Starting phenix.real_space_refine on Thu Mar 5 10:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.map" model { file = "/net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mks_9137/03_2026/6mks_9137.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.000 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 217 5.16 5 C 14508 2.51 5 N 3906 2.21 5 O 4123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22754 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e Time building chain proxies: 1.65, per 1000 atoms: 0.07 Number of scatterers: 22754 At special positions: 0 Unit cell: (91.08, 91.08, 192.72, 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 217 16.00 O 4123 8.00 N 3906 7.00 C 14508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 980.6 milliseconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 4.292A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 Processing helix chain 'E' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 Processing helix chain 'F' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 61 Processing helix chain 'G' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 61 Processing helix chain 'H' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 15 Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 61 Processing helix chain 'I' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 15 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 61 Processing helix chain 'J' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 15 Processing helix chain 'K' and resid 16 through 30 Processing helix chain 'K' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 61 Processing helix chain 'K' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 15 Processing helix chain 'L' and resid 16 through 30 Processing helix chain 'L' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 61 Processing helix chain 'L' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 15 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU M 44 " --> pdb=" O ILE M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 61 Processing helix chain 'M' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER M 65 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 15 Processing helix chain 'N' and resid 16 through 30 Processing helix chain 'N' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 61 Processing helix chain 'N' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER N 65 " --> pdb=" O LYS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 15 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU O 44 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER O 65 " --> pdb=" O LYS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 15 Processing helix chain 'P' and resid 16 through 30 Processing helix chain 'P' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU P 44 " --> pdb=" O ILE P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 61 Processing helix chain 'P' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER P 65 " --> pdb=" O LYS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 7 through 15 Processing helix chain 'Q' and resid 16 through 30 Processing helix chain 'Q' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 Processing helix chain 'Q' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 85 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 7 through 15 Processing helix chain 'R' and resid 16 through 30 Processing helix chain 'R' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 61 Processing helix chain 'R' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 7 through 15 Processing helix chain 'S' and resid 16 through 30 Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU S 44 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 61 Processing helix chain 'S' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER S 65 " --> pdb=" O LYS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 85 Processing helix chain 'T' and resid 2 through 7 Processing helix chain 'T' and resid 7 through 15 Processing helix chain 'T' and resid 16 through 30 Processing helix chain 'T' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 61 Processing helix chain 'T' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER T 65 " --> pdb=" O LYS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 85 Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 7 through 15 Processing helix chain 'U' and resid 16 through 30 Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU U 44 " --> pdb=" O ILE U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 61 Processing helix chain 'U' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER U 65 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 85 Processing helix chain 'V' and resid 2 through 7 Processing helix chain 'V' and resid 7 through 15 Processing helix chain 'V' and resid 16 through 30 Processing helix chain 'V' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU V 44 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 61 Processing helix chain 'V' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER V 65 " --> pdb=" O LYS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 85 Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 7 through 15 Processing helix chain 'W' and resid 16 through 30 Processing helix chain 'W' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU W 44 " --> pdb=" O ILE W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 61 Processing helix chain 'W' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 85 Processing helix chain 'X' and resid 2 through 7 Processing helix chain 'X' and resid 7 through 15 Processing helix chain 'X' and resid 16 through 30 Processing helix chain 'X' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 61 Processing helix chain 'X' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER X 65 " --> pdb=" O LYS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 85 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 7 through 15 Processing helix chain 'Y' and resid 16 through 30 Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Y 44 " --> pdb=" O ILE Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 Processing helix chain 'Y' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER Y 65 " --> pdb=" O LYS Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 85 Processing helix chain 'Z' and resid 2 through 7 Processing helix chain 'Z' and resid 7 through 15 Processing helix chain 'Z' and resid 16 through 30 Processing helix chain 'Z' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Z 44 " --> pdb=" O ILE Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 61 Processing helix chain 'Z' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 77 through 85 Processing helix chain 'a' and resid 2 through 7 Processing helix chain 'a' and resid 7 through 15 Processing helix chain 'a' and resid 16 through 30 Processing helix chain 'a' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU a 44 " --> pdb=" O ILE a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 61 Processing helix chain 'a' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER a 65 " --> pdb=" O LYS a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 85 Processing helix chain 'b' and resid 2 through 7 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 16 through 30 Processing helix chain 'b' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU b 44 " --> pdb=" O ILE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 61 Processing helix chain 'b' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER b 65 " --> pdb=" O LYS b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 85 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 7 through 15 Processing helix chain 'c' and resid 16 through 30 Processing helix chain 'c' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU c 44 " --> pdb=" O ILE c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 61 Processing helix chain 'c' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER c 65 " --> pdb=" O LYS c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 7 through 15 Processing helix chain 'd' and resid 16 through 30 Processing helix chain 'd' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU d 44 " --> pdb=" O ILE d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 61 Processing helix chain 'd' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER d 65 " --> pdb=" O LYS d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 Processing helix chain 'e' and resid 2 through 7 Processing helix chain 'e' and resid 7 through 15 Processing helix chain 'e' and resid 16 through 30 Processing helix chain 'e' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU e 44 " --> pdb=" O ILE e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 61 Processing helix chain 'e' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 85 1643 hydrogen bonds defined for protein. 4929 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: 3.81 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6507 1.33 - 1.45: 3463 1.45 - 1.57: 12784 1.57 - 1.69: 0 1.69 - 1.81: 341 Bond restraints: 23095 Sorted by residual: bond pdb=" CB VAL O 32 " pdb=" CG1 VAL O 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB VAL C 32 " pdb=" CG1 VAL C 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL P 32 " pdb=" CG1 VAL P 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL S 32 " pdb=" CG1 VAL S 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.40e+00 bond pdb=" CB VAL N 32 " pdb=" CG1 VAL N 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.38e+00 ... (remaining 23090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 26522 1.27 - 2.54: 3577 2.54 - 3.80: 590 3.80 - 5.07: 280 5.07 - 6.34: 31 Bond angle restraints: 31000 Sorted by residual: angle pdb=" N GLY a 62 " pdb=" CA GLY a 62 " pdb=" C GLY a 62 " ideal model delta sigma weight residual 112.17 116.26 -4.09 1.40e+00 5.10e-01 8.51e+00 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 112.17 116.24 -4.07 1.40e+00 5.10e-01 8.44e+00 angle pdb=" N GLY d 62 " pdb=" CA GLY d 62 " pdb=" C GLY d 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.42e+00 angle pdb=" N GLY Q 62 " pdb=" CA GLY Q 62 " pdb=" C GLY Q 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.40e+00 angle pdb=" N GLY D 62 " pdb=" CA GLY D 62 " pdb=" C GLY D 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 30995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 13500 14.40 - 28.81: 433 28.81 - 43.21: 141 43.21 - 57.62: 0 57.62 - 72.02: 31 Dihedral angle restraints: 14105 sinusoidal: 5983 harmonic: 8122 Sorted by residual: dihedral pdb=" C GLU V 64 " pdb=" N GLU V 64 " pdb=" CA GLU V 64 " pdb=" CB GLU V 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Y 64 " pdb=" N GLU Y 64 " pdb=" CA GLU Y 64 " pdb=" CB GLU Y 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Z 64 " pdb=" N GLU Z 64 " pdb=" CA GLU Z 64 " pdb=" CB GLU Z 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 14102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2690 0.071 - 0.142: 689 0.142 - 0.212: 58 0.212 - 0.283: 4 0.283 - 0.354: 31 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA GLU Y 64 " pdb=" N GLU Y 64 " pdb=" C GLU Y 64 " pdb=" CB GLU Y 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA GLU V 64 " pdb=" N GLU V 64 " pdb=" C GLU V 64 " pdb=" CB GLU V 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA GLU O 64 " pdb=" N GLU O 64 " pdb=" C GLU O 64 " pdb=" CB GLU O 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 3469 not shown) Planarity restraints: 3937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 53 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" C GLY Q 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY Q 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE Q 54 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 53 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C GLY b 53 " 0.020 2.00e-02 2.50e+03 pdb=" O GLY b 53 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE b 54 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 53 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C GLY J 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY J 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 54 " 0.007 2.00e-02 2.50e+03 ... (remaining 3934 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 7884 2.87 - 3.38: 26030 3.38 - 3.89: 40131 3.89 - 4.39: 46241 4.39 - 4.90: 77147 Nonbonded interactions: 197433 Sorted by model distance: nonbonded pdb=" OD2 ASP d 26 " pdb=" NE1 TRP d 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP P 26 " pdb=" NE1 TRP P 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP W 26 " pdb=" NE1 TRP W 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP X 26 " pdb=" NE1 TRP X 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP T 26 " pdb=" NE1 TRP T 76 " model vdw 2.367 3.120 ... (remaining 197428 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 0.050 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.180 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.012 0.084 23095 Z= 0.505 Angle : 1.000 6.341 31000 Z= 0.560 Chirality : 0.067 0.354 3472 Planarity : 0.004 0.012 3937 Dihedral : 9.700 72.020 8773 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -1.30 (0.15), residues: 2728 helix: -0.59 (0.09), residues: 2449 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 52 TYR 0.006 0.002 TYR e 78 PHE 0.009 0.003 PHE N 3 TRP 0.006 0.002 TRP I 30 HIS 0.002 0.001 HIS O 56 Details of bonding type rmsd covalent geometry : bond 0.01190 (23095) covalent geometry : angle 1.00001 (31000) hydrogen bonds : bond 0.11542 ( 1643) hydrogen bonds : angle 5.43910 ( 4929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1755 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.7270 (t160) cc_final: 0.6769 (t0) REVERT: A 66 CYS cc_start: 0.8627 (m) cc_final: 0.8314 (m) REVERT: A 76 TRP cc_start: 0.8492 (m100) cc_final: 0.7983 (m100) REVERT: B 6 ASP cc_start: 0.8289 (m-30) cc_final: 0.8056 (m-30) REVERT: B 17 MET cc_start: 0.8124 (tpp) cc_final: 0.7759 (tpt) REVERT: B 19 VAL cc_start: 0.9206 (t) cc_final: 0.8980 (t) REVERT: B 33 LEU cc_start: 0.9004 (mt) cc_final: 0.8677 (mt) REVERT: B 34 ASN cc_start: 0.7590 (t160) cc_final: 0.6870 (t0) REVERT: B 39 ASN cc_start: 0.7888 (m-40) cc_final: 0.7624 (m-40) REVERT: B 66 CYS cc_start: 0.8602 (m) cc_final: 0.8358 (m) REVERT: B 83 ASP cc_start: 0.8552 (t70) cc_final: 0.8308 (t0) REVERT: C 3 PHE cc_start: 0.8737 (t80) cc_final: 0.8497 (t80) REVERT: C 19 VAL cc_start: 0.9339 (t) cc_final: 0.9129 (t) REVERT: C 39 ASN cc_start: 0.7774 (m-40) cc_final: 0.7524 (m110) REVERT: C 60 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8141 (mtpp) REVERT: C 83 ASP cc_start: 0.8575 (t70) cc_final: 0.8358 (t70) REVERT: D 13 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8739 (mm-40) REVERT: D 35 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6856 (tpp80) REVERT: D 39 ASN cc_start: 0.7737 (m-40) cc_final: 0.7304 (m110) REVERT: D 43 CYS cc_start: 0.7877 (p) cc_final: 0.7052 (p) REVERT: D 66 CYS cc_start: 0.8461 (m) cc_final: 0.8244 (m) REVERT: D 74 LYS cc_start: 0.8662 (tttt) cc_final: 0.8423 (ttpp) REVERT: D 76 TRP cc_start: 0.8347 (m100) cc_final: 0.8024 (m100) REVERT: D 87 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7790 (mm110) REVERT: E 13 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8890 (mm110) REVERT: E 17 MET cc_start: 0.8091 (tpp) cc_final: 0.7828 (tpt) REVERT: E 40 ILE cc_start: 0.8708 (mt) cc_final: 0.8494 (pt) REVERT: E 82 GLN cc_start: 0.8825 (mm110) cc_final: 0.8616 (mm110) REVERT: F 19 VAL cc_start: 0.9248 (t) cc_final: 0.8870 (t) REVERT: F 34 ASN cc_start: 0.7392 (t160) cc_final: 0.7134 (t160) REVERT: F 40 ILE cc_start: 0.8870 (mt) cc_final: 0.8648 (pt) REVERT: F 66 CYS cc_start: 0.8736 (m) cc_final: 0.8387 (m) REVERT: F 82 GLN cc_start: 0.8569 (mm110) cc_final: 0.8302 (mm-40) REVERT: G 18 THR cc_start: 0.8815 (p) cc_final: 0.8582 (p) REVERT: G 33 LEU cc_start: 0.9030 (mt) cc_final: 0.8800 (mt) REVERT: G 34 ASN cc_start: 0.7192 (t160) cc_final: 0.6210 (t0) REVERT: G 35 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6668 (tpp80) REVERT: G 39 ASN cc_start: 0.7809 (m-40) cc_final: 0.7554 (m110) REVERT: G 48 GLN cc_start: 0.8393 (mp10) cc_final: 0.7722 (mp10) REVERT: G 83 ASP cc_start: 0.8527 (t70) cc_final: 0.8304 (t0) REVERT: H 3 PHE cc_start: 0.8631 (t80) cc_final: 0.8374 (t80) REVERT: H 17 MET cc_start: 0.8015 (tpp) cc_final: 0.7803 (tpt) REVERT: H 31 ASN cc_start: 0.9165 (m-40) cc_final: 0.8915 (m-40) REVERT: H 76 TRP cc_start: 0.8425 (m100) cc_final: 0.7875 (m100) REVERT: H 87 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7864 (mm110) REVERT: I 13 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8766 (mm-40) REVERT: I 17 MET cc_start: 0.8192 (tpp) cc_final: 0.7978 (tpt) REVERT: I 34 ASN cc_start: 0.7683 (t160) cc_final: 0.7133 (t160) REVERT: I 76 TRP cc_start: 0.8322 (m100) cc_final: 0.7582 (m100) REVERT: J 5 LYS cc_start: 0.8554 (tttm) cc_final: 0.8335 (tttt) REVERT: J 8 SER cc_start: 0.8929 (p) cc_final: 0.8692 (p) REVERT: J 12 ILE cc_start: 0.9483 (mt) cc_final: 0.9206 (mp) REVERT: J 17 MET cc_start: 0.8444 (tpp) cc_final: 0.8167 (tpp) REVERT: J 19 VAL cc_start: 0.9363 (t) cc_final: 0.9127 (t) REVERT: J 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6818 (tpp80) REVERT: J 39 ASN cc_start: 0.8096 (m-40) cc_final: 0.7743 (m110) REVERT: J 48 GLN cc_start: 0.8529 (mp10) cc_final: 0.8322 (mp10) REVERT: J 76 TRP cc_start: 0.8486 (m100) cc_final: 0.8046 (m100) REVERT: K 3 PHE cc_start: 0.8709 (t80) cc_final: 0.8401 (t80) REVERT: K 13 GLN cc_start: 0.9090 (mm-40) cc_final: 0.7755 (mm-40) REVERT: K 21 LYS cc_start: 0.8668 (mttt) cc_final: 0.8443 (mttp) REVERT: K 25 ASP cc_start: 0.8104 (m-30) cc_final: 0.7196 (m-30) REVERT: K 39 ASN cc_start: 0.8117 (m-40) cc_final: 0.7839 (m110) REVERT: K 60 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7920 (mtpt) REVERT: K 66 CYS cc_start: 0.8538 (m) cc_final: 0.8211 (m) REVERT: K 83 ASP cc_start: 0.8615 (t70) cc_final: 0.8101 (t0) REVERT: K 87 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7075 (mm110) REVERT: L 6 ASP cc_start: 0.8340 (m-30) cc_final: 0.8088 (m-30) REVERT: L 35 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6884 (ttm-80) REVERT: L 66 CYS cc_start: 0.8336 (m) cc_final: 0.7962 (m) REVERT: L 87 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7643 (mm110) REVERT: M 13 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8081 (mm-40) REVERT: M 39 ASN cc_start: 0.8025 (m-40) cc_final: 0.7425 (m110) REVERT: M 77 ASN cc_start: 0.9238 (t0) cc_final: 0.9027 (t0) REVERT: N 39 ASN cc_start: 0.7782 (m-40) cc_final: 0.7525 (m110) REVERT: O 34 ASN cc_start: 0.7612 (t160) cc_final: 0.6630 (t0) REVERT: O 35 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6870 (ttp-110) REVERT: O 39 ASN cc_start: 0.7849 (m-40) cc_final: 0.7513 (m110) REVERT: O 48 GLN cc_start: 0.8435 (mp10) cc_final: 0.7977 (mp10) REVERT: O 61 LYS cc_start: 0.8895 (mttm) cc_final: 0.8650 (mttm) REVERT: P 12 ILE cc_start: 0.9366 (mt) cc_final: 0.9079 (mm) REVERT: P 13 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8033 (mm110) REVERT: P 66 CYS cc_start: 0.8584 (m) cc_final: 0.8187 (m) REVERT: P 67 ASN cc_start: 0.8777 (m-40) cc_final: 0.8434 (m-40) REVERT: Q 76 TRP cc_start: 0.8258 (m100) cc_final: 0.7476 (m100) REVERT: Q 82 GLN cc_start: 0.8454 (mm110) cc_final: 0.8211 (mm-40) REVERT: R 5 LYS cc_start: 0.8713 (tttm) cc_final: 0.8497 (tttt) REVERT: R 8 SER cc_start: 0.9050 (p) cc_final: 0.8809 (p) REVERT: R 13 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8740 (mm110) REVERT: R 32 VAL cc_start: 0.9186 (m) cc_final: 0.8942 (p) REVERT: R 35 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6745 (tpp80) REVERT: R 39 ASN cc_start: 0.7893 (m-40) cc_final: 0.7079 (m110) REVERT: R 61 LYS cc_start: 0.9090 (mttm) cc_final: 0.8438 (mttm) REVERT: R 70 LEU cc_start: 0.9300 (mt) cc_final: 0.9031 (mt) REVERT: R 77 ASN cc_start: 0.9263 (t0) cc_final: 0.8702 (t0) REVERT: S 3 PHE cc_start: 0.8259 (t80) cc_final: 0.7798 (t80) REVERT: S 19 VAL cc_start: 0.9229 (t) cc_final: 0.8945 (t) REVERT: S 39 ASN cc_start: 0.7746 (m-40) cc_final: 0.7484 (m110) REVERT: S 48 GLN cc_start: 0.8310 (mp10) cc_final: 0.8076 (mp10) REVERT: S 60 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8290 (mtpt) REVERT: S 66 CYS cc_start: 0.8570 (m) cc_final: 0.8059 (m) REVERT: S 82 GLN cc_start: 0.8617 (mm110) cc_final: 0.8389 (mm-40) REVERT: T 13 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8889 (mm110) REVERT: T 17 MET cc_start: 0.8062 (tpp) cc_final: 0.7829 (tpp) REVERT: T 34 ASN cc_start: 0.7743 (t160) cc_final: 0.7079 (t0) REVERT: T 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6693 (ttm-80) REVERT: T 39 ASN cc_start: 0.7794 (m-40) cc_final: 0.7361 (m110) REVERT: T 82 GLN cc_start: 0.8502 (mm110) cc_final: 0.8167 (mm-40) REVERT: T 83 ASP cc_start: 0.8645 (t70) cc_final: 0.8274 (t70) REVERT: U 25 ASP cc_start: 0.8325 (m-30) cc_final: 0.7897 (m-30) REVERT: U 39 ASN cc_start: 0.7550 (m-40) cc_final: 0.7334 (m110) REVERT: U 49 ASP cc_start: 0.8515 (m-30) cc_final: 0.8292 (m-30) REVERT: V 35 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6841 (ttm110) REVERT: V 39 ASN cc_start: 0.7947 (m-40) cc_final: 0.7610 (m-40) REVERT: V 66 CYS cc_start: 0.8665 (m) cc_final: 0.8364 (m) REVERT: V 87 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7436 (mm110) REVERT: W 4 ILE cc_start: 0.8915 (mt) cc_final: 0.8507 (mt) REVERT: W 6 ASP cc_start: 0.8376 (m-30) cc_final: 0.8116 (m-30) REVERT: W 12 ILE cc_start: 0.9419 (mt) cc_final: 0.9206 (mt) REVERT: W 13 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8442 (mm-40) REVERT: W 17 MET cc_start: 0.7951 (tpp) cc_final: 0.7620 (tpt) REVERT: W 33 LEU cc_start: 0.9068 (mt) cc_final: 0.8826 (mt) REVERT: W 34 ASN cc_start: 0.7543 (t160) cc_final: 0.6694 (t0) REVERT: W 66 CYS cc_start: 0.8650 (m) cc_final: 0.8429 (t) REVERT: W 76 TRP cc_start: 0.8384 (m100) cc_final: 0.8069 (m100) REVERT: X 3 PHE cc_start: 0.8879 (t80) cc_final: 0.8651 (t80) REVERT: X 25 ASP cc_start: 0.8313 (m-30) cc_final: 0.7970 (m-30) REVERT: X 48 GLN cc_start: 0.8459 (mp10) cc_final: 0.8152 (mp10) REVERT: X 66 CYS cc_start: 0.8844 (m) cc_final: 0.8279 (m) REVERT: X 82 GLN cc_start: 0.8532 (mm110) cc_final: 0.8301 (mm110) REVERT: X 87 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7474 (mm-40) REVERT: Y 5 LYS cc_start: 0.8416 (tttm) cc_final: 0.8206 (tttt) REVERT: Y 13 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8814 (mm110) REVERT: Y 17 MET cc_start: 0.8083 (tpp) cc_final: 0.7821 (tpt) REVERT: Y 19 VAL cc_start: 0.9410 (t) cc_final: 0.9116 (t) REVERT: Y 25 ASP cc_start: 0.8163 (m-30) cc_final: 0.7756 (m-30) REVERT: Y 35 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7123 (ttp-110) REVERT: Y 39 ASN cc_start: 0.7715 (m-40) cc_final: 0.7341 (m-40) REVERT: Y 55 ILE cc_start: 0.9135 (mt) cc_final: 0.8827 (tt) REVERT: Y 60 LYS cc_start: 0.8991 (mtmt) cc_final: 0.7713 (tptt) REVERT: Y 61 LYS cc_start: 0.8678 (mttm) cc_final: 0.8296 (mttt) REVERT: Y 66 CYS cc_start: 0.8484 (m) cc_final: 0.8012 (m) REVERT: Z 8 SER cc_start: 0.8825 (p) cc_final: 0.8571 (p) REVERT: Z 12 ILE cc_start: 0.9465 (mt) cc_final: 0.9090 (mp) REVERT: Z 17 MET cc_start: 0.7915 (tpp) cc_final: 0.7486 (tpt) REVERT: Z 34 ASN cc_start: 0.7797 (t160) cc_final: 0.7034 (t0) REVERT: Z 36 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6801 (mt-10) REVERT: Z 48 GLN cc_start: 0.8487 (mp10) cc_final: 0.8176 (mp10) REVERT: Z 66 CYS cc_start: 0.8490 (m) cc_final: 0.8132 (m) REVERT: Z 77 ASN cc_start: 0.8985 (t0) cc_final: 0.8456 (t0) REVERT: a 3 PHE cc_start: 0.8669 (t80) cc_final: 0.8395 (t80) REVERT: a 5 LYS cc_start: 0.8766 (tttm) cc_final: 0.8362 (tptt) REVERT: a 8 SER cc_start: 0.9250 (p) cc_final: 0.8907 (p) REVERT: a 9 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7476 (mmt-90) REVERT: a 12 ILE cc_start: 0.9346 (mt) cc_final: 0.9007 (mp) REVERT: a 27 LEU cc_start: 0.8787 (mt) cc_final: 0.8488 (mt) REVERT: a 31 ASN cc_start: 0.9112 (m-40) cc_final: 0.8893 (m-40) REVERT: a 34 ASN cc_start: 0.7737 (t160) cc_final: 0.7164 (t0) REVERT: a 35 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7131 (ttm-80) REVERT: a 39 ASN cc_start: 0.8156 (m-40) cc_final: 0.7908 (m110) REVERT: a 83 ASP cc_start: 0.8535 (t70) cc_final: 0.8327 (t0) REVERT: a 87 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7305 (mm-40) REVERT: b 23 ILE cc_start: 0.8821 (mt) cc_final: 0.8616 (mt) REVERT: b 36 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6747 (mt-10) REVERT: b 39 ASN cc_start: 0.7840 (m-40) cc_final: 0.7516 (m110) REVERT: b 49 ASP cc_start: 0.8403 (m-30) cc_final: 0.8175 (m-30) REVERT: b 66 CYS cc_start: 0.8568 (m) cc_final: 0.8353 (m) REVERT: c 17 MET cc_start: 0.8383 (tpp) cc_final: 0.8157 (tpt) REVERT: c 19 VAL cc_start: 0.9349 (t) cc_final: 0.8978 (t) REVERT: c 39 ASN cc_start: 0.7626 (m-40) cc_final: 0.6903 (m110) REVERT: c 87 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7077 (mm110) REVERT: d 3 PHE cc_start: 0.8733 (t80) cc_final: 0.8528 (t80) REVERT: d 13 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8505 (mm110) REVERT: d 33 LEU cc_start: 0.9052 (mt) cc_final: 0.8729 (mt) REVERT: d 40 ILE cc_start: 0.8699 (mt) cc_final: 0.8442 (pt) REVERT: d 66 CYS cc_start: 0.8666 (m) cc_final: 0.8423 (m) REVERT: d 82 GLN cc_start: 0.8888 (mm110) cc_final: 0.8672 (mm-40) REVERT: d 83 ASP cc_start: 0.8460 (t70) cc_final: 0.8236 (t0) REVERT: e 13 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8708 (mm-40) REVERT: e 34 ASN cc_start: 0.7798 (t160) cc_final: 0.7394 (t0) REVERT: e 35 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6650 (tpp80) REVERT: e 39 ASN cc_start: 0.7689 (m-40) cc_final: 0.6489 (m110) REVERT: e 70 LEU cc_start: 0.8976 (mt) cc_final: 0.8718 (mt) REVERT: e 74 LYS cc_start: 0.8709 (tttt) cc_final: 0.8456 (ttpp) REVERT: e 87 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8409 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1755 average time/residue: 0.1649 time to fit residues: 438.7714 Evaluate side-chains 1495 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1495 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 82 GLN B 13 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 67 ASN B 82 GLN C 31 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 56 HIS E 34 ASN E 39 ASN E 56 HIS E 67 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 34 ASN G 39 ASN G 67 ASN G 82 GLN H 13 GLN H 67 ASN H 82 GLN I 13 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 HIS I 82 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN J 56 HIS J 67 ASN J 82 GLN K 31 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 56 HIS L 13 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 56 HIS L 67 ASN L 82 GLN M 22 GLN M 39 ASN M 56 HIS ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 ASN N 56 HIS N 67 ASN O 13 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN O 56 HIS O 67 ASN O 82 GLN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS P 82 GLN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN R 39 ASN R 56 HIS R 82 GLN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 HIS ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 ASN T 56 HIS ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 56 HIS U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 82 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 HIS V 82 GLN W 34 ASN W 67 ASN W 82 GLN X 67 ASN Y 13 GLN Y 39 ASN Y 67 ASN Y 82 GLN ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 HIS Z 67 ASN Z 82 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN ** a 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 ASN c 39 ASN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 HIS d 67 ASN e 34 ASN e 67 ASN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.086256 restraints weight = 37789.448| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.41 r_work: 0.2901 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23095 Z= 0.167 Angle : 0.574 5.896 31000 Z= 0.315 Chirality : 0.042 0.223 3472 Planarity : 0.004 0.055 3937 Dihedral : 3.999 14.994 2914 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 5.09 % Allowed : 13.76 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.03 (0.15), residues: 2728 helix: 1.00 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 35 TYR 0.012 0.002 TYR N 78 PHE 0.021 0.002 PHE I 28 TRP 0.018 0.003 TRP Q 76 HIS 0.009 0.001 HIS W 56 Details of bonding type rmsd covalent geometry : bond 0.00395 (23095) covalent geometry : angle 0.57420 (31000) hydrogen bonds : bond 0.03846 ( 1643) hydrogen bonds : angle 4.21857 ( 4929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1854 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1723 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7248 (tpp) cc_final: 0.6918 (tpp) REVERT: A 9 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8185 (ttp-110) REVERT: A 22 GLN cc_start: 0.8570 (mt0) cc_final: 0.8303 (mt0) REVERT: A 26 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (m-30) REVERT: A 34 ASN cc_start: 0.7832 (t160) cc_final: 0.6359 (t0) REVERT: A 36 GLU cc_start: 0.7531 (mp0) cc_final: 0.7314 (mp0) REVERT: A 43 CYS cc_start: 0.8122 (p) cc_final: 0.7859 (m) REVERT: A 47 GLU cc_start: 0.7577 (tt0) cc_final: 0.7229 (tt0) REVERT: A 66 CYS cc_start: 0.9088 (m) cc_final: 0.8681 (m) REVERT: A 74 LYS cc_start: 0.9290 (mtpp) cc_final: 0.8893 (ttpp) REVERT: B 34 ASN cc_start: 0.8112 (t160) cc_final: 0.7853 (m-40) REVERT: B 37 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 39 ASN cc_start: 0.8942 (m110) cc_final: 0.8602 (m-40) REVERT: B 52 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7984 (mtt-85) REVERT: B 60 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8773 (mtmm) REVERT: B 66 CYS cc_start: 0.8887 (m) cc_final: 0.8601 (m) REVERT: B 83 ASP cc_start: 0.8687 (t70) cc_final: 0.8464 (t0) REVERT: C 2 ASN cc_start: 0.7875 (m-40) cc_final: 0.7214 (m-40) REVERT: C 12 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9138 (mp) REVERT: C 34 ASN cc_start: 0.8206 (t0) cc_final: 0.7508 (t0) REVERT: C 35 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7698 (ttm110) REVERT: C 48 GLN cc_start: 0.8569 (mp10) cc_final: 0.8340 (mp10) REVERT: C 60 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8687 (mtpp) REVERT: C 78 TYR cc_start: 0.9124 (t80) cc_final: 0.8915 (t80) REVERT: C 83 ASP cc_start: 0.8810 (t70) cc_final: 0.8547 (t0) REVERT: D 13 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8878 (mm-40) REVERT: D 35 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7629 (tpp80) REVERT: D 39 ASN cc_start: 0.8352 (m110) cc_final: 0.7821 (m-40) REVERT: D 60 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8535 (mtpp) REVERT: D 74 LYS cc_start: 0.9023 (tttt) cc_final: 0.8765 (ttpp) REVERT: D 77 ASN cc_start: 0.9220 (t0) cc_final: 0.8947 (t0) REVERT: D 87 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8201 (mm110) REVERT: E 1 MET cc_start: 0.7244 (tpp) cc_final: 0.6907 (tpt) REVERT: E 17 MET cc_start: 0.8362 (tpp) cc_final: 0.8148 (tpp) REVERT: E 34 ASN cc_start: 0.8498 (t0) cc_final: 0.7481 (p0) REVERT: E 37 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7196 (mt-10) REVERT: E 60 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8659 (mtpp) REVERT: E 78 TYR cc_start: 0.9031 (t80) cc_final: 0.8822 (t80) REVERT: E 82 GLN cc_start: 0.8798 (mm110) cc_final: 0.8433 (mm110) REVERT: F 2 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7900 (m-40) REVERT: F 6 ASP cc_start: 0.8462 (m-30) cc_final: 0.8095 (p0) REVERT: F 74 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8822 (ttmm) REVERT: F 82 GLN cc_start: 0.8756 (mm110) cc_final: 0.8453 (mm110) REVERT: F 87 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7774 (mm110) REVERT: G 35 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7699 (ttp-110) REVERT: G 39 ASN cc_start: 0.8481 (m110) cc_final: 0.8131 (m110) REVERT: G 67 ASN cc_start: 0.8955 (m-40) cc_final: 0.8714 (m110) REVERT: G 76 TRP cc_start: 0.8913 (m100) cc_final: 0.7971 (m100) REVERT: G 77 ASN cc_start: 0.9147 (t0) cc_final: 0.8798 (t0) REVERT: G 83 ASP cc_start: 0.8613 (t70) cc_final: 0.8359 (t0) REVERT: H 2 ASN cc_start: 0.7489 (m-40) cc_final: 0.7057 (m110) REVERT: H 6 ASP cc_start: 0.8433 (m-30) cc_final: 0.8142 (m-30) REVERT: H 7 ASN cc_start: 0.8978 (m-40) cc_final: 0.8586 (m110) REVERT: H 31 ASN cc_start: 0.9181 (m-40) cc_final: 0.8946 (m-40) REVERT: H 34 ASN cc_start: 0.7741 (t0) cc_final: 0.6849 (t0) REVERT: H 60 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8351 (mtpt) REVERT: H 83 ASP cc_start: 0.8673 (t0) cc_final: 0.8462 (t0) REVERT: I 7 ASN cc_start: 0.9045 (m-40) cc_final: 0.8809 (m110) REVERT: I 31 ASN cc_start: 0.8899 (m-40) cc_final: 0.8696 (m-40) REVERT: I 37 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8096 (mt-10) REVERT: I 57 MET cc_start: 0.8581 (mtp) cc_final: 0.8221 (mtt) REVERT: J 34 ASN cc_start: 0.8273 (t0) cc_final: 0.7679 (t0) REVERT: J 35 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7750 (ttp-170) REVERT: J 39 ASN cc_start: 0.8480 (m110) cc_final: 0.7918 (m110) REVERT: J 40 ILE cc_start: 0.9161 (tt) cc_final: 0.8929 (tt) REVERT: J 43 CYS cc_start: 0.8046 (p) cc_final: 0.7747 (p) REVERT: J 60 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8594 (mttt) REVERT: J 71 LYS cc_start: 0.9235 (ttmt) cc_final: 0.9025 (ttmm) REVERT: J 77 ASN cc_start: 0.9225 (t0) cc_final: 0.8860 (t0) REVERT: K 21 LYS cc_start: 0.9207 (mttt) cc_final: 0.8860 (mttp) REVERT: K 25 ASP cc_start: 0.8222 (m-30) cc_final: 0.7755 (m-30) REVERT: K 34 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.6870 (t0) REVERT: K 60 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8401 (mtpp) REVERT: K 66 CYS cc_start: 0.8940 (m) cc_final: 0.8694 (m) REVERT: K 78 TYR cc_start: 0.9194 (t80) cc_final: 0.8911 (t80) REVERT: K 83 ASP cc_start: 0.8822 (t70) cc_final: 0.8407 (t0) REVERT: L 6 ASP cc_start: 0.8643 (m-30) cc_final: 0.8403 (m-30) REVERT: L 21 LYS cc_start: 0.9432 (mttp) cc_final: 0.9155 (mttm) REVERT: L 35 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7621 (tpp80) REVERT: L 77 ASN cc_start: 0.9330 (t0) cc_final: 0.9118 (t0) REVERT: M 1 MET cc_start: 0.6623 (tpp) cc_final: 0.6384 (tpp) REVERT: M 39 ASN cc_start: 0.8668 (m110) cc_final: 0.8180 (m-40) REVERT: M 48 GLN cc_start: 0.8789 (mp10) cc_final: 0.8586 (mp10) REVERT: N 20 ILE cc_start: 0.9333 (mt) cc_final: 0.9109 (mp) REVERT: N 34 ASN cc_start: 0.8392 (t0) cc_final: 0.7451 (t0) REVERT: N 39 ASN cc_start: 0.8506 (m110) cc_final: 0.8275 (m110) REVERT: N 60 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8428 (mtpt) REVERT: N 66 CYS cc_start: 0.9030 (m) cc_final: 0.8649 (m) REVERT: N 89 LEU cc_start: 0.6950 (tp) cc_final: 0.6747 (tp) REVERT: O 35 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7124 (tpp80) REVERT: O 39 ASN cc_start: 0.8566 (m110) cc_final: 0.7898 (m110) REVERT: O 44 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7829 (mm-30) REVERT: P 25 ASP cc_start: 0.8249 (m-30) cc_final: 0.8021 (m-30) REVERT: P 34 ASN cc_start: 0.7943 (t160) cc_final: 0.7609 (t0) REVERT: P 60 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8790 (mtpt) REVERT: P 66 CYS cc_start: 0.9095 (m) cc_final: 0.8654 (m) REVERT: P 67 ASN cc_start: 0.9066 (m-40) cc_final: 0.8706 (m-40) REVERT: Q 7 ASN cc_start: 0.8725 (m-40) cc_final: 0.8188 (m110) REVERT: Q 34 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7553 (t0) REVERT: Q 66 CYS cc_start: 0.8933 (m) cc_final: 0.8382 (m) REVERT: Q 89 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6928 (tt) REVERT: R 1 MET cc_start: 0.7267 (tpp) cc_final: 0.6997 (tpp) REVERT: R 21 LYS cc_start: 0.9396 (mttt) cc_final: 0.8815 (mttt) REVERT: R 35 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7607 (tpp80) REVERT: R 36 GLU cc_start: 0.7433 (mp0) cc_final: 0.7127 (mp0) REVERT: R 39 ASN cc_start: 0.8505 (m110) cc_final: 0.8159 (m-40) REVERT: R 60 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8593 (mttt) REVERT: R 66 CYS cc_start: 0.8804 (m) cc_final: 0.8449 (m) REVERT: S 2 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: S 34 ASN cc_start: 0.8180 (t0) cc_final: 0.7490 (t0) REVERT: S 35 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7780 (tpp80) REVERT: S 39 ASN cc_start: 0.8613 (m-40) cc_final: 0.7982 (m110) REVERT: S 56 HIS cc_start: 0.8247 (m90) cc_final: 0.7705 (m-70) REVERT: S 60 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8787 (mtpt) REVERT: S 66 CYS cc_start: 0.9089 (m) cc_final: 0.8751 (m) REVERT: T 35 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7529 (ttp-110) REVERT: T 39 ASN cc_start: 0.8434 (m110) cc_final: 0.7795 (m110) REVERT: T 77 ASN cc_start: 0.9258 (t0) cc_final: 0.9034 (t0) REVERT: T 83 ASP cc_start: 0.8886 (t70) cc_final: 0.8614 (t70) REVERT: U 2 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: U 34 ASN cc_start: 0.8241 (t0) cc_final: 0.7799 (t0) REVERT: U 35 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7183 (ttm-80) REVERT: U 39 ASN cc_start: 0.8459 (m110) cc_final: 0.7844 (m110) REVERT: U 47 GLU cc_start: 0.7858 (tt0) cc_final: 0.7215 (tt0) REVERT: U 49 ASP cc_start: 0.8656 (m-30) cc_final: 0.8388 (m-30) REVERT: U 60 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8633 (mtpp) REVERT: V 35 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7760 (ttm170) REVERT: V 39 ASN cc_start: 0.8585 (m-40) cc_final: 0.8316 (m110) REVERT: V 66 CYS cc_start: 0.9019 (m) cc_final: 0.8681 (m) REVERT: V 78 TYR cc_start: 0.9064 (t80) cc_final: 0.8857 (t80) REVERT: W 6 ASP cc_start: 0.8547 (m-30) cc_final: 0.8291 (m-30) REVERT: W 35 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7541 (ttp-110) REVERT: W 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.7824 (m110) REVERT: W 60 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8580 (mtmm) REVERT: W 66 CYS cc_start: 0.8999 (m) cc_final: 0.8775 (t) REVERT: X 21 LYS cc_start: 0.9273 (mttp) cc_final: 0.8613 (mttp) REVERT: X 25 ASP cc_start: 0.8349 (m-30) cc_final: 0.8028 (m-30) REVERT: X 35 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7541 (tpp80) REVERT: X 39 ASN cc_start: 0.8618 (m110) cc_final: 0.8255 (m-40) REVERT: X 60 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8698 (mtpt) REVERT: X 66 CYS cc_start: 0.9132 (m) cc_final: 0.8501 (m) REVERT: X 82 GLN cc_start: 0.8742 (mm110) cc_final: 0.8426 (mm110) REVERT: X 87 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7600 (mm-40) REVERT: Y 21 LYS cc_start: 0.9237 (mttp) cc_final: 0.8957 (mttm) REVERT: Y 25 ASP cc_start: 0.8577 (m-30) cc_final: 0.7904 (m-30) REVERT: Y 31 ASN cc_start: 0.9045 (m-40) cc_final: 0.8842 (m-40) REVERT: Y 60 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8034 (tptt) REVERT: Y 66 CYS cc_start: 0.8899 (m) cc_final: 0.8515 (m) REVERT: Z 2 ASN cc_start: 0.8182 (m-40) cc_final: 0.7756 (m110) REVERT: Z 6 ASP cc_start: 0.8382 (m-30) cc_final: 0.8142 (m-30) REVERT: Z 9 ARG cc_start: 0.8349 (mtp85) cc_final: 0.8052 (mtp85) REVERT: Z 13 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8238 (mm-40) REVERT: Z 44 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7800 (mm-30) REVERT: Z 60 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8519 (mtpt) REVERT: Z 61 LYS cc_start: 0.8864 (mttp) cc_final: 0.8655 (mttm) REVERT: Z 66 CYS cc_start: 0.8774 (m) cc_final: 0.8562 (m) REVERT: Z 77 ASN cc_start: 0.9041 (t0) cc_final: 0.8335 (t0) REVERT: a 2 ASN cc_start: 0.8129 (m-40) cc_final: 0.7761 (m110) REVERT: a 3 PHE cc_start: 0.8918 (t80) cc_final: 0.8718 (t80) REVERT: a 5 LYS cc_start: 0.8836 (tttm) cc_final: 0.8077 (tptt) REVERT: a 6 ASP cc_start: 0.8700 (m-30) cc_final: 0.8497 (m-30) REVERT: a 8 SER cc_start: 0.9237 (p) cc_final: 0.8955 (m) REVERT: a 9 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7658 (mmt-90) REVERT: a 35 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7431 (ttm110) REVERT: a 45 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7758 (tttp) REVERT: a 60 LYS cc_start: 0.9057 (mtmt) cc_final: 0.7903 (tptm) REVERT: a 74 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8984 (ttmm) REVERT: b 39 ASN cc_start: 0.8231 (m110) cc_final: 0.7834 (m110) REVERT: b 57 MET cc_start: 0.8701 (mtp) cc_final: 0.8462 (mtp) REVERT: b 58 ILE cc_start: 0.9208 (tp) cc_final: 0.8954 (tp) REVERT: b 66 CYS cc_start: 0.8796 (m) cc_final: 0.8580 (m) REVERT: b 74 LYS cc_start: 0.9254 (ttpt) cc_final: 0.9053 (ttmm) REVERT: b 77 ASN cc_start: 0.9168 (t0) cc_final: 0.8860 (t0) REVERT: c 20 ILE cc_start: 0.9292 (mt) cc_final: 0.9080 (mp) REVERT: c 21 LYS cc_start: 0.9301 (mttm) cc_final: 0.8753 (mttm) REVERT: c 25 ASP cc_start: 0.8313 (m-30) cc_final: 0.7987 (m-30) REVERT: c 34 ASN cc_start: 0.7478 (t0) cc_final: 0.6466 (t0) REVERT: c 39 ASN cc_start: 0.8827 (m110) cc_final: 0.8468 (m110) REVERT: c 44 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7775 (mm-30) REVERT: c 48 GLN cc_start: 0.8728 (mp10) cc_final: 0.8204 (mp10) REVERT: c 58 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9069 (tp) REVERT: d 1 MET cc_start: 0.7548 (tpp) cc_final: 0.7200 (tpt) REVERT: d 2 ASN cc_start: 0.8415 (m-40) cc_final: 0.8208 (m-40) REVERT: d 3 PHE cc_start: 0.8940 (t80) cc_final: 0.8634 (t80) REVERT: d 13 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8804 (mm110) REVERT: d 34 ASN cc_start: 0.7840 (t160) cc_final: 0.7376 (p0) REVERT: d 60 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8512 (mtpp) REVERT: d 63 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8875 (p) REVERT: d 82 GLN cc_start: 0.9103 (mm110) cc_final: 0.8891 (mm-40) REVERT: d 83 ASP cc_start: 0.8746 (t70) cc_final: 0.8468 (t0) REVERT: e 34 ASN cc_start: 0.8314 (t0) cc_final: 0.7927 (t0) REVERT: e 35 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7438 (ttp-110) REVERT: e 36 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6359 (mm-30) REVERT: e 39 ASN cc_start: 0.8612 (m-40) cc_final: 0.7640 (m110) REVERT: e 74 LYS cc_start: 0.9006 (tttt) cc_final: 0.8761 (ttpp) REVERT: e 77 ASN cc_start: 0.9202 (t0) cc_final: 0.8725 (t0) REVERT: e 82 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8531 (mm110) outliers start: 131 outliers final: 59 residues processed: 1759 average time/residue: 0.1679 time to fit residues: 445.4528 Evaluate side-chains 1625 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1556 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 42 CYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 37 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 98 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 34 ASN A 82 GLN B 31 ASN B 34 ASN B 67 ASN C 39 ASN D 82 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 39 ASN H 67 ASN I 22 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN J 67 ASN K 34 ASN K 39 ASN L 31 ASN L 82 GLN M 39 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN P 34 ASN P 39 ASN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 ASN S 39 ASN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN T 13 GLN T 22 GLN T 34 ASN V 39 ASN W 22 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 ASN W 67 ASN Y 67 ASN Z 82 GLN a 39 ASN b 82 GLN b 87 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 39 ASN d 67 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.084160 restraints weight = 38202.453| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.41 r_work: 0.2873 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23095 Z= 0.145 Angle : 0.561 7.904 31000 Z= 0.308 Chirality : 0.041 0.174 3472 Planarity : 0.004 0.043 3937 Dihedral : 3.783 13.829 2914 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 5.91 % Allowed : 18.73 % Favored : 75.36 % 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: 1.33 (0.15), residues: 2728 helix: 1.18 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.09 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 9 TYR 0.017 0.002 TYR a 78 PHE 0.017 0.001 PHE C 3 TRP 0.015 0.002 TRP I 30 HIS 0.011 0.001 HIS S 56 Details of bonding type rmsd covalent geometry : bond 0.00346 (23095) covalent geometry : angle 0.56127 (31000) hydrogen bonds : bond 0.03635 ( 1643) hydrogen bonds : angle 4.26271 ( 4929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1809 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1657 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8323 (t0) cc_final: 0.7992 (t0) REVERT: A 37 GLU cc_start: 0.9059 (mp0) cc_final: 0.8815 (mp0) REVERT: A 47 GLU cc_start: 0.7618 (tt0) cc_final: 0.7175 (tt0) REVERT: A 66 CYS cc_start: 0.8977 (m) cc_final: 0.8726 (m) REVERT: A 74 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8865 (ttpp) REVERT: B 35 ARG cc_start: 0.7581 (tpp80) cc_final: 0.6995 (tpp80) REVERT: B 39 ASN cc_start: 0.8876 (m110) cc_final: 0.8246 (m110) REVERT: B 52 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7875 (mtt-85) REVERT: B 66 CYS cc_start: 0.8786 (m) cc_final: 0.8521 (m) REVERT: B 83 ASP cc_start: 0.8785 (t70) cc_final: 0.8535 (t0) REVERT: C 2 ASN cc_start: 0.8239 (m-40) cc_final: 0.7818 (m110) REVERT: C 39 ASN cc_start: 0.8632 (m-40) cc_final: 0.8166 (m-40) REVERT: C 60 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8633 (mtpp) REVERT: C 78 TYR cc_start: 0.9050 (t80) cc_final: 0.8843 (t80) REVERT: C 83 ASP cc_start: 0.8744 (t70) cc_final: 0.8490 (t0) REVERT: D 13 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8768 (mm-40) REVERT: D 35 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7616 (tpp80) REVERT: D 39 ASN cc_start: 0.8265 (m110) cc_final: 0.7672 (m110) REVERT: D 60 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8532 (mtpp) REVERT: D 74 LYS cc_start: 0.9121 (tttt) cc_final: 0.8843 (ttpp) REVERT: E 1 MET cc_start: 0.6720 (tpp) cc_final: 0.6441 (tpt) REVERT: E 9 ARG cc_start: 0.8707 (mtp-110) cc_final: 0.8445 (mtp-110) REVERT: E 20 ILE cc_start: 0.9370 (mt) cc_final: 0.9062 (mp) REVERT: E 34 ASN cc_start: 0.8121 (t0) cc_final: 0.7385 (t0) REVERT: E 39 ASN cc_start: 0.8530 (m110) cc_final: 0.7909 (m110) REVERT: E 47 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: E 57 MET cc_start: 0.8411 (mtm) cc_final: 0.8169 (mtp) REVERT: E 60 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8605 (mtpp) REVERT: E 78 TYR cc_start: 0.9013 (t80) cc_final: 0.8755 (t80) REVERT: E 82 GLN cc_start: 0.8778 (mm110) cc_final: 0.8474 (mm-40) REVERT: F 2 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: F 39 ASN cc_start: 0.8574 (m-40) cc_final: 0.8336 (m110) REVERT: F 82 GLN cc_start: 0.8844 (mm110) cc_final: 0.8636 (mm110) REVERT: G 1 MET cc_start: 0.6668 (tpp) cc_final: 0.6350 (tpp) REVERT: G 35 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7668 (ttp-110) REVERT: G 39 ASN cc_start: 0.8609 (m110) cc_final: 0.8207 (m110) REVERT: G 77 ASN cc_start: 0.9136 (t0) cc_final: 0.8785 (t0) REVERT: G 83 ASP cc_start: 0.8609 (t70) cc_final: 0.8330 (t0) REVERT: H 2 ASN cc_start: 0.7749 (m-40) cc_final: 0.7364 (m110) REVERT: H 34 ASN cc_start: 0.8160 (t0) cc_final: 0.7493 (t0) REVERT: H 35 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7616 (tpp80) REVERT: H 60 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8361 (mtpt) REVERT: I 31 ASN cc_start: 0.8918 (m-40) cc_final: 0.8709 (m-40) REVERT: I 35 ARG cc_start: 0.7663 (tpp80) cc_final: 0.7335 (tpp80) REVERT: I 82 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8223 (mm110) REVERT: J 39 ASN cc_start: 0.8540 (m110) cc_final: 0.7967 (m110) REVERT: J 77 ASN cc_start: 0.9249 (t0) cc_final: 0.8748 (t0) REVERT: K 13 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8359 (mm110) REVERT: K 22 GLN cc_start: 0.8847 (mt0) cc_final: 0.8615 (mt0) REVERT: K 34 ASN cc_start: 0.8266 (t0) cc_final: 0.7629 (t0) REVERT: K 37 GLU cc_start: 0.8991 (mp0) cc_final: 0.8426 (mp0) REVERT: K 60 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8316 (mtpp) REVERT: K 66 CYS cc_start: 0.8867 (m) cc_final: 0.8666 (m) REVERT: K 78 TYR cc_start: 0.9059 (t80) cc_final: 0.8847 (t80) REVERT: K 83 ASP cc_start: 0.8804 (t70) cc_final: 0.8430 (t0) REVERT: M 1 MET cc_start: 0.6518 (tpp) cc_final: 0.6103 (tpp) REVERT: M 13 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8727 (mm-40) REVERT: M 34 ASN cc_start: 0.8317 (t0) cc_final: 0.7922 (t0) REVERT: M 39 ASN cc_start: 0.8911 (m-40) cc_final: 0.8517 (m110) REVERT: M 78 TYR cc_start: 0.8828 (t80) cc_final: 0.8620 (t80) REVERT: N 2 ASN cc_start: 0.8585 (m-40) cc_final: 0.8119 (m110) REVERT: N 39 ASN cc_start: 0.8414 (m110) cc_final: 0.8189 (m-40) REVERT: N 60 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8455 (mtpp) REVERT: N 71 LYS cc_start: 0.9250 (ttmm) cc_final: 0.9024 (ptmt) REVERT: N 74 LYS cc_start: 0.9307 (ttpp) cc_final: 0.9083 (ttmm) REVERT: N 77 ASN cc_start: 0.9230 (t0) cc_final: 0.8964 (t0) REVERT: N 89 LEU cc_start: 0.6607 (tp) cc_final: 0.6231 (tp) REVERT: O 1 MET cc_start: 0.6372 (tpp) cc_final: 0.6149 (tpp) REVERT: O 39 ASN cc_start: 0.8751 (m110) cc_final: 0.8513 (m110) REVERT: O 44 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7790 (mm-30) REVERT: O 60 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8555 (mttt) REVERT: P 25 ASP cc_start: 0.8354 (m-30) cc_final: 0.8149 (m-30) REVERT: P 41 ILE cc_start: 0.9299 (mm) cc_final: 0.9087 (mt) REVERT: P 47 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: P 48 GLN cc_start: 0.8633 (mp10) cc_final: 0.8293 (mp10) REVERT: P 60 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8636 (mtpt) REVERT: P 66 CYS cc_start: 0.8894 (m) cc_final: 0.8483 (m) REVERT: P 67 ASN cc_start: 0.8982 (m-40) cc_final: 0.8515 (m-40) REVERT: Q 7 ASN cc_start: 0.8846 (m-40) cc_final: 0.8409 (m110) REVERT: Q 66 CYS cc_start: 0.8847 (m) cc_final: 0.8263 (m) REVERT: R 36 GLU cc_start: 0.7600 (mp0) cc_final: 0.6834 (mp0) REVERT: R 44 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7691 (mm-30) REVERT: R 60 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8760 (mttt) REVERT: S 2 ASN cc_start: 0.8195 (m-40) cc_final: 0.7751 (m110) REVERT: S 39 ASN cc_start: 0.8648 (m110) cc_final: 0.8348 (m-40) REVERT: S 60 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8726 (mtpp) REVERT: S 66 CYS cc_start: 0.8935 (m) cc_final: 0.8630 (m) REVERT: T 33 LEU cc_start: 0.9042 (mm) cc_final: 0.8698 (mt) REVERT: T 34 ASN cc_start: 0.8235 (t0) cc_final: 0.7856 (t0) REVERT: T 35 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7543 (ttp-110) REVERT: T 39 ASN cc_start: 0.8424 (m110) cc_final: 0.7811 (m110) REVERT: T 45 LYS cc_start: 0.8277 (tttm) cc_final: 0.7897 (tttm) REVERT: T 77 ASN cc_start: 0.9250 (t0) cc_final: 0.9010 (t0) REVERT: T 83 ASP cc_start: 0.8971 (t70) cc_final: 0.8757 (t70) REVERT: U 1 MET cc_start: 0.5985 (tpp) cc_final: 0.5734 (tpt) REVERT: U 2 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8118 (m110) REVERT: U 35 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7329 (ttp-110) REVERT: U 39 ASN cc_start: 0.8490 (m110) cc_final: 0.7906 (m110) REVERT: U 47 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: U 49 ASP cc_start: 0.8653 (m-30) cc_final: 0.8391 (m-30) REVERT: V 34 ASN cc_start: 0.8258 (t0) cc_final: 0.7850 (t0) REVERT: V 39 ASN cc_start: 0.8604 (m110) cc_final: 0.8167 (m110) REVERT: V 66 CYS cc_start: 0.8895 (m) cc_final: 0.8617 (m) REVERT: W 6 ASP cc_start: 0.8681 (m-30) cc_final: 0.8372 (m-30) REVERT: W 13 GLN cc_start: 0.9080 (mm110) cc_final: 0.8876 (mm110) REVERT: W 35 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7621 (ttp-110) REVERT: W 39 ASN cc_start: 0.8294 (m110) cc_final: 0.8000 (m110) REVERT: W 60 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8735 (mtmm) REVERT: W 66 CYS cc_start: 0.8927 (m) cc_final: 0.8711 (t) REVERT: X 7 ASN cc_start: 0.9158 (m-40) cc_final: 0.8827 (m110) REVERT: X 17 MET cc_start: 0.8418 (tpp) cc_final: 0.8154 (tpp) REVERT: X 21 LYS cc_start: 0.9263 (mttp) cc_final: 0.8781 (mttp) REVERT: X 25 ASP cc_start: 0.8435 (m-30) cc_final: 0.7905 (m-30) REVERT: X 60 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8608 (mtpt) REVERT: X 66 CYS cc_start: 0.9009 (m) cc_final: 0.8424 (m) REVERT: X 81 PHE cc_start: 0.9208 (t80) cc_final: 0.8996 (t80) REVERT: X 82 GLN cc_start: 0.8765 (mm110) cc_final: 0.8537 (mm110) REVERT: Y 7 ASN cc_start: 0.8767 (m-40) cc_final: 0.8363 (m-40) REVERT: Y 31 ASN cc_start: 0.9114 (m-40) cc_final: 0.8895 (m-40) REVERT: Y 36 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8151 (mm-30) REVERT: Y 43 CYS cc_start: 0.8369 (p) cc_final: 0.8007 (p) REVERT: Y 60 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8069 (tptt) REVERT: Y 66 CYS cc_start: 0.8901 (m) cc_final: 0.8532 (m) REVERT: Z 2 ASN cc_start: 0.8350 (m-40) cc_final: 0.7879 (m110) REVERT: Z 6 ASP cc_start: 0.8470 (m-30) cc_final: 0.8240 (m-30) REVERT: Z 34 ASN cc_start: 0.7952 (t0) cc_final: 0.7566 (t0) REVERT: Z 44 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7937 (mm-30) REVERT: Z 60 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8626 (mtpt) REVERT: Z 66 CYS cc_start: 0.8843 (m) cc_final: 0.8626 (m) REVERT: Z 77 ASN cc_start: 0.9013 (t0) cc_final: 0.8355 (t0) REVERT: a 2 ASN cc_start: 0.8173 (m-40) cc_final: 0.7741 (m110) REVERT: a 3 PHE cc_start: 0.8895 (t80) cc_final: 0.8654 (t80) REVERT: a 5 LYS cc_start: 0.8889 (tttm) cc_final: 0.8239 (tptt) REVERT: a 6 ASP cc_start: 0.8799 (m-30) cc_final: 0.8581 (m-30) REVERT: a 9 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7719 (mmt-90) REVERT: a 34 ASN cc_start: 0.7455 (t0) cc_final: 0.6798 (t0) REVERT: a 60 LYS cc_start: 0.9102 (mtmt) cc_final: 0.7820 (tptm) REVERT: b 39 ASN cc_start: 0.8415 (m110) cc_final: 0.7888 (m110) REVERT: b 74 LYS cc_start: 0.9219 (ttpt) cc_final: 0.9018 (ttmm) REVERT: b 77 ASN cc_start: 0.9128 (t0) cc_final: 0.8763 (t0) REVERT: b 78 TYR cc_start: 0.9008 (t80) cc_final: 0.8775 (t80) REVERT: b 82 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8334 (mm110) REVERT: c 1 MET cc_start: 0.6349 (tpp) cc_final: 0.6041 (tpp) REVERT: c 8 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (m) REVERT: c 21 LYS cc_start: 0.9430 (mttm) cc_final: 0.9019 (mttm) REVERT: c 25 ASP cc_start: 0.8394 (m-30) cc_final: 0.7883 (m-30) REVERT: c 34 ASN cc_start: 0.8315 (t0) cc_final: 0.7710 (t0) REVERT: c 37 GLU cc_start: 0.9079 (mp0) cc_final: 0.8853 (mp0) REVERT: c 39 ASN cc_start: 0.8784 (m110) cc_final: 0.8316 (m110) REVERT: c 44 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7970 (mm-30) REVERT: c 58 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8973 (tp) REVERT: d 1 MET cc_start: 0.7317 (tpp) cc_final: 0.7062 (tpt) REVERT: d 2 ASN cc_start: 0.8505 (m-40) cc_final: 0.8272 (m-40) REVERT: d 3 PHE cc_start: 0.8996 (t80) cc_final: 0.8757 (t80) REVERT: d 13 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8846 (mm-40) REVERT: d 26 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8105 (t0) REVERT: d 39 ASN cc_start: 0.8463 (m110) cc_final: 0.8231 (m110) REVERT: d 60 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8613 (mtpp) REVERT: d 83 ASP cc_start: 0.8700 (t70) cc_final: 0.8367 (t0) REVERT: e 34 ASN cc_start: 0.8556 (t0) cc_final: 0.8187 (t0) REVERT: e 74 LYS cc_start: 0.9046 (tttt) cc_final: 0.8793 (ttpp) outliers start: 152 outliers final: 84 residues processed: 1697 average time/residue: 0.1712 time to fit residues: 436.1725 Evaluate side-chains 1637 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1545 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 15 MET Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 58 ILE Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 47 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 34 ASN B 67 ASN C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 67 ASN G 82 GLN H 13 GLN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN I 77 ASN J 31 ASN J 67 ASN J 82 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN M 22 GLN M 39 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN R 31 ASN R 39 ASN S 22 GLN ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN V 22 GLN W 67 ASN X 34 ASN X 67 ASN Y 13 GLN Y 22 GLN Y 67 ASN Y 82 GLN Z 82 GLN Z 87 GLN a 82 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 67 ASN e 82 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.089589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.077355 restraints weight = 38955.482| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.31 r_work: 0.2768 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23095 Z= 0.261 Angle : 0.648 7.832 31000 Z= 0.357 Chirality : 0.046 0.202 3472 Planarity : 0.004 0.040 3937 Dihedral : 3.948 14.464 2914 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 7.38 % Allowed : 20.40 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2728 helix: 0.96 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 9 TYR 0.018 0.002 TYR N 78 PHE 0.022 0.002 PHE P 3 TRP 0.011 0.002 TRP L 30 HIS 0.005 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00635 (23095) covalent geometry : angle 0.64768 (31000) hydrogen bonds : bond 0.04182 ( 1643) hydrogen bonds : angle 4.34023 ( 4929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1817 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1627 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6710 (tpp) cc_final: 0.6253 (tpt) REVERT: A 47 GLU cc_start: 0.7751 (tt0) cc_final: 0.7408 (tt0) REVERT: A 66 CYS cc_start: 0.8991 (m) cc_final: 0.8742 (m) REVERT: B 39 ASN cc_start: 0.8854 (m110) cc_final: 0.8543 (m-40) REVERT: B 45 LYS cc_start: 0.8674 (tttm) cc_final: 0.8373 (tmtt) REVERT: B 66 CYS cc_start: 0.8816 (m) cc_final: 0.8563 (m) REVERT: C 2 ASN cc_start: 0.8361 (m-40) cc_final: 0.7969 (m-40) REVERT: C 31 ASN cc_start: 0.9081 (m-40) cc_final: 0.8791 (m110) REVERT: C 34 ASN cc_start: 0.8006 (t0) cc_final: 0.7770 (t0) REVERT: C 57 MET cc_start: 0.8688 (ttp) cc_final: 0.8268 (mtm) REVERT: C 60 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8657 (mtpp) REVERT: C 82 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8458 (mm-40) REVERT: C 83 ASP cc_start: 0.8778 (t70) cc_final: 0.8417 (t0) REVERT: D 13 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8824 (mm-40) REVERT: D 34 ASN cc_start: 0.8546 (t0) cc_final: 0.7806 (t0) REVERT: D 35 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7850 (ttm-80) REVERT: D 43 CYS cc_start: 0.8286 (p) cc_final: 0.8057 (p) REVERT: D 74 LYS cc_start: 0.9186 (tttt) cc_final: 0.8879 (ttpp) REVERT: E 9 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.8482 (mtp-110) REVERT: E 37 GLU cc_start: 0.8833 (mp0) cc_final: 0.8629 (mp0) REVERT: E 39 ASN cc_start: 0.8517 (m110) cc_final: 0.7831 (m110) REVERT: E 57 MET cc_start: 0.8623 (mtm) cc_final: 0.8257 (mtp) REVERT: E 60 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8635 (mtpp) REVERT: E 78 TYR cc_start: 0.9093 (t80) cc_final: 0.8848 (t80) REVERT: F 9 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8290 (mtp-110) REVERT: G 26 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: G 66 CYS cc_start: 0.8808 (m) cc_final: 0.8583 (m) REVERT: H 2 ASN cc_start: 0.7952 (m-40) cc_final: 0.7740 (m110) REVERT: H 14 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7693 (mmm-85) REVERT: H 57 MET cc_start: 0.8651 (mtp) cc_final: 0.8388 (mtp) REVERT: H 60 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8088 (mtpt) REVERT: J 22 GLN cc_start: 0.9036 (mt0) cc_final: 0.8834 (mt0) REVERT: J 37 GLU cc_start: 0.8837 (pm20) cc_final: 0.8615 (mp0) REVERT: J 39 ASN cc_start: 0.8640 (m110) cc_final: 0.7942 (m110) REVERT: J 60 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8712 (mttt) REVERT: J 87 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7626 (mm-40) REVERT: K 25 ASP cc_start: 0.8356 (m-30) cc_final: 0.8045 (m-30) REVERT: K 60 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8398 (mtpp) REVERT: K 66 CYS cc_start: 0.8811 (m) cc_final: 0.8570 (m) REVERT: K 83 ASP cc_start: 0.8900 (t70) cc_final: 0.8442 (t0) REVERT: L 89 LEU cc_start: 0.7898 (tp) cc_final: 0.7668 (tp) REVERT: M 1 MET cc_start: 0.7215 (tpp) cc_final: 0.6981 (tpt) REVERT: M 5 LYS cc_start: 0.8896 (tptm) cc_final: 0.8452 (tptm) REVERT: M 35 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7791 (tpp80) REVERT: M 39 ASN cc_start: 0.8802 (m110) cc_final: 0.8122 (m-40) REVERT: N 1 MET cc_start: 0.7810 (tpp) cc_final: 0.7506 (tpt) REVERT: N 60 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8445 (mtpp) REVERT: N 71 LYS cc_start: 0.9345 (ttmm) cc_final: 0.9138 (ptmt) REVERT: N 89 LEU cc_start: 0.7050 (tp) cc_final: 0.6625 (tp) REVERT: O 39 ASN cc_start: 0.8822 (m110) cc_final: 0.8429 (m110) REVERT: O 44 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7977 (mm-30) REVERT: O 45 LYS cc_start: 0.8862 (pttt) cc_final: 0.8646 (ttpt) REVERT: O 52 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8207 (mtt-85) REVERT: O 60 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8428 (mttt) REVERT: P 37 GLU cc_start: 0.9032 (mp0) cc_final: 0.8767 (mp0) REVERT: P 47 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: P 60 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8661 (mtpp) REVERT: P 66 CYS cc_start: 0.8906 (m) cc_final: 0.8545 (m) REVERT: P 67 ASN cc_start: 0.9132 (m-40) cc_final: 0.8814 (m-40) REVERT: Q 60 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8739 (mtmm) REVERT: Q 78 TYR cc_start: 0.9089 (t80) cc_final: 0.8829 (t80) REVERT: Q 89 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7177 (tt) REVERT: R 60 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8812 (mttt) REVERT: S 2 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8146 (m-40) REVERT: S 60 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8754 (mtpp) REVERT: S 66 CYS cc_start: 0.8910 (m) cc_final: 0.8657 (m) REVERT: T 1 MET cc_start: 0.7076 (tpp) cc_final: 0.6717 (tpt) REVERT: T 2 ASN cc_start: 0.8464 (m-40) cc_final: 0.8182 (m-40) REVERT: T 78 TYR cc_start: 0.9041 (t80) cc_final: 0.8817 (t80) REVERT: U 25 ASP cc_start: 0.8254 (m-30) cc_final: 0.7885 (m-30) REVERT: U 35 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7510 (ttp-110) REVERT: U 39 ASN cc_start: 0.8714 (m110) cc_final: 0.8162 (m110) REVERT: U 47 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: U 49 ASP cc_start: 0.8758 (m-30) cc_final: 0.8548 (m-30) REVERT: V 1 MET cc_start: 0.7665 (tpp) cc_final: 0.7433 (tpt) REVERT: V 34 ASN cc_start: 0.8356 (t0) cc_final: 0.8156 (t0) REVERT: V 47 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: V 57 MET cc_start: 0.8764 (mtm) cc_final: 0.8532 (mtp) REVERT: V 66 CYS cc_start: 0.8922 (m) cc_final: 0.8648 (m) REVERT: W 6 ASP cc_start: 0.8544 (m-30) cc_final: 0.8323 (m-30) REVERT: W 34 ASN cc_start: 0.8334 (t0) cc_final: 0.8076 (t0) REVERT: W 47 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: W 60 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8775 (mtmm) REVERT: X 14 ARG cc_start: 0.8135 (mtt180) cc_final: 0.6388 (tpt170) REVERT: X 17 MET cc_start: 0.8709 (tpp) cc_final: 0.8443 (tpp) REVERT: X 21 LYS cc_start: 0.9366 (mttp) cc_final: 0.8981 (mttp) REVERT: X 25 ASP cc_start: 0.8388 (m-30) cc_final: 0.8018 (m-30) REVERT: X 37 GLU cc_start: 0.8929 (mp0) cc_final: 0.8726 (mp0) REVERT: X 60 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8662 (mtpt) REVERT: X 66 CYS cc_start: 0.8937 (m) cc_final: 0.8429 (m) REVERT: Y 1 MET cc_start: 0.7381 (tpp) cc_final: 0.6827 (tpt) REVERT: Y 2 ASN cc_start: 0.8491 (m-40) cc_final: 0.8219 (m110) REVERT: Y 31 ASN cc_start: 0.9211 (m-40) cc_final: 0.8990 (m-40) REVERT: Y 60 LYS cc_start: 0.9267 (mtmt) cc_final: 0.8102 (tptt) REVERT: Y 82 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8225 (mp10) REVERT: Z 2 ASN cc_start: 0.8553 (m-40) cc_final: 0.8255 (m110) REVERT: Z 33 LEU cc_start: 0.9003 (mt) cc_final: 0.8799 (mt) REVERT: Z 44 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8037 (mm-30) REVERT: Z 60 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8859 (mtmm) REVERT: a 2 ASN cc_start: 0.8493 (m-40) cc_final: 0.7953 (m110) REVERT: a 5 LYS cc_start: 0.8807 (tttm) cc_final: 0.8397 (tptt) REVERT: a 6 ASP cc_start: 0.8789 (m-30) cc_final: 0.8558 (m-30) REVERT: a 9 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7713 (mmt-90) REVERT: a 34 ASN cc_start: 0.8260 (t0) cc_final: 0.7766 (t0) REVERT: a 37 GLU cc_start: 0.8988 (mp0) cc_final: 0.8739 (mp0) REVERT: a 60 LYS cc_start: 0.9156 (mtmt) cc_final: 0.7811 (tptm) REVERT: b 34 ASN cc_start: 0.7869 (t0) cc_final: 0.7594 (t0) REVERT: b 39 ASN cc_start: 0.8643 (m110) cc_final: 0.8148 (m110) REVERT: b 78 TYR cc_start: 0.9226 (t80) cc_final: 0.9007 (t80) REVERT: b 82 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8509 (mm110) REVERT: c 1 MET cc_start: 0.7125 (tpp) cc_final: 0.6697 (tpp) REVERT: c 25 ASP cc_start: 0.8532 (m-30) cc_final: 0.8042 (m-30) REVERT: c 26 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (t70) REVERT: c 44 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8101 (mm-30) REVERT: c 58 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9105 (tp) REVERT: c 68 LEU cc_start: 0.9498 (mt) cc_final: 0.9295 (mp) REVERT: d 26 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8343 (t70) REVERT: d 60 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8550 (mtpp) REVERT: d 83 ASP cc_start: 0.8638 (t70) cc_final: 0.8412 (t70) REVERT: e 34 ASN cc_start: 0.8724 (t0) cc_final: 0.8421 (t0) REVERT: e 74 LYS cc_start: 0.9089 (tttt) cc_final: 0.8816 (ttpp) outliers start: 190 outliers final: 127 residues processed: 1677 average time/residue: 0.1694 time to fit residues: 427.1757 Evaluate side-chains 1690 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1553 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 15 MET Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 54 ILE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 58 ILE Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 271 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 31 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN C 34 ASN C 77 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 82 GLN F 31 ASN F 82 GLN G 31 ASN G 67 ASN H 13 GLN H 67 ASN H 82 GLN I 77 ASN I 82 GLN J 31 ASN J 67 ASN J 82 GLN K 22 GLN L 82 GLN M 22 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN P 22 GLN P 82 GLN Q 82 GLN R 2 ASN R 31 ASN ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN U 22 GLN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN W 87 GLN X 82 GLN Y 13 GLN Y 67 ASN a 82 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 ASN d 13 GLN d 39 ASN d 67 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085317 restraints weight = 37965.521| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.32 r_work: 0.2893 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23095 Z= 0.129 Angle : 0.581 6.438 31000 Z= 0.320 Chirality : 0.041 0.208 3472 Planarity : 0.004 0.057 3937 Dihedral : 3.874 13.225 2914 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.02 % Allowed : 24.56 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2728 helix: 0.95 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 9 TYR 0.015 0.002 TYR D 78 PHE 0.019 0.001 PHE C 3 TRP 0.010 0.001 TRP E 30 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00299 (23095) covalent geometry : angle 0.58108 (31000) hydrogen bonds : bond 0.03480 ( 1643) hydrogen bonds : angle 4.44283 ( 4929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1857 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1702 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.9372 (mp) cc_final: 0.9149 (mp) REVERT: A 34 ASN cc_start: 0.7858 (t0) cc_final: 0.7135 (t0) REVERT: A 36 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 37 GLU cc_start: 0.9105 (mp0) cc_final: 0.8641 (mp0) REVERT: A 39 ASN cc_start: 0.8830 (m-40) cc_final: 0.8315 (m-40) REVERT: A 43 CYS cc_start: 0.8380 (p) cc_final: 0.8030 (p) REVERT: A 44 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 47 GLU cc_start: 0.7708 (tt0) cc_final: 0.7313 (tt0) REVERT: A 57 MET cc_start: 0.8347 (mtm) cc_final: 0.8145 (mtm) REVERT: A 81 PHE cc_start: 0.9072 (t80) cc_final: 0.8788 (t80) REVERT: B 35 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7572 (tpp-160) REVERT: B 66 CYS cc_start: 0.8890 (m) cc_final: 0.8584 (m) REVERT: C 2 ASN cc_start: 0.8421 (m-40) cc_final: 0.8211 (m-40) REVERT: C 48 GLN cc_start: 0.8191 (mp10) cc_final: 0.7798 (mp10) REVERT: C 60 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8633 (mtpp) REVERT: C 82 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8168 (mm110) REVERT: D 13 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8680 (mm-40) REVERT: D 39 ASN cc_start: 0.8223 (m110) cc_final: 0.7715 (t0) REVERT: D 45 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8026 (ttpt) REVERT: D 74 LYS cc_start: 0.9135 (tttt) cc_final: 0.8847 (ttpp) REVERT: D 78 TYR cc_start: 0.8595 (t80) cc_final: 0.8210 (t80) REVERT: D 82 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8458 (mp10) REVERT: E 39 ASN cc_start: 0.8463 (m110) cc_final: 0.7598 (m110) REVERT: E 57 MET cc_start: 0.8627 (mtm) cc_final: 0.8274 (mtp) REVERT: E 60 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8671 (mtpp) REVERT: E 78 TYR cc_start: 0.8951 (t80) cc_final: 0.8564 (t80) REVERT: E 80 LEU cc_start: 0.9014 (tp) cc_final: 0.8810 (tp) REVERT: F 1 MET cc_start: 0.6852 (tpp) cc_final: 0.6607 (tpp) REVERT: G 35 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7697 (ttp-110) REVERT: G 36 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: G 39 ASN cc_start: 0.8692 (m110) cc_final: 0.8402 (m110) REVERT: G 45 LYS cc_start: 0.8438 (pttt) cc_final: 0.8123 (ptmt) REVERT: G 77 ASN cc_start: 0.9081 (t0) cc_final: 0.8748 (t0) REVERT: G 83 ASP cc_start: 0.8697 (t70) cc_final: 0.8359 (t0) REVERT: H 14 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.6907 (mtp180) REVERT: H 35 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7317 (tpp80) REVERT: H 48 GLN cc_start: 0.8490 (mp10) cc_final: 0.8279 (mp10) REVERT: H 57 MET cc_start: 0.8722 (mtp) cc_final: 0.8459 (mtp) REVERT: H 60 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8390 (mtpt) REVERT: H 67 ASN cc_start: 0.8880 (m-40) cc_final: 0.8611 (m110) REVERT: H 74 LYS cc_start: 0.9289 (ttpp) cc_final: 0.8974 (ttmm) REVERT: I 14 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7545 (mtp180) REVERT: I 39 ASN cc_start: 0.8743 (m-40) cc_final: 0.8497 (m-40) REVERT: J 1 MET cc_start: 0.7199 (tpp) cc_final: 0.6972 (tpt) REVERT: J 39 ASN cc_start: 0.8645 (m110) cc_final: 0.7769 (m110) REVERT: K 25 ASP cc_start: 0.8278 (m-30) cc_final: 0.7743 (m-30) REVERT: K 37 GLU cc_start: 0.9008 (mp0) cc_final: 0.8378 (mp0) REVERT: K 38 VAL cc_start: 0.9056 (t) cc_final: 0.8835 (m) REVERT: K 56 HIS cc_start: 0.8309 (m-70) cc_final: 0.8032 (m-70) REVERT: K 60 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8330 (mttt) REVERT: K 66 CYS cc_start: 0.8834 (m) cc_final: 0.8616 (m) REVERT: K 83 ASP cc_start: 0.8846 (t70) cc_final: 0.8512 (t0) REVERT: L 77 ASN cc_start: 0.9321 (t0) cc_final: 0.8974 (t0) REVERT: L 80 LEU cc_start: 0.9398 (tp) cc_final: 0.9176 (tp) REVERT: L 82 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8196 (mp10) REVERT: L 89 LEU cc_start: 0.7709 (tp) cc_final: 0.7464 (tp) REVERT: M 1 MET cc_start: 0.6933 (tpp) cc_final: 0.6501 (tpt) REVERT: M 35 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7446 (tpp-160) REVERT: M 39 ASN cc_start: 0.8536 (m110) cc_final: 0.7951 (m110) REVERT: M 58 ILE cc_start: 0.9362 (tp) cc_final: 0.8835 (tp) REVERT: M 60 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8353 (mtpp) REVERT: M 78 TYR cc_start: 0.8768 (t80) cc_final: 0.8388 (t80) REVERT: N 1 MET cc_start: 0.7613 (tpp) cc_final: 0.7333 (tpt) REVERT: N 60 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8466 (mtpp) REVERT: N 89 LEU cc_start: 0.7035 (tp) cc_final: 0.6351 (tp) REVERT: O 18 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8693 (m) REVERT: O 35 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7024 (tpp80) REVERT: O 39 ASN cc_start: 0.8723 (m110) cc_final: 0.7613 (m110) REVERT: O 44 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7811 (mm-30) REVERT: O 45 LYS cc_start: 0.8758 (pttt) cc_final: 0.8476 (ttpp) REVERT: O 52 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7910 (mtt-85) REVERT: O 60 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8409 (mttt) REVERT: P 34 ASN cc_start: 0.7992 (t0) cc_final: 0.7777 (t0) REVERT: P 35 ARG cc_start: 0.8482 (ttm170) cc_final: 0.8245 (tpp80) REVERT: P 60 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8390 (mtpt) REVERT: P 66 CYS cc_start: 0.8888 (m) cc_final: 0.8472 (m) REVERT: P 67 ASN cc_start: 0.9033 (m-40) cc_final: 0.8612 (m-40) REVERT: P 82 GLN cc_start: 0.8738 (mm-40) cc_final: 0.7980 (mp10) REVERT: Q 1 MET cc_start: 0.6521 (tpp) cc_final: 0.6229 (tpt) REVERT: Q 14 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7866 (mtp180) REVERT: Q 89 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7288 (tt) REVERT: R 36 GLU cc_start: 0.7530 (mp0) cc_final: 0.7277 (mp0) REVERT: R 39 ASN cc_start: 0.8629 (m-40) cc_final: 0.8417 (m110) REVERT: R 44 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7637 (mm-30) REVERT: R 60 LYS cc_start: 0.9054 (mtmt) cc_final: 0.8767 (mttt) REVERT: R 74 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8865 (mtpp) REVERT: S 1 MET cc_start: 0.6877 (tpp) cc_final: 0.6463 (tpt) REVERT: S 2 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8023 (m-40) REVERT: S 60 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8695 (mtpp) REVERT: S 66 CYS cc_start: 0.9054 (m) cc_final: 0.8741 (m) REVERT: T 1 MET cc_start: 0.6873 (tpp) cc_final: 0.6543 (tpt) REVERT: T 34 ASN cc_start: 0.8102 (t0) cc_final: 0.7814 (t0) REVERT: T 39 ASN cc_start: 0.8604 (m110) cc_final: 0.7747 (m-40) REVERT: T 45 LYS cc_start: 0.8191 (tttm) cc_final: 0.7740 (tttm) REVERT: T 77 ASN cc_start: 0.9257 (t0) cc_final: 0.9001 (t0) REVERT: U 2 ASN cc_start: 0.8782 (m110) cc_final: 0.8457 (m-40) REVERT: U 25 ASP cc_start: 0.8311 (m-30) cc_final: 0.7919 (m-30) REVERT: U 35 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7362 (ttp-110) REVERT: U 39 ASN cc_start: 0.8590 (m110) cc_final: 0.7972 (m110) REVERT: U 44 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8120 (mm-30) REVERT: U 49 ASP cc_start: 0.8628 (m-30) cc_final: 0.8135 (m-30) REVERT: U 74 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8879 (ptmm) REVERT: V 1 MET cc_start: 0.7290 (tpp) cc_final: 0.7063 (tpt) REVERT: V 2 ASN cc_start: 0.8509 (m-40) cc_final: 0.8281 (m-40) REVERT: V 39 ASN cc_start: 0.8648 (m-40) cc_final: 0.8192 (m110) REVERT: V 47 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: V 66 CYS cc_start: 0.8894 (m) cc_final: 0.8652 (m) REVERT: W 60 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8657 (mtmm) REVERT: X 17 MET cc_start: 0.8510 (tpp) cc_final: 0.8289 (tpp) REVERT: X 21 LYS cc_start: 0.9344 (mttp) cc_final: 0.8798 (mttp) REVERT: X 22 GLN cc_start: 0.8816 (mt0) cc_final: 0.8603 (mt0) REVERT: X 25 ASP cc_start: 0.8374 (m-30) cc_final: 0.8090 (m-30) REVERT: X 37 GLU cc_start: 0.8987 (mp0) cc_final: 0.8761 (mp0) REVERT: X 60 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8522 (mtpp) REVERT: X 66 CYS cc_start: 0.8983 (m) cc_final: 0.8397 (m) REVERT: X 78 TYR cc_start: 0.9092 (t80) cc_final: 0.8670 (t80) REVERT: X 82 GLN cc_start: 0.8820 (mm-40) cc_final: 0.7915 (mp10) REVERT: Y 1 MET cc_start: 0.7096 (tpp) cc_final: 0.6814 (tpt) REVERT: Y 2 ASN cc_start: 0.8583 (m-40) cc_final: 0.8241 (m110) REVERT: Y 7 ASN cc_start: 0.8803 (m-40) cc_final: 0.8158 (m110) REVERT: Y 60 LYS cc_start: 0.9232 (mtmt) cc_final: 0.8157 (tmtt) REVERT: Z 2 ASN cc_start: 0.8639 (m-40) cc_final: 0.8230 (m110) REVERT: Z 44 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7913 (mm-30) REVERT: Z 60 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8699 (mttt) REVERT: Z 74 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8785 (ttpp) REVERT: Z 77 ASN cc_start: 0.9009 (t0) cc_final: 0.8337 (t0) REVERT: Z 78 TYR cc_start: 0.8886 (t80) cc_final: 0.8678 (t80) REVERT: Z 82 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8385 (mp10) REVERT: a 2 ASN cc_start: 0.8580 (m-40) cc_final: 0.8106 (m110) REVERT: a 5 LYS cc_start: 0.8902 (tttm) cc_final: 0.8628 (tptt) REVERT: a 9 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7649 (mmt-90) REVERT: a 34 ASN cc_start: 0.8304 (t0) cc_final: 0.7818 (t0) REVERT: a 60 LYS cc_start: 0.9125 (mtmt) cc_final: 0.7859 (tptm) REVERT: b 20 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9087 (mp) REVERT: b 39 ASN cc_start: 0.8476 (m110) cc_final: 0.7892 (m110) REVERT: b 74 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8958 (ptmm) REVERT: b 82 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8571 (mm110) REVERT: c 1 MET cc_start: 0.6895 (tpp) cc_final: 0.6513 (tpp) REVERT: c 26 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8229 (t70) REVERT: c 45 LYS cc_start: 0.8825 (pttt) cc_final: 0.8595 (pttt) REVERT: c 58 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9002 (tp) REVERT: c 68 LEU cc_start: 0.9451 (mt) cc_final: 0.9096 (mp) REVERT: c 74 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8651 (ttpp) REVERT: c 82 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8595 (mm110) REVERT: c 87 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7556 (mm-40) REVERT: d 26 ASP cc_start: 0.8618 (t70) cc_final: 0.8286 (t70) REVERT: d 34 ASN cc_start: 0.8069 (t0) cc_final: 0.7793 (t0) REVERT: d 39 ASN cc_start: 0.8784 (m-40) cc_final: 0.8524 (m110) REVERT: d 56 HIS cc_start: 0.8239 (m-70) cc_final: 0.7914 (m-70) REVERT: d 60 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8407 (mtpt) REVERT: d 78 TYR cc_start: 0.9117 (t80) cc_final: 0.8881 (t80) REVERT: d 83 ASP cc_start: 0.8699 (t70) cc_final: 0.8250 (t0) REVERT: e 13 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8694 (mm-40) REVERT: e 34 ASN cc_start: 0.8747 (t0) cc_final: 0.8342 (t0) REVERT: e 74 LYS cc_start: 0.9126 (tttt) cc_final: 0.8836 (ttpp) REVERT: e 77 ASN cc_start: 0.9313 (t0) cc_final: 0.8761 (t0) REVERT: e 78 TYR cc_start: 0.9043 (t80) cc_final: 0.8702 (t80) REVERT: e 82 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8270 (mp10) outliers start: 155 outliers final: 92 residues processed: 1748 average time/residue: 0.1694 time to fit residues: 445.0045 Evaluate side-chains 1703 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1601 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 15 MET Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 77 ASN B 31 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 77 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 67 ASN F 2 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 67 ASN H 2 ASN H 13 GLN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN I 22 GLN I 67 ASN I 77 ASN I 82 GLN J 56 HIS J 67 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 67 ASN Q 2 ASN Q 22 GLN R 31 ASN R 39 ASN T 82 GLN U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN X 67 ASN X 77 ASN Y 13 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 ASN Y 82 GLN b 22 GLN b 67 ASN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN d 82 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.082185 restraints weight = 38615.929| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.31 r_work: 0.2846 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23095 Z= 0.171 Angle : 0.634 8.372 31000 Z= 0.351 Chirality : 0.043 0.201 3472 Planarity : 0.005 0.106 3937 Dihedral : 3.909 14.272 2914 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.30 % Allowed : 25.57 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2728 helix: 0.85 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.72 (0.30), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 52 TYR 0.020 0.002 TYR F 78 PHE 0.033 0.001 PHE X 81 TRP 0.020 0.001 TRP E 30 HIS 0.004 0.001 HIS Z 56 Details of bonding type rmsd covalent geometry : bond 0.00424 (23095) covalent geometry : angle 0.63403 (31000) hydrogen bonds : bond 0.03798 ( 1643) hydrogen bonds : angle 4.47998 ( 4929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1636 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8953 (tttm) cc_final: 0.8685 (tmtt) REVERT: A 25 ASP cc_start: 0.8421 (m-30) cc_final: 0.8111 (m-30) REVERT: A 39 ASN cc_start: 0.8781 (m-40) cc_final: 0.8496 (m-40) REVERT: A 43 CYS cc_start: 0.8402 (p) cc_final: 0.8169 (p) REVERT: A 44 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 47 GLU cc_start: 0.7790 (tt0) cc_final: 0.7478 (tt0) REVERT: B 39 ASN cc_start: 0.8753 (m-40) cc_final: 0.8381 (m110) REVERT: B 57 MET cc_start: 0.8610 (mtp) cc_final: 0.8320 (mtp) REVERT: B 60 LYS cc_start: 0.8865 (mttp) cc_final: 0.8593 (mttp) REVERT: B 66 CYS cc_start: 0.8898 (m) cc_final: 0.8675 (t) REVERT: C 2 ASN cc_start: 0.8401 (m-40) cc_final: 0.7998 (m-40) REVERT: C 47 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 60 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8592 (mtpp) REVERT: C 82 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8305 (mm110) REVERT: D 13 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8715 (mm-40) REVERT: D 35 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7379 (tpp80) REVERT: D 39 ASN cc_start: 0.8352 (m110) cc_final: 0.7873 (m110) REVERT: D 45 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8157 (ttpt) REVERT: D 74 LYS cc_start: 0.9189 (tttt) cc_final: 0.8902 (ttpp) REVERT: E 1 MET cc_start: 0.6017 (tpt) cc_final: 0.5619 (tpt) REVERT: E 39 ASN cc_start: 0.8490 (m110) cc_final: 0.7755 (m110) REVERT: E 57 MET cc_start: 0.8688 (mtm) cc_final: 0.8384 (mtp) REVERT: E 60 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8575 (mtpp) REVERT: E 75 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8403 (tm-30) REVERT: E 78 TYR cc_start: 0.8989 (t80) cc_final: 0.8714 (t80) REVERT: F 1 MET cc_start: 0.6948 (tpp) cc_final: 0.6139 (tpt) REVERT: F 2 ASN cc_start: 0.8529 (m110) cc_final: 0.8252 (m110) REVERT: G 26 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: G 35 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7822 (ttp-110) REVERT: G 39 ASN cc_start: 0.8763 (m110) cc_final: 0.8292 (m110) REVERT: G 45 LYS cc_start: 0.8518 (pttt) cc_final: 0.8202 (pttt) REVERT: H 14 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7279 (mtp180) REVERT: H 35 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7608 (tpp80) REVERT: H 57 MET cc_start: 0.8704 (mtp) cc_final: 0.8471 (mtp) REVERT: H 60 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8366 (mtpt) REVERT: H 83 ASP cc_start: 0.8592 (t0) cc_final: 0.8374 (t0) REVERT: I 14 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7564 (mtp180) REVERT: I 36 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8100 (mm-30) REVERT: I 37 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8346 (mt-10) REVERT: I 57 MET cc_start: 0.8880 (mtp) cc_final: 0.8671 (mtp) REVERT: J 2 ASN cc_start: 0.8815 (m-40) cc_final: 0.8583 (m110) REVERT: J 25 ASP cc_start: 0.8861 (m-30) cc_final: 0.8643 (m-30) REVERT: J 39 ASN cc_start: 0.8622 (m110) cc_final: 0.8410 (m110) REVERT: J 87 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7611 (mm-40) REVERT: K 13 GLN cc_start: 0.8894 (mm110) cc_final: 0.8643 (mm110) REVERT: K 25 ASP cc_start: 0.8338 (m-30) cc_final: 0.7788 (m-30) REVERT: K 37 GLU cc_start: 0.8955 (mp0) cc_final: 0.7975 (mp0) REVERT: K 38 VAL cc_start: 0.9092 (t) cc_final: 0.8844 (m) REVERT: K 44 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8238 (mm-30) REVERT: K 48 GLN cc_start: 0.8338 (mp10) cc_final: 0.7995 (mp10) REVERT: K 60 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8307 (mtpp) REVERT: K 66 CYS cc_start: 0.8780 (m) cc_final: 0.8370 (m) REVERT: K 83 ASP cc_start: 0.8747 (t70) cc_final: 0.8248 (t0) REVERT: L 89 LEU cc_start: 0.7825 (tp) cc_final: 0.7607 (tp) REVERT: M 1 MET cc_start: 0.7261 (tpp) cc_final: 0.6952 (tpt) REVERT: M 35 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7655 (tpp-160) REVERT: M 39 ASN cc_start: 0.8387 (m110) cc_final: 0.7798 (m110) REVERT: M 48 GLN cc_start: 0.8828 (mp10) cc_final: 0.8594 (mp10) REVERT: M 56 HIS cc_start: 0.8291 (m-70) cc_final: 0.8053 (m-70) REVERT: M 58 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8859 (tp) REVERT: M 60 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8531 (mtpp) REVERT: M 78 TYR cc_start: 0.9040 (t80) cc_final: 0.8625 (t80) REVERT: N 1 MET cc_start: 0.7620 (tpp) cc_final: 0.7269 (tpt) REVERT: N 2 ASN cc_start: 0.8893 (m110) cc_final: 0.8617 (m-40) REVERT: N 60 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8493 (mttt) REVERT: N 89 LEU cc_start: 0.7473 (tp) cc_final: 0.7159 (tp) REVERT: O 39 ASN cc_start: 0.8690 (m110) cc_final: 0.8355 (m110) REVERT: O 44 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7816 (mm-30) REVERT: O 52 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.8042 (mtt-85) REVERT: P 1 MET cc_start: 0.6375 (tpp) cc_final: 0.6138 (tpp) REVERT: P 5 LYS cc_start: 0.9211 (tptm) cc_final: 0.8837 (tptm) REVERT: P 35 ARG cc_start: 0.8476 (ttm170) cc_final: 0.8206 (tpp80) REVERT: P 60 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8418 (mtpt) REVERT: P 66 CYS cc_start: 0.8920 (m) cc_final: 0.8528 (m) REVERT: P 67 ASN cc_start: 0.9060 (m-40) cc_final: 0.8593 (m-40) REVERT: P 82 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8092 (mp10) REVERT: Q 14 ARG cc_start: 0.8412 (mtp180) cc_final: 0.8159 (mtp180) REVERT: Q 15 MET cc_start: 0.8349 (ttm) cc_final: 0.8100 (ttp) REVERT: Q 60 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8460 (mtmm) REVERT: Q 89 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7172 (tt) REVERT: R 39 ASN cc_start: 0.8616 (m110) cc_final: 0.8323 (m110) REVERT: R 44 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7701 (mm-30) REVERT: R 52 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7703 (mtt-85) REVERT: R 60 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8765 (mttt) REVERT: S 1 MET cc_start: 0.6948 (tpp) cc_final: 0.6634 (tpt) REVERT: S 2 ASN cc_start: 0.8418 (m-40) cc_final: 0.7959 (m-40) REVERT: S 60 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8687 (mtpp) REVERT: S 66 CYS cc_start: 0.9064 (m) cc_final: 0.8721 (m) REVERT: T 1 MET cc_start: 0.6993 (tpp) cc_final: 0.6690 (tpt) REVERT: T 39 ASN cc_start: 0.8363 (m110) cc_final: 0.7754 (m110) REVERT: T 45 LYS cc_start: 0.8382 (tttm) cc_final: 0.7975 (tttm) REVERT: U 2 ASN cc_start: 0.8880 (m110) cc_final: 0.8572 (m-40) REVERT: U 35 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7313 (ttp-110) REVERT: U 37 GLU cc_start: 0.9184 (pm20) cc_final: 0.8838 (pm20) REVERT: U 39 ASN cc_start: 0.8514 (m110) cc_final: 0.7651 (m110) REVERT: U 44 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8191 (mm-30) REVERT: U 49 ASP cc_start: 0.8705 (m-30) cc_final: 0.8262 (m-30) REVERT: V 3 PHE cc_start: 0.9171 (t80) cc_final: 0.8965 (t80) REVERT: V 39 ASN cc_start: 0.8672 (m-40) cc_final: 0.8215 (m110) REVERT: V 47 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: V 66 CYS cc_start: 0.8902 (m) cc_final: 0.8550 (m) REVERT: W 60 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8736 (mtmm) REVERT: W 66 CYS cc_start: 0.9100 (t) cc_final: 0.8787 (t) REVERT: X 14 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6547 (tpt170) REVERT: X 17 MET cc_start: 0.8539 (tpp) cc_final: 0.8311 (tpp) REVERT: X 21 LYS cc_start: 0.9347 (mttp) cc_final: 0.8836 (mttp) REVERT: X 22 GLN cc_start: 0.8834 (mt0) cc_final: 0.8598 (mt0) REVERT: X 25 ASP cc_start: 0.8400 (m-30) cc_final: 0.8105 (m-30) REVERT: X 60 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8619 (mtpt) REVERT: X 66 CYS cc_start: 0.8971 (m) cc_final: 0.8419 (m) REVERT: X 78 TYR cc_start: 0.9171 (t80) cc_final: 0.8701 (t80) REVERT: X 82 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8242 (mp10) REVERT: Y 7 ASN cc_start: 0.8869 (m-40) cc_final: 0.8271 (m-40) REVERT: Y 60 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8124 (tmtt) REVERT: Y 74 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8894 (ttmm) REVERT: Y 78 TYR cc_start: 0.9115 (t80) cc_final: 0.8823 (t80) REVERT: Y 82 GLN cc_start: 0.8770 (mm-40) cc_final: 0.7981 (mp10) REVERT: Y 87 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7438 (mm-40) REVERT: Z 44 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8023 (mm-30) REVERT: Z 74 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8797 (ttpp) REVERT: a 5 LYS cc_start: 0.8859 (tttm) cc_final: 0.8573 (tptt) REVERT: a 9 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7644 (mmt-90) REVERT: a 60 LYS cc_start: 0.9120 (mtmt) cc_final: 0.7707 (tptm) REVERT: b 20 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9080 (mp) REVERT: b 39 ASN cc_start: 0.8586 (m110) cc_final: 0.7994 (m110) REVERT: b 74 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8946 (ptmm) REVERT: c 1 MET cc_start: 0.6981 (tpp) cc_final: 0.6585 (tpt) REVERT: c 37 GLU cc_start: 0.9131 (mp0) cc_final: 0.8772 (mp0) REVERT: c 58 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9008 (tp) REVERT: c 74 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8668 (ttpp) REVERT: c 87 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7599 (mm-40) REVERT: d 13 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8620 (mm110) REVERT: d 26 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8325 (t70) REVERT: d 39 ASN cc_start: 0.8860 (m-40) cc_final: 0.8525 (m110) REVERT: d 56 HIS cc_start: 0.8338 (m-70) cc_final: 0.7878 (m-70) REVERT: d 58 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9273 (tp) REVERT: d 83 ASP cc_start: 0.8718 (t70) cc_final: 0.8219 (t0) REVERT: e 13 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8680 (mm-40) REVERT: e 34 ASN cc_start: 0.8754 (t0) cc_final: 0.8355 (t0) REVERT: e 74 LYS cc_start: 0.9119 (tttt) cc_final: 0.8859 (ttpp) REVERT: e 82 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8707 (mm110) outliers start: 162 outliers final: 114 residues processed: 1687 average time/residue: 0.1718 time to fit residues: 435.6352 Evaluate side-chains 1708 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1584 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 71 LYS Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 2 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 82 GLN G 67 ASN H 2 ASN H 13 GLN H 82 GLN I 67 ASN J 22 GLN J 67 ASN L 31 ASN L 82 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 67 ASN Q 2 ASN Q 22 GLN R 31 ASN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN Y 2 ASN Y 13 GLN Y 67 ASN Z 2 ASN Z 82 GLN a 2 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 GLN b 67 ASN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 GLN d 67 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082933 restraints weight = 39057.644| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.39 r_work: 0.2845 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23095 Z= 0.163 Angle : 0.642 7.082 31000 Z= 0.358 Chirality : 0.043 0.206 3472 Planarity : 0.005 0.084 3937 Dihedral : 3.934 14.998 2914 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.68 % Allowed : 26.74 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2728 helix: 0.76 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.78 (0.29), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 52 TYR 0.014 0.002 TYR C 78 PHE 0.017 0.001 PHE a 3 TRP 0.014 0.001 TRP E 30 HIS 0.004 0.001 HIS P 56 Details of bonding type rmsd covalent geometry : bond 0.00407 (23095) covalent geometry : angle 0.64189 (31000) hydrogen bonds : bond 0.03735 ( 1643) hydrogen bonds : angle 4.51853 ( 4929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1806 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1634 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.9103 (mp0) cc_final: 0.8570 (mp0) REVERT: A 39 ASN cc_start: 0.8829 (m-40) cc_final: 0.8343 (m-40) REVERT: A 43 CYS cc_start: 0.8344 (p) cc_final: 0.7896 (p) REVERT: A 44 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 47 GLU cc_start: 0.7766 (tt0) cc_final: 0.7406 (tt0) REVERT: A 74 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8883 (mtpp) REVERT: A 87 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7747 (mp10) REVERT: B 35 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7575 (tpp-160) REVERT: B 39 ASN cc_start: 0.8734 (m-40) cc_final: 0.8360 (m110) REVERT: B 60 LYS cc_start: 0.8906 (mttp) cc_final: 0.8630 (mttp) REVERT: B 66 CYS cc_start: 0.8892 (m) cc_final: 0.8668 (t) REVERT: C 47 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: C 60 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8588 (mtpp) REVERT: C 82 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8425 (mm110) REVERT: D 13 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8652 (mm-40) REVERT: D 39 ASN cc_start: 0.8273 (m110) cc_final: 0.7933 (t0) REVERT: D 45 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8192 (ttpt) REVERT: D 74 LYS cc_start: 0.9165 (tttt) cc_final: 0.8902 (ttpp) REVERT: E 39 ASN cc_start: 0.8506 (m110) cc_final: 0.7786 (m110) REVERT: E 57 MET cc_start: 0.8603 (mtm) cc_final: 0.8294 (mtp) REVERT: E 60 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8581 (mtpp) REVERT: E 75 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 78 TYR cc_start: 0.9026 (t80) cc_final: 0.8659 (t80) REVERT: F 1 MET cc_start: 0.7059 (tpp) cc_final: 0.6289 (tpt) REVERT: F 2 ASN cc_start: 0.8582 (m110) cc_final: 0.8323 (m110) REVERT: F 82 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8529 (mm110) REVERT: G 26 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: G 36 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: G 39 ASN cc_start: 0.8761 (m110) cc_final: 0.8512 (m110) REVERT: H 14 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7426 (mtp180) REVERT: H 35 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7308 (tpp80) REVERT: H 60 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8513 (mtpt) REVERT: H 67 ASN cc_start: 0.8880 (m-40) cc_final: 0.8619 (m110) REVERT: H 74 LYS cc_start: 0.9249 (ttpp) cc_final: 0.8919 (ttmm) REVERT: H 83 ASP cc_start: 0.8615 (t0) cc_final: 0.8274 (t0) REVERT: I 14 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7614 (mtp180) REVERT: I 36 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7874 (mm-30) REVERT: I 37 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8490 (mt-10) REVERT: I 57 MET cc_start: 0.8777 (mtp) cc_final: 0.8475 (mtp) REVERT: I 66 CYS cc_start: 0.9002 (t) cc_final: 0.8504 (m) REVERT: J 39 ASN cc_start: 0.8533 (m110) cc_final: 0.8295 (m110) REVERT: J 87 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7678 (mm-40) REVERT: K 13 GLN cc_start: 0.8886 (mm110) cc_final: 0.8664 (mm110) REVERT: K 25 ASP cc_start: 0.8305 (m-30) cc_final: 0.7786 (m-30) REVERT: K 48 GLN cc_start: 0.8254 (mp10) cc_final: 0.7861 (mp10) REVERT: K 56 HIS cc_start: 0.8548 (m-70) cc_final: 0.8232 (m-70) REVERT: K 60 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8344 (mtpp) REVERT: K 66 CYS cc_start: 0.8825 (m) cc_final: 0.8430 (m) REVERT: K 83 ASP cc_start: 0.8776 (t70) cc_final: 0.8251 (t0) REVERT: L 74 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8872 (ttmm) REVERT: L 78 TYR cc_start: 0.9110 (t80) cc_final: 0.8843 (t80) REVERT: L 89 LEU cc_start: 0.8072 (tp) cc_final: 0.7779 (tp) REVERT: M 35 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7289 (tpp-160) REVERT: M 39 ASN cc_start: 0.8476 (m110) cc_final: 0.7642 (m110) REVERT: M 58 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8861 (tp) REVERT: N 1 MET cc_start: 0.7686 (tpp) cc_final: 0.7247 (tpt) REVERT: N 60 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8490 (mttt) REVERT: N 89 LEU cc_start: 0.7449 (tp) cc_final: 0.7214 (tp) REVERT: O 1 MET cc_start: 0.7137 (tpp) cc_final: 0.6758 (tpt) REVERT: O 26 ASP cc_start: 0.9086 (t0) cc_final: 0.8886 (t70) REVERT: O 35 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7277 (tpp80) REVERT: O 39 ASN cc_start: 0.8704 (m110) cc_final: 0.7918 (m110) REVERT: O 43 CYS cc_start: 0.8167 (p) cc_final: 0.7928 (p) REVERT: O 44 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7826 (mm-30) REVERT: O 60 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8888 (mttt) REVERT: P 5 LYS cc_start: 0.9186 (tptm) cc_final: 0.8810 (tptm) REVERT: P 60 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8492 (mtpt) REVERT: P 66 CYS cc_start: 0.8919 (m) cc_final: 0.8512 (m) REVERT: P 67 ASN cc_start: 0.9115 (m-40) cc_final: 0.8789 (m-40) REVERT: Q 5 LYS cc_start: 0.8826 (tptm) cc_final: 0.8546 (tptm) REVERT: Q 14 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8239 (mtp180) REVERT: Q 15 MET cc_start: 0.8360 (ttm) cc_final: 0.8122 (ttp) REVERT: Q 60 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8548 (mtmm) REVERT: Q 66 CYS cc_start: 0.8914 (m) cc_final: 0.8486 (m) REVERT: Q 89 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7203 (tt) REVERT: R 39 ASN cc_start: 0.8578 (m110) cc_final: 0.8158 (t0) REVERT: R 44 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7640 (mm-30) REVERT: R 52 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7821 (mtt-85) REVERT: R 60 LYS cc_start: 0.9054 (mtmt) cc_final: 0.8789 (mttt) REVERT: S 1 MET cc_start: 0.6894 (tpp) cc_final: 0.6598 (tpt) REVERT: S 2 ASN cc_start: 0.8358 (m-40) cc_final: 0.7957 (m-40) REVERT: S 60 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8751 (mtpp) REVERT: S 66 CYS cc_start: 0.9040 (m) cc_final: 0.8746 (m) REVERT: T 2 ASN cc_start: 0.8619 (m-40) cc_final: 0.8122 (t0) REVERT: T 37 GLU cc_start: 0.8781 (pm20) cc_final: 0.8562 (pm20) REVERT: T 39 ASN cc_start: 0.8419 (m110) cc_final: 0.7719 (m110) REVERT: T 45 LYS cc_start: 0.8288 (tttm) cc_final: 0.7879 (tttm) REVERT: U 35 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7173 (ttp-110) REVERT: U 39 ASN cc_start: 0.8401 (m110) cc_final: 0.7873 (m110) REVERT: U 44 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8098 (mm-30) REVERT: U 47 GLU cc_start: 0.7754 (tt0) cc_final: 0.7483 (tt0) REVERT: U 49 ASP cc_start: 0.8501 (m-30) cc_final: 0.8071 (m-30) REVERT: U 67 ASN cc_start: 0.9091 (m-40) cc_final: 0.8885 (m110) REVERT: U 74 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8787 (ttpp) REVERT: V 34 ASN cc_start: 0.8393 (t0) cc_final: 0.8187 (t0) REVERT: V 39 ASN cc_start: 0.8739 (m-40) cc_final: 0.8256 (m110) REVERT: V 48 GLN cc_start: 0.8875 (mp10) cc_final: 0.8662 (mp10) REVERT: V 60 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8794 (mtpt) REVERT: V 66 CYS cc_start: 0.9032 (m) cc_final: 0.8647 (m) REVERT: V 87 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7914 (mp10) REVERT: W 60 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8677 (mtmm) REVERT: X 14 ARG cc_start: 0.8247 (mtt180) cc_final: 0.6639 (tpt170) REVERT: X 17 MET cc_start: 0.8554 (tpp) cc_final: 0.8346 (tpp) REVERT: X 21 LYS cc_start: 0.9382 (mttp) cc_final: 0.8846 (mttp) REVERT: X 22 GLN cc_start: 0.8819 (mt0) cc_final: 0.8586 (mt0) REVERT: X 35 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7128 (tpp80) REVERT: X 60 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8557 (mtpt) REVERT: X 66 CYS cc_start: 0.8931 (m) cc_final: 0.8316 (m) REVERT: X 78 TYR cc_start: 0.9154 (t80) cc_final: 0.8533 (t80) REVERT: X 82 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8227 (mp10) REVERT: Y 7 ASN cc_start: 0.8758 (m-40) cc_final: 0.8150 (m-40) REVERT: Y 60 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8184 (tmtt) REVERT: Y 74 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8921 (ttmm) REVERT: Y 87 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7552 (mm-40) REVERT: Z 44 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7940 (mm-30) REVERT: Z 74 LYS cc_start: 0.9053 (ttpt) cc_final: 0.8785 (ttpp) REVERT: a 5 LYS cc_start: 0.8852 (tttm) cc_final: 0.8588 (tptt) REVERT: a 9 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7729 (mmt-90) REVERT: a 60 LYS cc_start: 0.9102 (mtmt) cc_final: 0.7703 (tptm) REVERT: b 20 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9140 (mp) REVERT: b 39 ASN cc_start: 0.8566 (m110) cc_final: 0.7980 (m110) REVERT: b 74 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8945 (ptmm) REVERT: b 78 TYR cc_start: 0.9190 (t80) cc_final: 0.8783 (t80) REVERT: c 9 ARG cc_start: 0.5379 (mmt-90) cc_final: 0.4748 (mtt-85) REVERT: c 35 ARG cc_start: 0.7724 (tpt170) cc_final: 0.7450 (tpp80) REVERT: c 37 GLU cc_start: 0.9086 (mp0) cc_final: 0.8797 (mp0) REVERT: c 58 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9019 (tp) REVERT: c 61 LYS cc_start: 0.6847 (mttm) cc_final: 0.6474 (mttm) REVERT: c 74 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8644 (ttpp) REVERT: c 87 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7517 (mm-40) REVERT: d 13 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8507 (mm110) REVERT: d 26 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8276 (t0) REVERT: d 39 ASN cc_start: 0.8756 (m-40) cc_final: 0.8508 (m-40) REVERT: d 56 HIS cc_start: 0.8157 (m-70) cc_final: 0.7340 (m-70) REVERT: d 83 ASP cc_start: 0.8692 (t70) cc_final: 0.8464 (t70) REVERT: e 13 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8730 (mm-40) REVERT: e 34 ASN cc_start: 0.8661 (t0) cc_final: 0.8399 (t0) REVERT: e 67 ASN cc_start: 0.9004 (m-40) cc_final: 0.8797 (m110) REVERT: e 74 LYS cc_start: 0.9112 (tttt) cc_final: 0.8852 (ttpp) REVERT: e 87 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8407 (mm-40) outliers start: 172 outliers final: 129 residues processed: 1692 average time/residue: 0.1656 time to fit residues: 422.2106 Evaluate side-chains 1721 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1582 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 71 LYS Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 13 GLN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 55 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 109 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 13 GLN B 2 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN E 67 ASN E 82 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 39 ASN G 67 ASN H 2 ASN H 13 GLN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 2 ASN J 13 GLN J 67 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 82 GLN M 82 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 13 GLN O 67 ASN P 82 GLN Q 2 ASN Q 67 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 ASN W 67 ASN X 67 ASN Y 2 ASN Y 67 ASN Y 82 GLN Z 2 ASN Z 13 GLN a 2 ASN b 67 ASN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.081392 restraints weight = 38178.912| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.30 r_work: 0.2830 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23095 Z= 0.195 Angle : 0.684 7.092 31000 Z= 0.380 Chirality : 0.045 0.224 3472 Planarity : 0.005 0.081 3937 Dihedral : 3.992 14.209 2914 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.76 % Allowed : 27.63 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2728 helix: 0.64 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 9 TYR 0.018 0.002 TYR N 78 PHE 0.016 0.001 PHE K 3 TRP 0.018 0.001 TRP E 30 HIS 0.006 0.001 HIS Z 56 Details of bonding type rmsd covalent geometry : bond 0.00491 (23095) covalent geometry : angle 0.68449 (31000) hydrogen bonds : bond 0.03951 ( 1643) hydrogen bonds : angle 4.53929 ( 4929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1789 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1615 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8079 (t0) cc_final: 0.7811 (t0) REVERT: A 39 ASN cc_start: 0.8814 (m-40) cc_final: 0.8574 (m-40) REVERT: A 43 CYS cc_start: 0.8355 (p) cc_final: 0.7992 (p) REVERT: A 44 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 47 GLU cc_start: 0.7880 (tt0) cc_final: 0.7474 (tt0) REVERT: A 87 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7749 (mp10) REVERT: B 35 ARG cc_start: 0.7888 (tpp-160) cc_final: 0.7615 (tpp-160) REVERT: B 37 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 39 ASN cc_start: 0.8585 (m-40) cc_final: 0.8316 (m110) REVERT: B 60 LYS cc_start: 0.8971 (mttp) cc_final: 0.8708 (mttp) REVERT: B 66 CYS cc_start: 0.8871 (m) cc_final: 0.8634 (t) REVERT: C 1 MET cc_start: 0.6612 (tpt) cc_final: 0.6038 (tpt) REVERT: C 9 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8067 (mmm-85) REVERT: C 31 ASN cc_start: 0.9071 (m-40) cc_final: 0.8776 (m-40) REVERT: C 37 GLU cc_start: 0.8900 (pm20) cc_final: 0.8576 (mp0) REVERT: C 47 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: C 60 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8630 (mtpp) REVERT: C 82 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8455 (mm110) REVERT: D 13 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8696 (mm-40) REVERT: D 35 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7609 (tpp80) REVERT: D 37 GLU cc_start: 0.8989 (pm20) cc_final: 0.8787 (pm20) REVERT: D 39 ASN cc_start: 0.8498 (m110) cc_final: 0.8141 (m110) REVERT: D 74 LYS cc_start: 0.9193 (tttt) cc_final: 0.8880 (ttpp) REVERT: D 78 TYR cc_start: 0.8935 (t80) cc_final: 0.8578 (t80) REVERT: E 39 ASN cc_start: 0.8567 (m110) cc_final: 0.7858 (m110) REVERT: E 57 MET cc_start: 0.8515 (mtm) cc_final: 0.8274 (mtp) REVERT: E 60 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8564 (mtpp) REVERT: E 75 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8311 (tm-30) REVERT: E 78 TYR cc_start: 0.9012 (t80) cc_final: 0.8664 (t80) REVERT: F 1 MET cc_start: 0.7106 (tpp) cc_final: 0.6633 (tpt) REVERT: F 3 PHE cc_start: 0.9172 (t80) cc_final: 0.8959 (t80) REVERT: F 17 MET cc_start: 0.8479 (tpt) cc_final: 0.8238 (ttt) REVERT: F 82 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8503 (mm110) REVERT: G 5 LYS cc_start: 0.8857 (tttt) cc_final: 0.8636 (tttt) REVERT: G 26 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: G 36 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: G 39 ASN cc_start: 0.8753 (m-40) cc_final: 0.8524 (m-40) REVERT: H 14 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7502 (mtp180) REVERT: H 35 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7272 (tpp80) REVERT: H 60 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8553 (mtpt) REVERT: H 67 ASN cc_start: 0.8883 (m-40) cc_final: 0.8595 (m110) REVERT: I 14 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7536 (mtp180) REVERT: I 36 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7786 (mm-30) REVERT: I 37 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8446 (mt-10) REVERT: I 57 MET cc_start: 0.8732 (mtp) cc_final: 0.8486 (mtp) REVERT: I 66 CYS cc_start: 0.9012 (t) cc_final: 0.8564 (m) REVERT: J 36 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: J 39 ASN cc_start: 0.8457 (m110) cc_final: 0.7759 (m-40) REVERT: K 12 ILE cc_start: 0.9535 (mt) cc_final: 0.9324 (mt) REVERT: K 25 ASP cc_start: 0.8343 (m-30) cc_final: 0.7967 (m-30) REVERT: K 38 VAL cc_start: 0.9121 (t) cc_final: 0.8878 (m) REVERT: K 48 GLN cc_start: 0.8436 (mp10) cc_final: 0.7898 (mp10) REVERT: K 60 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8296 (mtpp) REVERT: K 66 CYS cc_start: 0.8819 (m) cc_final: 0.8384 (m) REVERT: K 83 ASP cc_start: 0.8708 (t70) cc_final: 0.8150 (t0) REVERT: L 39 ASN cc_start: 0.8616 (m110) cc_final: 0.8088 (t0) REVERT: L 78 TYR cc_start: 0.9095 (t80) cc_final: 0.8890 (t80) REVERT: L 89 LEU cc_start: 0.8092 (tp) cc_final: 0.7813 (tp) REVERT: M 36 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: M 39 ASN cc_start: 0.8513 (m110) cc_final: 0.8042 (t0) REVERT: M 58 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.8882 (tp) REVERT: M 75 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8767 (tm-30) REVERT: N 60 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8487 (mttt) REVERT: N 89 LEU cc_start: 0.7383 (tp) cc_final: 0.7051 (tp) REVERT: O 35 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7276 (tpp80) REVERT: O 39 ASN cc_start: 0.8595 (m110) cc_final: 0.7779 (m110) REVERT: O 44 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8004 (mm-30) REVERT: O 60 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8960 (mttt) REVERT: P 5 LYS cc_start: 0.9191 (tptm) cc_final: 0.8897 (tptm) REVERT: P 35 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8390 (tpp80) REVERT: P 37 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: P 60 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8544 (mtpt) REVERT: P 66 CYS cc_start: 0.8914 (m) cc_final: 0.8451 (m) REVERT: P 67 ASN cc_start: 0.9141 (m-40) cc_final: 0.8776 (m-40) REVERT: Q 5 LYS cc_start: 0.8999 (tptm) cc_final: 0.8704 (tptm) REVERT: Q 14 ARG cc_start: 0.8595 (mtp180) cc_final: 0.8256 (mtp180) REVERT: Q 15 MET cc_start: 0.8377 (ttm) cc_final: 0.8166 (ttp) REVERT: Q 60 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8542 (mtmm) REVERT: Q 66 CYS cc_start: 0.8905 (m) cc_final: 0.8432 (m) REVERT: Q 89 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7223 (tt) REVERT: R 35 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.7941 (tpp80) REVERT: R 60 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8777 (mttt) REVERT: S 2 ASN cc_start: 0.8232 (m-40) cc_final: 0.7991 (m-40) REVERT: S 37 GLU cc_start: 0.9067 (pm20) cc_final: 0.8865 (pm20) REVERT: S 44 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8242 (mm-30) REVERT: S 60 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8715 (mtpp) REVERT: S 66 CYS cc_start: 0.9029 (m) cc_final: 0.8679 (m) REVERT: T 39 ASN cc_start: 0.8423 (m110) cc_final: 0.7718 (m110) REVERT: T 45 LYS cc_start: 0.8347 (tttm) cc_final: 0.7906 (tttm) REVERT: T 74 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8911 (ttpp) REVERT: U 25 ASP cc_start: 0.8221 (m-30) cc_final: 0.7995 (m-30) REVERT: U 35 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7231 (ttp-110) REVERT: U 37 GLU cc_start: 0.9186 (pm20) cc_final: 0.8923 (pm20) REVERT: U 39 ASN cc_start: 0.8436 (m110) cc_final: 0.7861 (m110) REVERT: U 44 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8236 (mm-30) REVERT: U 49 ASP cc_start: 0.8675 (m-30) cc_final: 0.8198 (m-30) REVERT: U 74 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8803 (ttpp) REVERT: V 39 ASN cc_start: 0.8724 (m-40) cc_final: 0.8279 (m110) REVERT: V 60 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8716 (mtpt) REVERT: V 66 CYS cc_start: 0.9016 (m) cc_final: 0.8591 (m) REVERT: V 87 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7938 (mp10) REVERT: W 4 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8610 (pt) REVERT: W 60 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8623 (mtmm) REVERT: X 14 ARG cc_start: 0.8245 (mtt180) cc_final: 0.6630 (tpt170) REVERT: X 17 MET cc_start: 0.8591 (tpp) cc_final: 0.8319 (tpp) REVERT: X 60 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8546 (mtpt) REVERT: X 66 CYS cc_start: 0.8969 (m) cc_final: 0.8360 (m) REVERT: X 78 TYR cc_start: 0.9210 (t80) cc_final: 0.8565 (t80) REVERT: X 82 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8288 (mp10) REVERT: Y 60 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8013 (tptt) REVERT: Y 83 ASP cc_start: 0.8582 (t0) cc_final: 0.8328 (t0) REVERT: Y 87 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7721 (mm-40) REVERT: Z 44 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8097 (mm-30) REVERT: Z 74 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8855 (ttpp) REVERT: Z 82 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8378 (mp10) REVERT: a 5 LYS cc_start: 0.8864 (tttm) cc_final: 0.8566 (tptt) REVERT: a 9 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7695 (mmt-90) REVERT: a 60 LYS cc_start: 0.9085 (mtmt) cc_final: 0.7653 (tptm) REVERT: b 20 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9093 (mp) REVERT: b 26 ASP cc_start: 0.8130 (t70) cc_final: 0.7810 (t0) REVERT: b 39 ASN cc_start: 0.8520 (m110) cc_final: 0.7917 (m110) REVERT: b 74 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8937 (ptmm) REVERT: b 78 TYR cc_start: 0.9329 (t80) cc_final: 0.9023 (t80) REVERT: c 6 ASP cc_start: 0.8506 (m-30) cc_final: 0.7847 (p0) REVERT: c 9 ARG cc_start: 0.5443 (mmt-90) cc_final: 0.4838 (mtt-85) REVERT: c 35 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7492 (tpp80) REVERT: c 58 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9038 (tp) REVERT: c 61 LYS cc_start: 0.6676 (mttm) cc_final: 0.6297 (mttm) REVERT: c 87 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7654 (mm-40) REVERT: d 13 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8558 (mm-40) REVERT: d 26 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8382 (t70) REVERT: d 39 ASN cc_start: 0.8837 (m-40) cc_final: 0.8507 (m110) REVERT: d 56 HIS cc_start: 0.8198 (m-70) cc_final: 0.7863 (m-70) REVERT: d 83 ASP cc_start: 0.8647 (t70) cc_final: 0.8012 (t0) REVERT: e 13 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8675 (mm-40) REVERT: e 34 ASN cc_start: 0.8806 (t0) cc_final: 0.8528 (t0) REVERT: e 67 ASN cc_start: 0.9016 (m-40) cc_final: 0.8807 (m110) REVERT: e 74 LYS cc_start: 0.9199 (tttt) cc_final: 0.8898 (ttpp) REVERT: e 87 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8423 (mp10) outliers start: 174 outliers final: 140 residues processed: 1670 average time/residue: 0.1664 time to fit residues: 418.7045 Evaluate side-chains 1735 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1581 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 71 LYS Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 15 MET Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 55 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 71 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 31 ASN E 82 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 67 ASN H 2 ASN H 13 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 2 ASN J 13 GLN J 67 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN Q 67 ASN Q 77 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN X 67 ASN Y 2 ASN Y 67 ASN Z 2 ASN a 2 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN d 82 GLN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084758 restraints weight = 38233.297| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.31 r_work: 0.2885 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23095 Z= 0.159 Angle : 0.689 9.654 31000 Z= 0.382 Chirality : 0.044 0.231 3472 Planarity : 0.005 0.079 3937 Dihedral : 4.042 13.452 2914 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.99 % Allowed : 29.42 % Favored : 64.59 % 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: 0.32 (0.16), residues: 2728 helix: 0.57 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.99 (0.27), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 9 TYR 0.014 0.002 TYR L 78 PHE 0.025 0.001 PHE C 3 TRP 0.020 0.001 TRP E 30 HIS 0.003 0.001 HIS O 56 Details of bonding type rmsd covalent geometry : bond 0.00396 (23095) covalent geometry : angle 0.68875 (31000) hydrogen bonds : bond 0.03781 ( 1643) hydrogen bonds : angle 4.66328 ( 4929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1800 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1646 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8706 (m-40) cc_final: 0.8284 (m-40) REVERT: A 43 CYS cc_start: 0.8278 (p) cc_final: 0.7868 (p) REVERT: A 44 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 47 GLU cc_start: 0.7684 (tt0) cc_final: 0.7327 (tt0) REVERT: A 71 LYS cc_start: 0.9383 (ttmt) cc_final: 0.8910 (ttpp) REVERT: A 87 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7787 (mp10) REVERT: B 35 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7613 (tpp-160) REVERT: B 39 ASN cc_start: 0.8569 (m-40) cc_final: 0.8078 (m110) REVERT: B 60 LYS cc_start: 0.8953 (mttp) cc_final: 0.8714 (mttp) REVERT: B 66 CYS cc_start: 0.8889 (m) cc_final: 0.8682 (t) REVERT: C 1 MET cc_start: 0.6775 (tpt) cc_final: 0.6328 (tpt) REVERT: C 31 ASN cc_start: 0.9007 (m-40) cc_final: 0.8703 (m-40) REVERT: C 34 ASN cc_start: 0.8060 (t0) cc_final: 0.7661 (t0) REVERT: C 37 GLU cc_start: 0.9004 (pm20) cc_final: 0.8680 (mp0) REVERT: C 60 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8649 (mttt) REVERT: C 71 LYS cc_start: 0.9374 (ttmm) cc_final: 0.9170 (ptmt) REVERT: C 82 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8528 (mm-40) REVERT: D 13 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8680 (mm-40) REVERT: D 35 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7729 (tpp-160) REVERT: D 37 GLU cc_start: 0.8989 (pm20) cc_final: 0.8744 (pm20) REVERT: D 39 ASN cc_start: 0.8361 (m110) cc_final: 0.7860 (m110) REVERT: D 74 LYS cc_start: 0.9169 (tttt) cc_final: 0.8851 (ttpp) REVERT: D 78 TYR cc_start: 0.8902 (t80) cc_final: 0.8615 (t80) REVERT: D 87 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8714 (mm-40) REVERT: E 9 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8479 (mtp-110) REVERT: E 39 ASN cc_start: 0.8493 (m110) cc_final: 0.7779 (m110) REVERT: E 57 MET cc_start: 0.8460 (mtm) cc_final: 0.8117 (mtp) REVERT: E 60 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8554 (mtpp) REVERT: E 78 TYR cc_start: 0.8956 (t80) cc_final: 0.8663 (t80) REVERT: F 1 MET cc_start: 0.7164 (tpp) cc_final: 0.6886 (tpt) REVERT: F 17 MET cc_start: 0.8407 (tpt) cc_final: 0.8179 (ttt) REVERT: F 82 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8478 (mm110) REVERT: G 26 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: G 35 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7557 (ttm110) REVERT: G 36 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: G 39 ASN cc_start: 0.8636 (m-40) cc_final: 0.8405 (m110) REVERT: H 14 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7996 (mtp-110) REVERT: H 35 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7441 (tpp80) REVERT: H 44 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8048 (mm-30) REVERT: H 45 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7766 (tttm) REVERT: H 60 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8479 (mtpt) REVERT: H 67 ASN cc_start: 0.8867 (m-40) cc_final: 0.8590 (m-40) REVERT: H 78 TYR cc_start: 0.9076 (t80) cc_final: 0.8741 (t80) REVERT: I 14 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7652 (mtp180) REVERT: I 36 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8028 (mm-30) REVERT: I 37 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8174 (mt-10) REVERT: I 57 MET cc_start: 0.8795 (mtp) cc_final: 0.8514 (mtp) REVERT: I 66 CYS cc_start: 0.9040 (t) cc_final: 0.8553 (m) REVERT: J 39 ASN cc_start: 0.8353 (m110) cc_final: 0.7703 (m-40) REVERT: J 77 ASN cc_start: 0.9247 (t0) cc_final: 0.8613 (t0) REVERT: J 87 GLN cc_start: 0.7718 (mm110) cc_final: 0.7478 (mp10) REVERT: K 12 ILE cc_start: 0.9545 (mt) cc_final: 0.9307 (mt) REVERT: K 25 ASP cc_start: 0.8331 (m-30) cc_final: 0.7443 (m-30) REVERT: K 38 VAL cc_start: 0.9134 (t) cc_final: 0.8840 (m) REVERT: K 48 GLN cc_start: 0.8466 (mp10) cc_final: 0.7895 (mp10) REVERT: K 60 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8371 (mtpp) REVERT: K 66 CYS cc_start: 0.8861 (m) cc_final: 0.8414 (m) REVERT: K 83 ASP cc_start: 0.8851 (t70) cc_final: 0.8166 (t0) REVERT: L 77 ASN cc_start: 0.9133 (t0) cc_final: 0.8819 (t0) REVERT: L 78 TYR cc_start: 0.9024 (t80) cc_final: 0.8760 (t80) REVERT: L 82 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8607 (mp10) REVERT: M 35 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7937 (tpp-160) REVERT: M 39 ASN cc_start: 0.8516 (m110) cc_final: 0.7845 (m110) REVERT: M 58 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8825 (tp) REVERT: M 71 LYS cc_start: 0.9242 (ttmm) cc_final: 0.9010 (ptmt) REVERT: M 75 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8774 (tm-30) REVERT: M 78 TYR cc_start: 0.8818 (t80) cc_final: 0.8484 (t80) REVERT: N 60 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8494 (mttt) REVERT: N 89 LEU cc_start: 0.7410 (tp) cc_final: 0.7016 (tp) REVERT: O 1 MET cc_start: 0.6768 (tpt) cc_final: 0.6161 (tpt) REVERT: O 35 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7314 (tpp80) REVERT: O 44 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7953 (mm-30) REVERT: O 60 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8899 (mttt) REVERT: P 5 LYS cc_start: 0.9228 (tptm) cc_final: 0.8927 (tptm) REVERT: P 35 ARG cc_start: 0.8669 (ttm170) cc_final: 0.8307 (tpp80) REVERT: P 47 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: P 60 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8592 (mtpt) REVERT: P 67 ASN cc_start: 0.9085 (m-40) cc_final: 0.8761 (m-40) REVERT: P 82 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8312 (mp10) REVERT: Q 5 LYS cc_start: 0.8770 (tptm) cc_final: 0.8535 (tptm) REVERT: Q 14 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8258 (mtp180) REVERT: Q 15 MET cc_start: 0.8433 (ttm) cc_final: 0.8232 (ttp) REVERT: Q 52 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7918 (mtt-85) REVERT: Q 60 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8548 (mtmm) REVERT: Q 66 CYS cc_start: 0.8912 (m) cc_final: 0.8425 (m) REVERT: Q 89 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7320 (tt) REVERT: R 35 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7809 (tpp80) REVERT: R 60 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8746 (mttt) REVERT: S 2 ASN cc_start: 0.8247 (m-40) cc_final: 0.7971 (m-40) REVERT: S 37 GLU cc_start: 0.8980 (pm20) cc_final: 0.8670 (pm20) REVERT: S 44 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8170 (mm-30) REVERT: S 60 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8717 (mtpp) REVERT: S 66 CYS cc_start: 0.9104 (m) cc_final: 0.8772 (m) REVERT: T 35 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7454 (ttp-110) REVERT: T 39 ASN cc_start: 0.8426 (m110) cc_final: 0.7517 (m110) REVERT: T 45 LYS cc_start: 0.8342 (tttm) cc_final: 0.7941 (tttm) REVERT: T 74 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8929 (ttpp) REVERT: U 35 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7262 (ttp-110) REVERT: U 37 GLU cc_start: 0.9233 (pm20) cc_final: 0.8940 (pm20) REVERT: U 39 ASN cc_start: 0.8555 (m110) cc_final: 0.7877 (m110) REVERT: U 49 ASP cc_start: 0.8596 (m-30) cc_final: 0.8377 (m-30) REVERT: U 56 HIS cc_start: 0.8099 (m90) cc_final: 0.7478 (m90) REVERT: U 67 ASN cc_start: 0.9015 (m-40) cc_final: 0.8754 (m110) REVERT: U 68 LEU cc_start: 0.9364 (mt) cc_final: 0.9141 (mp) REVERT: U 74 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8778 (ttpp) REVERT: V 39 ASN cc_start: 0.8588 (m-40) cc_final: 0.8048 (m110) REVERT: V 66 CYS cc_start: 0.9041 (m) cc_final: 0.8642 (m) REVERT: V 87 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7964 (mp10) REVERT: W 4 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8518 (pt) REVERT: W 36 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: W 60 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8622 (mtmm) REVERT: W 78 TYR cc_start: 0.8905 (t80) cc_final: 0.8580 (t80) REVERT: X 7 ASN cc_start: 0.9070 (m-40) cc_final: 0.8634 (m110) REVERT: X 14 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6658 (tpt170) REVERT: X 35 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7576 (tpp80) REVERT: X 60 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8569 (mtpt) REVERT: X 66 CYS cc_start: 0.8918 (m) cc_final: 0.8430 (m) REVERT: X 78 TYR cc_start: 0.9162 (t80) cc_final: 0.8530 (t80) REVERT: X 82 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8233 (mp10) REVERT: Y 60 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8026 (tptt) REVERT: Y 74 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8890 (ttmm) REVERT: Y 78 TYR cc_start: 0.9080 (t80) cc_final: 0.8716 (t80) REVERT: Y 82 GLN cc_start: 0.8717 (mm-40) cc_final: 0.7834 (mp10) REVERT: Y 87 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7735 (mp10) REVERT: Z 60 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8720 (mttt) REVERT: Z 74 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8894 (ttpp) REVERT: Z 82 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8336 (mp10) REVERT: a 5 LYS cc_start: 0.8861 (tttm) cc_final: 0.8588 (tptt) REVERT: a 9 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7704 (mmt-90) REVERT: a 60 LYS cc_start: 0.9069 (mtmt) cc_final: 0.7644 (tptm) REVERT: b 20 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9136 (mp) REVERT: b 26 ASP cc_start: 0.8095 (t70) cc_final: 0.7768 (t0) REVERT: b 39 ASN cc_start: 0.8401 (m110) cc_final: 0.7805 (m-40) REVERT: b 71 LYS cc_start: 0.9412 (ptmt) cc_final: 0.9199 (ptmt) REVERT: b 74 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8970 (ptmm) REVERT: b 78 TYR cc_start: 0.9241 (t80) cc_final: 0.8860 (t80) REVERT: c 6 ASP cc_start: 0.8428 (m-30) cc_final: 0.7798 (p0) REVERT: c 9 ARG cc_start: 0.5316 (mmt-90) cc_final: 0.4665 (mtt-85) REVERT: c 21 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8744 (mmmm) REVERT: c 35 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7426 (tpp80) REVERT: c 37 GLU cc_start: 0.9057 (mp0) cc_final: 0.8719 (mp0) REVERT: c 58 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9060 (tp) REVERT: c 61 LYS cc_start: 0.6635 (mttm) cc_final: 0.6287 (mttm) REVERT: c 68 LEU cc_start: 0.9218 (mp) cc_final: 0.9016 (mt) REVERT: c 71 LYS cc_start: 0.9244 (ptmt) cc_final: 0.9005 (ptmt) REVERT: c 87 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7575 (mm-40) REVERT: d 13 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8604 (mm110) REVERT: d 26 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8320 (t70) REVERT: d 39 ASN cc_start: 0.8787 (m-40) cc_final: 0.8426 (m110) REVERT: d 52 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8184 (mtt-85) REVERT: d 56 HIS cc_start: 0.8102 (m-70) cc_final: 0.7841 (m-70) REVERT: d 83 ASP cc_start: 0.8698 (t70) cc_final: 0.8040 (t0) REVERT: e 9 ARG cc_start: 0.6373 (tpt170) cc_final: 0.6104 (ttt90) REVERT: e 13 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8647 (mm-40) REVERT: e 34 ASN cc_start: 0.8692 (t0) cc_final: 0.8424 (t0) REVERT: e 39 ASN cc_start: 0.8664 (m-40) cc_final: 0.8397 (m110) REVERT: e 74 LYS cc_start: 0.9202 (tttt) cc_final: 0.8917 (ttpp) REVERT: e 78 TYR cc_start: 0.8987 (t80) cc_final: 0.8564 (t80) REVERT: e 87 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8452 (mp10) outliers start: 154 outliers final: 122 residues processed: 1693 average time/residue: 0.1628 time to fit residues: 415.2774 Evaluate side-chains 1727 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1594 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 15 MET Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 55 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 64 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 22 GLN G 67 ASN H 2 ASN H 82 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 2 ASN J 67 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 82 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN N 82 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 ASN Q 77 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN W 82 GLN X 67 ASN Y 2 ASN Y 67 ASN Z 2 ASN a 2 ASN b 22 GLN b 67 ASN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 GLN d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 67 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.094081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.081422 restraints weight = 38827.546| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.36 r_work: 0.2832 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23095 Z= 0.194 Angle : 0.730 12.932 31000 Z= 0.404 Chirality : 0.047 0.272 3472 Planarity : 0.005 0.079 3937 Dihedral : 4.144 18.893 2914 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.64 % Allowed : 30.04 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2728 helix: 0.50 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.91 (0.28), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 9 TYR 0.023 0.003 TYR a 78 PHE 0.023 0.001 PHE D 3 TRP 0.020 0.001 TRP E 30 HIS 0.006 0.001 HIS Z 56 Details of bonding type rmsd covalent geometry : bond 0.00488 (23095) covalent geometry : angle 0.73036 (31000) hydrogen bonds : bond 0.04040 ( 1643) hydrogen bonds : angle 4.67671 ( 4929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1765 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1620 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8830 (m-40) cc_final: 0.8587 (m-40) REVERT: A 43 CYS cc_start: 0.8242 (p) cc_final: 0.7897 (p) REVERT: A 44 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 47 GLU cc_start: 0.7814 (tt0) cc_final: 0.7479 (tt0) REVERT: A 87 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7947 (mp10) REVERT: B 35 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7683 (tpp-160) REVERT: B 52 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8390 (mtt-85) REVERT: B 60 LYS cc_start: 0.8945 (mttp) cc_final: 0.8712 (mttp) REVERT: B 66 CYS cc_start: 0.8870 (m) cc_final: 0.8606 (t) REVERT: C 1 MET cc_start: 0.6871 (tpt) cc_final: 0.6470 (tpt) REVERT: C 31 ASN cc_start: 0.9093 (m-40) cc_final: 0.8800 (m-40) REVERT: C 47 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: C 71 LYS cc_start: 0.9386 (ttmm) cc_final: 0.9185 (ptmt) REVERT: D 13 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8671 (mm-40) REVERT: D 35 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7832 (tpp-160) REVERT: D 39 ASN cc_start: 0.8414 (m110) cc_final: 0.7876 (m110) REVERT: D 74 LYS cc_start: 0.9139 (tttt) cc_final: 0.8830 (ttpp) REVERT: D 78 TYR cc_start: 0.8892 (t80) cc_final: 0.8590 (t80) REVERT: E 39 ASN cc_start: 0.8529 (m110) cc_final: 0.7827 (m110) REVERT: E 57 MET cc_start: 0.8535 (mtm) cc_final: 0.8275 (mtp) REVERT: E 74 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8870 (ttmm) REVERT: E 78 TYR cc_start: 0.8976 (t80) cc_final: 0.8578 (t80) REVERT: F 17 MET cc_start: 0.8430 (tpt) cc_final: 0.8207 (ttt) REVERT: F 82 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8532 (mm110) REVERT: G 26 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: G 35 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7653 (ttm110) REVERT: G 36 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: G 39 ASN cc_start: 0.8720 (m-40) cc_final: 0.8487 (m110) REVERT: H 14 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8021 (mtp-110) REVERT: H 35 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7510 (tpp80) REVERT: H 44 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8126 (mm-30) REVERT: H 48 GLN cc_start: 0.8654 (mp10) cc_final: 0.8314 (mp10) REVERT: H 60 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8522 (mtpt) REVERT: H 67 ASN cc_start: 0.8878 (m-40) cc_final: 0.8591 (m-40) REVERT: I 14 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7664 (mtp180) REVERT: I 36 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7593 (mm-30) REVERT: I 37 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8395 (mt-10) REVERT: I 45 LYS cc_start: 0.8461 (pttt) cc_final: 0.8114 (pttt) REVERT: I 57 MET cc_start: 0.8726 (mtp) cc_final: 0.8448 (mtp) REVERT: I 66 CYS cc_start: 0.9039 (t) cc_final: 0.8539 (m) REVERT: J 36 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: J 39 ASN cc_start: 0.8366 (m110) cc_final: 0.7617 (m-40) REVERT: J 87 GLN cc_start: 0.7776 (mm110) cc_final: 0.7168 (mp10) REVERT: K 12 ILE cc_start: 0.9540 (mt) cc_final: 0.9286 (mt) REVERT: K 25 ASP cc_start: 0.8452 (m-30) cc_final: 0.7960 (m-30) REVERT: K 38 VAL cc_start: 0.9106 (t) cc_final: 0.8831 (m) REVERT: K 48 GLN cc_start: 0.8334 (mp10) cc_final: 0.7873 (mp10) REVERT: K 60 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8415 (mtpp) REVERT: K 66 CYS cc_start: 0.8822 (m) cc_final: 0.8353 (m) REVERT: K 83 ASP cc_start: 0.8899 (t70) cc_final: 0.8288 (t0) REVERT: L 39 ASN cc_start: 0.8672 (m110) cc_final: 0.8154 (t0) REVERT: L 78 TYR cc_start: 0.9061 (t80) cc_final: 0.8732 (t80) REVERT: L 82 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8608 (mp10) REVERT: M 35 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7979 (tpp-160) REVERT: M 39 ASN cc_start: 0.8573 (m110) cc_final: 0.7970 (m110) REVERT: M 58 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.8892 (tp) REVERT: M 75 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8779 (tm-30) REVERT: M 78 TYR cc_start: 0.8862 (t80) cc_final: 0.8514 (t80) REVERT: N 35 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7430 (tpp80) REVERT: N 60 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8476 (mttt) REVERT: O 1 MET cc_start: 0.6724 (tpt) cc_final: 0.6358 (tpt) REVERT: O 35 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7364 (tpp80) REVERT: O 44 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8041 (mm-30) REVERT: O 60 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8909 (mttt) REVERT: P 2 ASN cc_start: 0.8735 (m-40) cc_final: 0.8480 (t0) REVERT: P 35 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8130 (tpp80) REVERT: P 47 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: P 60 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8658 (mtpt) REVERT: P 67 ASN cc_start: 0.9040 (m-40) cc_final: 0.8610 (m-40) REVERT: Q 5 LYS cc_start: 0.8972 (tptm) cc_final: 0.8697 (tptm) REVERT: Q 14 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8270 (mtp180) REVERT: Q 15 MET cc_start: 0.8423 (ttm) cc_final: 0.8201 (ttp) REVERT: Q 52 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.7963 (mtt-85) REVERT: Q 60 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8429 (mtmm) REVERT: Q 66 CYS cc_start: 0.8967 (m) cc_final: 0.8470 (m) REVERT: Q 76 TRP cc_start: 0.8459 (m100) cc_final: 0.8194 (m100) REVERT: R 35 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.8001 (tpp80) REVERT: R 43 CYS cc_start: 0.8260 (p) cc_final: 0.7766 (p) REVERT: R 60 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8745 (mttt) REVERT: S 37 GLU cc_start: 0.8985 (pm20) cc_final: 0.8628 (pm20) REVERT: S 44 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8187 (mm-30) REVERT: S 60 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8742 (mtpp) REVERT: S 66 CYS cc_start: 0.9047 (m) cc_final: 0.8571 (m) REVERT: T 36 GLU cc_start: 0.8801 (tp30) cc_final: 0.8428 (tp30) REVERT: T 39 ASN cc_start: 0.8426 (m110) cc_final: 0.7697 (t0) REVERT: T 43 CYS cc_start: 0.8182 (p) cc_final: 0.7918 (p) REVERT: U 35 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7324 (ttp-110) REVERT: U 39 ASN cc_start: 0.8525 (m110) cc_final: 0.7945 (m110) REVERT: U 44 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8121 (mm-30) REVERT: U 49 ASP cc_start: 0.8659 (m-30) cc_final: 0.8183 (m-30) REVERT: U 56 HIS cc_start: 0.8089 (m90) cc_final: 0.7557 (m90) REVERT: U 60 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8613 (mtpp) REVERT: U 68 LEU cc_start: 0.9327 (mt) cc_final: 0.9114 (mp) REVERT: V 39 ASN cc_start: 0.8615 (m-40) cc_final: 0.8118 (m110) REVERT: V 66 CYS cc_start: 0.8937 (m) cc_final: 0.8403 (m) REVERT: V 87 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7944 (mp10) REVERT: W 4 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8543 (pt) REVERT: W 60 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8605 (mtmm) REVERT: X 14 ARG cc_start: 0.8258 (mtt180) cc_final: 0.6676 (tpt170) REVERT: X 35 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7568 (tpp80) REVERT: X 60 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8588 (mtpt) REVERT: X 66 CYS cc_start: 0.8991 (m) cc_final: 0.8518 (m) REVERT: X 71 LYS cc_start: 0.9203 (ttpp) cc_final: 0.8913 (ttpp) REVERT: Y 14 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7718 (mtp180) REVERT: Y 60 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8038 (tptt) REVERT: Y 74 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8871 (ttmm) REVERT: Y 82 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7639 (mp10) REVERT: Y 83 ASP cc_start: 0.8570 (t70) cc_final: 0.8338 (t0) REVERT: Y 87 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7780 (mp10) REVERT: Z 43 CYS cc_start: 0.8479 (p) cc_final: 0.8149 (p) REVERT: Z 74 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8806 (ttpp) REVERT: Z 82 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8334 (mp10) REVERT: a 5 LYS cc_start: 0.8870 (tttm) cc_final: 0.8580 (tptt) REVERT: a 9 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7688 (mmt-90) REVERT: a 60 LYS cc_start: 0.9082 (mtmt) cc_final: 0.7633 (tptm) REVERT: b 20 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9134 (mp) REVERT: b 39 ASN cc_start: 0.8347 (m110) cc_final: 0.7765 (m-40) REVERT: b 71 LYS cc_start: 0.9432 (ptmt) cc_final: 0.9204 (ptmt) REVERT: b 78 TYR cc_start: 0.9287 (t80) cc_final: 0.8918 (t80) REVERT: c 6 ASP cc_start: 0.8490 (m-30) cc_final: 0.7859 (p0) REVERT: c 9 ARG cc_start: 0.5457 (mmt-90) cc_final: 0.4814 (mtt-85) REVERT: c 21 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8791 (mmmm) REVERT: c 35 ARG cc_start: 0.7781 (tpt90) cc_final: 0.7515 (tpp80) REVERT: c 37 GLU cc_start: 0.9073 (mp0) cc_final: 0.8715 (mp0) REVERT: c 58 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9072 (tp) REVERT: c 61 LYS cc_start: 0.6657 (mttm) cc_final: 0.6277 (mttm) REVERT: c 87 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7583 (mm-40) REVERT: d 13 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8615 (mm-40) REVERT: d 26 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (t70) REVERT: d 37 GLU cc_start: 0.8818 (pm20) cc_final: 0.8404 (pm20) REVERT: d 39 ASN cc_start: 0.8870 (m-40) cc_final: 0.8526 (m110) REVERT: d 56 HIS cc_start: 0.8072 (m-70) cc_final: 0.7693 (m-70) REVERT: e 13 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8740 (mm-40) REVERT: e 34 ASN cc_start: 0.8764 (t0) cc_final: 0.8496 (t0) REVERT: e 39 ASN cc_start: 0.8690 (m-40) cc_final: 0.8416 (m110) REVERT: e 74 LYS cc_start: 0.9192 (tttt) cc_final: 0.8907 (ttpp) REVERT: e 78 TYR cc_start: 0.9001 (t80) cc_final: 0.8583 (t80) REVERT: e 87 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8542 (mp10) outliers start: 145 outliers final: 122 residues processed: 1669 average time/residue: 0.1679 time to fit residues: 422.7035 Evaluate side-chains 1730 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1598 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 71 LYS Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 15 MET Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 55 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 161 optimal weight: 0.0040 chunk 33 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 197 optimal weight: 0.0470 chunk 189 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN G 13 GLN G 67 ASN H 2 ASN H 13 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 2 ASN J 67 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN P 82 GLN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 ASN Q 77 ASN R 31 ASN ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 2 ASN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN X 67 ASN X 82 GLN Y 2 ASN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 ASN Z 2 ASN Z 22 GLN a 2 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 67 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.087060 restraints weight = 38142.728| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.30 r_work: 0.2937 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23095 Z= 0.155 Angle : 0.715 12.228 31000 Z= 0.396 Chirality : 0.044 0.244 3472 Planarity : 0.005 0.085 3937 Dihedral : 4.192 26.561 2914 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.05 % Allowed : 30.86 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2728 helix: 0.46 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 9 TYR 0.015 0.002 TYR D 78 PHE 0.025 0.001 PHE C 3 TRP 0.018 0.001 TRP E 30 HIS 0.004 0.001 HIS U 56 Details of bonding type rmsd covalent geometry : bond 0.00375 (23095) covalent geometry : angle 0.71529 (31000) hydrogen bonds : bond 0.03758 ( 1643) hydrogen bonds : angle 4.77115 ( 4929) =============================================================================== Job complete usr+sys time: 7021.78 seconds wall clock time: 120 minutes 44.56 seconds (7244.56 seconds total)