: U 239 MET cc_start: 0.7592 (mmt) cc_final: 0.7001 (mmm) REVERT: U 280 ASP cc_start: 0.8630 (p0) cc_final: 0.8414 (p0) REVERT: U 282 ASP cc_start: 0.8197 (m-30) cc_final: 0.7531 (m-30) REVERT: U 298 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8593 (tttp) REVERT: U 303 MET cc_start: 0.9047 (tpt) cc_final: 0.8729 (tpt) REVERT: V 51 LYS cc_start: 0.9004 (mptt) cc_final: 0.8701 (tmmt) REVERT: W 199 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.7703 (t60) REVERT: W 360 LYS cc_start: 0.4946 (mmtm) cc_final: 0.4643 (mmtt) REVERT: X 51 LYS cc_start: 0.9001 (mptt) cc_final: 0.8674 (tmmt) REVERT: Z 42 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8568 (m-40) REVERT: c 283 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: c 292 MET cc_start: 0.8691 (ttm) cc_final: 0.8304 (ttt) REVERT: c 298 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8798 (tttp) REVERT: d 51 LYS cc_start: 0.9250 (tppt) cc_final: 0.8852 (tmmt) REVERT: e 196 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7913 (ptt90) REVERT: e 303 MET cc_start: 0.8728 (tpt) cc_final: 0.8472 (tpt) REVERT: f 51 LYS cc_start: 0.9168 (tppt) cc_final: 0.8890 (tmmt) REVERT: g 196 ARG cc_start: 0.8416 (tmm-80) cc_final: 0.8074 (ptt90) REVERT: g 279 ASP cc_start: 0.8147 (p0) cc_final: 0.7738 (p0) REVERT: g 298 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8887 (tttp) REVERT: g 408 ARG cc_start: 0.7401 (mmp-170) cc_final: 0.7189 (mmm160) REVERT: h 51 LYS cc_start: 0.9122 (tppt) cc_final: 0.8873 (tmmt) outliers start: 218 outliers final: 173 residues processed: 717 average time/residue: 0.2254 time to fit residues: 235.8488 Evaluate side-chains 726 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 534 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 318 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 27 CYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 202 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 27 CYS Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 318 LEU Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 280 ASP Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 383 ASN Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 297 ILE Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 368 LYS Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain a residue 383 ASN Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 196 ARG Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 298 LYS Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain e residue 388 VAL Chi-restraints excluded: chain f residue 36 MET Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain g residue 388 VAL Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 351 optimal weight: 0.9990 chunk 224 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 281 optimal weight: 0.0000 chunk 312 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN P 52 GLN S 283 GLN S 383 ASN V 52 GLN b 52 GLN e 390 GLN g 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091989 restraints weight = 46493.402| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.92 r_work: 0.3035 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28475 Z= 0.115 Angle : 0.603 8.147 38301 Z= 0.302 Chirality : 0.042 0.175 4267 Planarity : 0.004 0.058 5015 Dihedral : 5.531 80.220 3964 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.34 % Allowed : 33.07 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3655 helix: 2.78 (0.16), residues: 1020 sheet: -1.85 (0.17), residues: 901 loop : -2.83 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG V 46 TYR 0.010 0.001 TYR S 373 PHE 0.008 0.001 PHE E 317 TRP 0.013 0.001 TRP Q 199 HIS 0.007 0.002 HIS W 374 Details of bonding type rmsd covalent geometry : bond 0.00275 (28441) covalent geometry : angle 0.60042 (38233) SS BOND : bond 0.00308 ( 34) SS BOND : angle 1.38438 ( 68) hydrogen bonds : bond 0.01876 ( 663) hydrogen bonds : angle 2.46200 ( 1989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 560 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.8416 (m-30) cc_final: 0.7823 (m-30) REVERT: A 298 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8728 (tttp) REVERT: B 51 LYS cc_start: 0.8767 (tmmt) cc_final: 0.8515 (tmmt) REVERT: C 199 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7321 (t60) REVERT: C 298 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8802 (tttp) REVERT: D 21 VAL cc_start: 0.8349 (m) cc_final: 0.8056 (p) REVERT: E 199 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7782 (t60) REVERT: E 298 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8899 (tttp) REVERT: E 408 ARG cc_start: 0.7267 (mmp-170) cc_final: 0.7019 (mmp-170) REVERT: G 199 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7470 (t60) REVERT: G 298 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8954 (tttp) REVERT: K 298 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8781 (tttp) REVERT: K 303 MET cc_start: 0.8685 (tpt) cc_final: 0.8415 (tpt) REVERT: M 282 ASP cc_start: 0.8225 (m-30) cc_final: 0.7342 (m-30) REVERT: M 360 LYS cc_start: 0.5036 (mmtm) cc_final: 0.4814 (mmtt) REVERT: O 199 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7716 (t60) REVERT: O 280 ASP cc_start: 0.8362 (m-30) cc_final: 0.7977 (m-30) REVERT: O 408 ARG cc_start: 0.6820 (tpm170) cc_final: 0.6580 (tpm170) REVERT: P 46 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7391 (mtm110) REVERT: Q 199 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.8002 (t-100) REVERT: Q 255 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8264 (mt-10) REVERT: Q 268 ARG cc_start: 0.8475 (ptt180) cc_final: 0.8081 (ttp80) REVERT: Q 298 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8731 (tttp) REVERT: Q 379 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8466 (mp) REVERT: S 268 ARG cc_start: 0.8433 (ptt180) cc_final: 0.8185 (ttp80) REVERT: U 239 MET cc_start: 0.7420 (mmt) cc_final: 0.6758 (mmm) REVERT: U 298 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8499 (tttp) REVERT: U 303 MET cc_start: 0.8974 (tpt) cc_final: 0.8506 (tpt) REVERT: W 199 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7662 (t60) REVERT: W 360 LYS cc_start: 0.5039 (mmtm) cc_final: 0.4426 (mmtt) REVERT: X 21 VAL cc_start: 0.8474 (m) cc_final: 0.8176 (p) REVERT: X 51 LYS cc_start: 0.8902 (mptt) cc_final: 0.8545 (tmmt) REVERT: Y 360 LYS cc_start: 0.5265 (mmtm) cc_final: 0.4866 (mmtt) REVERT: Z 36 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8378 (ptp) REVERT: Z 42 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: a 298 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9026 (tttp) REVERT: c 292 MET cc_start: 0.8551 (ttm) cc_final: 0.8133 (ttt) REVERT: c 298 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8882 (tttp) REVERT: d 51 LYS cc_start: 0.9191 (tppt) cc_final: 0.8821 (tmmt) REVERT: e 196 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7973 (ptt90) REVERT: e 303 MET cc_start: 0.8684 (tpt) cc_final: 0.8465 (tpt) REVERT: f 51 LYS cc_start: 0.9094 (tppt) cc_final: 0.8786 (tmmt) REVERT: g 196 ARG cc_start: 0.8295 (tmm-80) cc_final: 0.8010 (ptt90) REVERT: g 255 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8469 (mt-10) REVERT: g 279 ASP cc_start: 0.8098 (p0) cc_final: 0.7707 (p0) REVERT: g 298 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8862 (tttp) REVERT: g 303 MET cc_start: 0.8779 (tpt) cc_final: 0.8531 (tpt) REVERT: g 408 ARG cc_start: 0.7367 (mmp-170) cc_final: 0.7149 (mmm160) REVERT: h 51 LYS cc_start: 0.9063 (tppt) cc_final: 0.8811 (tmmt) outliers start: 156 outliers final: 119 residues processed: 672 average time/residue: 0.2299 time to fit residues: 224.7300 Evaluate side-chains 676 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 537 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 GLN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 42 ASN Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 196 ARG Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 387 LEU Chi-restraints excluded: chain e residue 388 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 298 LYS Chi-restraints excluded: chain h residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 136 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 256 optimal weight: 0.0570 chunk 329 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 334 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 GLN S 383 ASN V 52 GLN Y 383 ASN b 52 GLN g 295 ASN g 383 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092157 restraints weight = 46520.612| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.71 r_work: 0.3054 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28475 Z= 0.139 Angle : 0.600 8.661 38301 Z= 0.300 Chirality : 0.043 0.216 4267 Planarity : 0.004 0.064 5015 Dihedral : 5.398 80.213 3962 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.23 % Allowed : 32.97 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3655 helix: 2.83 (0.16), residues: 1020 sheet: -2.10 (0.15), residues: 1071 loop : -2.64 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG V 46 TYR 0.013 0.001 TYR K 373 PHE 0.008 0.001 PHE c 205 TRP 0.012 0.001 TRP O 199 HIS 0.006 0.002 HIS W 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (28441) covalent geometry : angle 0.59829 (38233) SS BOND : bond 0.00369 ( 34) SS BOND : angle 1.13186 ( 68) hydrogen bonds : bond 0.02076 ( 663) hydrogen bonds : angle 2.37530 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6831.80 seconds wall clock time: 117 minutes 26.12 seconds (7046.12 seconds total)