Starting phenix.real_space_refine on Sat Aug 23 07:50:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.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 { model { file = "/net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a7f_6993/08_2025/6a7f_6993.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 30 5.16 5 C 7050 2.51 5 N 1740 2.21 5 O 2010 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} 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 Time building chain proxies: 1.07, per 1000 atoms: 0.10 Number of scatterers: 10830 At special positions: 0 Unit cell: (76.7, 76.7, 165.1, 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 30 16.00 O 2010 8.00 N 1740 7.00 C 7050 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: 1.20 Conformation dependent library (CDL) restraints added in 359.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 95.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 4.020A pdb=" N ALA A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 30 - end of helix removed outlier: 4.020A pdb=" N ALA B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Proline residue: C 30 - end of helix removed outlier: 4.021A pdb=" N ALA C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 4.021A pdb=" N ALA D 38 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) Proline residue: E 30 - end of helix removed outlier: 4.021A pdb=" N ALA E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Proline residue: F 30 - end of helix removed outlier: 4.020A pdb=" N ALA F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) Proline residue: G 30 - end of helix removed outlier: 4.022A pdb=" N ALA G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Proline residue: H 30 - end of helix removed outlier: 4.021A pdb=" N ALA H 38 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS H 46 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 4.021A pdb=" N ALA I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 43 " --> pdb=" O GLY I 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Proline residue: J 30 - end of helix removed outlier: 4.021A pdb=" N ALA J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) Proline residue: K 30 - end of helix removed outlier: 4.021A pdb=" N ALA K 38 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 46 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) Proline residue: L 30 - end of helix removed outlier: 4.022A pdb=" N ALA L 38 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG L 43 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP M 23 " --> pdb=" O THR M 19 " (cutoff:3.500A) Proline residue: M 30 - end of helix removed outlier: 4.021A pdb=" N ALA M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS M 46 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP N 23 " --> pdb=" O THR N 19 " (cutoff:3.500A) Proline residue: N 30 - end of helix removed outlier: 4.020A pdb=" N ALA N 38 " --> pdb=" O THR N 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE N 42 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL N 53 " --> pdb=" O SER N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP O 23 " --> pdb=" O THR O 19 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 4.022A pdb=" N ALA O 38 " --> pdb=" O THR O 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG O 43 " --> pdb=" O GLY O 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS O 46 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL O 53 " --> pdb=" O SER O 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Proline residue: P 30 - end of helix removed outlier: 4.021A pdb=" N ALA P 38 " --> pdb=" O THR P 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE P 42 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG P 43 " --> pdb=" O GLY P 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS P 46 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL P 53 " --> pdb=" O SER P 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Q 23 " --> pdb=" O THR Q 19 " (cutoff:3.500A) Proline residue: Q 30 - end of helix removed outlier: 4.022A pdb=" N ALA Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 42 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG Q 43 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS Q 46 " --> pdb=" O ILE Q 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Q 53 " --> pdb=" O SER Q 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP R 23 " --> pdb=" O THR R 19 " (cutoff:3.500A) Proline residue: R 30 - end of helix removed outlier: 4.021A pdb=" N ALA R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL R 53 " --> pdb=" O SER R 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP S 23 " --> pdb=" O THR S 19 " (cutoff:3.500A) Proline residue: S 30 - end of helix removed outlier: 4.021A pdb=" N ALA S 38 " --> pdb=" O THR S 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG S 43 " --> pdb=" O GLY S 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP T 23 " --> pdb=" O THR T 19 " (cutoff:3.500A) Proline residue: T 30 - end of helix removed outlier: 4.021A pdb=" N ALA T 38 " --> pdb=" O THR T 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE T 42 " --> pdb=" O ALA T 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG T 43 " --> pdb=" O GLY T 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) Proline residue: U 30 - end of helix removed outlier: 4.021A pdb=" N ALA U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 42 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG U 43 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS U 46 " --> pdb=" O ILE U 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL U 53 " --> pdb=" O SER U 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP V 23 " --> pdb=" O THR V 19 " (cutoff:3.500A) Proline residue: V 30 - end of helix removed outlier: 4.022A pdb=" N ALA V 38 " --> pdb=" O THR V 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE V 42 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG V 43 " --> pdb=" O GLY V 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS V 46 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL V 53 " --> pdb=" O SER V 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP W 23 " --> pdb=" O THR W 19 " (cutoff:3.500A) Proline residue: W 30 - end of helix removed outlier: 4.021A pdb=" N ALA W 38 " --> pdb=" O THR W 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE W 42 " --> pdb=" O ALA W 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS W 46 " --> pdb=" O ILE W 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL W 53 " --> pdb=" O SER W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP X 23 " --> pdb=" O THR X 19 " (cutoff:3.500A) Proline residue: X 30 - end of helix removed outlier: 4.022A pdb=" N ALA X 38 " --> pdb=" O THR X 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE X 42 " --> pdb=" O ALA X 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG X 43 " --> pdb=" O GLY X 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS X 46 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL X 53 " --> pdb=" O SER X 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP Y 23 " --> pdb=" O THR Y 19 " (cutoff:3.500A) Proline residue: Y 30 - end of helix removed outlier: 4.021A pdb=" N ALA Y 38 " --> pdb=" O THR Y 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Y 43 " --> pdb=" O GLY Y 39 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Y 46 " --> pdb=" O ILE Y 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 53 removed outlier: 3.627A pdb=" N ASP Z 23 " --> pdb=" O THR Z 19 " (cutoff:3.500A) Proline residue: Z 30 - end of helix removed outlier: 4.021A pdb=" N ALA Z 38 " --> pdb=" O THR Z 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Z 42 " --> pdb=" O ALA Z 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Z 43 " --> pdb=" O GLY Z 39 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS Z 46 " --> pdb=" O ILE Z 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 53 removed outlier: 3.629A pdb=" N ASP a 23 " --> pdb=" O THR a 19 " (cutoff:3.500A) Proline residue: a 30 - end of helix removed outlier: 4.020A pdb=" N ALA a 38 " --> pdb=" O THR a 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 42 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS a 46 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL a 53 " --> pdb=" O SER a 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP b 23 " --> pdb=" O THR b 19 " (cutoff:3.500A) Proline residue: b 30 - end of helix removed outlier: 4.020A pdb=" N ALA b 38 " --> pdb=" O THR b 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 53 " --> pdb=" O SER b 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP c 23 " --> pdb=" O THR c 19 " (cutoff:3.500A) Proline residue: c 30 - end of helix removed outlier: 4.020A pdb=" N ALA c 38 " --> pdb=" O THR c 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE c 42 " --> pdb=" O ALA c 38 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL c 53 " --> pdb=" O SER c 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 53 removed outlier: 3.628A pdb=" N ASP d 23 " --> pdb=" O THR d 19 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 4.021A pdb=" N ALA d 38 " --> pdb=" O THR d 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE d 42 " --> pdb=" O ALA d 38 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS d 46 " --> pdb=" O ILE d 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL d 53 " --> pdb=" O SER d 49 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2880 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: 1.53 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3199 1.33 - 1.45: 1403 1.45 - 1.56: 6318 1.56 - 1.67: 0 1.67 - 1.79: 60 Bond restraints: 10980 Sorted by residual: bond pdb=" CB VAL X 32 " pdb=" CG2 VAL X 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB VAL M 32 " pdb=" CG2 VAL M 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL d 32 " pdb=" CG2 VAL d 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL H 32 " pdb=" CG2 VAL H 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL c 32 " pdb=" CG2 VAL c 32 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.73e+00 ... (remaining 10975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 12951 1.33 - 2.67: 1420 2.67 - 4.00: 239 4.00 - 5.34: 180 5.34 - 6.67: 150 Bond angle restraints: 14940 Sorted by residual: angle pdb=" N TRP I 29 " pdb=" CA TRP I 29 " pdb=" C TRP I 29 " ideal model delta sigma weight residual 113.45 117.78 -4.33 1.39e+00 5.18e-01 9.70e+00 angle pdb=" N TRP F 29 " pdb=" CA TRP F 29 " pdb=" C TRP F 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.68e+00 angle pdb=" N TRP U 29 " pdb=" CA TRP U 29 " pdb=" C TRP U 29 " ideal model delta sigma weight residual 113.45 117.77 -4.32 1.39e+00 5.18e-01 9.66e+00 angle pdb=" N TRP J 29 " pdb=" CA TRP J 29 " pdb=" C TRP J 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.63e+00 angle pdb=" N TRP a 29 " pdb=" CA TRP a 29 " pdb=" C TRP a 29 " ideal model delta sigma weight residual 113.45 117.76 -4.31 1.39e+00 5.18e-01 9.62e+00 ... (remaining 14935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 6120 14.33 - 28.65: 420 28.65 - 42.98: 30 42.98 - 57.30: 0 57.30 - 71.63: 30 Dihedral angle restraints: 6600 sinusoidal: 2430 harmonic: 4170 Sorted by residual: dihedral pdb=" CA THR G 7 " pdb=" C THR G 7 " pdb=" N ASN G 8 " pdb=" CA ASN G 8 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR R 7 " pdb=" C THR R 7 " pdb=" N ASN R 8 " pdb=" CA ASN R 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR C 7 " pdb=" C THR C 7 " pdb=" N ASN C 8 " pdb=" CA ASN C 8 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1023 0.042 - 0.083: 614 0.083 - 0.125: 209 0.125 - 0.166: 104 0.166 - 0.208: 30 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA TRP I 29 " pdb=" N TRP I 29 " pdb=" C TRP I 29 " pdb=" CB TRP I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TRP Q 29 " pdb=" N TRP Q 29 " pdb=" C TRP Q 29 " pdb=" CB TRP Q 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP d 29 " pdb=" N TRP d 29 " pdb=" C TRP d 29 " pdb=" CB TRP d 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1977 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL T 41 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C VAL T 41 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL T 41 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE T 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL W 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL W 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE W 42 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 41 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL b 41 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL b 41 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE b 42 " -0.011 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3091 2.80 - 3.32: 11247 3.32 - 3.85: 18366 3.85 - 4.37: 20225 4.37 - 4.90: 35192 Nonbonded interactions: 88121 Sorted by model distance: nonbonded pdb=" NZ LYS C 46 " pdb=" O LYS I 51 " model vdw 2.271 3.120 nonbonded pdb=" NZ LYS W 46 " pdb=" O VAL c 53 " model vdw 2.288 3.120 nonbonded pdb=" NZ LYS T 46 " pdb=" O VAL U 53 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS O 46 " pdb=" O VAL P 53 " model vdw 2.332 3.120 nonbonded pdb=" O ALA a 13 " pdb=" OG SER a 16 " model vdw 2.339 3.040 ... (remaining 88116 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: 0.04 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' } 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: 1.260 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.014 0.064 10980 Z= 0.597 Angle : 1.172 6.672 14940 Z= 0.615 Chirality : 0.064 0.208 1980 Planarity : 0.008 0.044 1740 Dihedral : 11.202 71.631 3840 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.18), residues: 1350 helix: -1.19 (0.11), residues: 1320 sheet: None (None), residues: 0 loop : -0.50 (0.01), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG A 43 TYR 0.003 0.001 TYR G 9 PHE 0.008 0.003 PHE Y 48 TRP 0.003 0.001 TRP S 29 Details of bonding type rmsd covalent geometry : bond 0.01424 (10980) covalent geometry : angle 1.17200 (14940) hydrogen bonds : bond 0.06220 ( 960) hydrogen bonds : angle 5.11291 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 833 time to evaluate : 0.436 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: A 14 MET cc_start: 0.9213 (mmt) cc_final: 0.8863 (mmt) REVERT: A 23 ASP cc_start: 0.8373 (m-30) cc_final: 0.8085 (m-30) REVERT: A 27 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8831 (tp-100) REVERT: A 47 LYS cc_start: 0.9241 (tttt) cc_final: 0.8748 (tppt) REVERT: B 42 ILE cc_start: 0.9521 (tt) cc_final: 0.9248 (tp) REVERT: B 47 LYS cc_start: 0.8973 (tttt) cc_final: 0.8658 (mmtt) REVERT: B 51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8607 (mttt) REVERT: C 9 TYR cc_start: 0.7565 (m-80) cc_final: 0.7326 (m-80) REVERT: C 42 ILE cc_start: 0.9470 (tt) cc_final: 0.9252 (tt) REVERT: C 47 LYS cc_start: 0.9055 (tttt) cc_final: 0.8539 (tptt) REVERT: D 23 ASP cc_start: 0.8346 (m-30) cc_final: 0.8017 (m-30) REVERT: D 47 LYS cc_start: 0.9197 (tttt) cc_final: 0.8818 (tptt) REVERT: E 15 ASP cc_start: 0.8656 (m-30) cc_final: 0.8454 (m-30) REVERT: E 20 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8663 (mm-40) REVERT: E 23 ASP cc_start: 0.8251 (m-30) cc_final: 0.7862 (m-30) REVERT: F 8 ASN cc_start: 0.8166 (t0) cc_final: 0.7146 (t0) REVERT: F 9 TYR cc_start: 0.7269 (m-80) cc_final: 0.7068 (m-80) REVERT: F 11 THR cc_start: 0.8286 (p) cc_final: 0.7624 (p) REVERT: F 23 ASP cc_start: 0.8463 (m-30) cc_final: 0.8232 (m-30) REVERT: F 51 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8413 (mtpp) REVERT: G 7 THR cc_start: 0.8273 (p) cc_final: 0.7934 (p) REVERT: G 8 ASN cc_start: 0.8012 (t0) cc_final: 0.6751 (m110) REVERT: G 23 ASP cc_start: 0.8490 (m-30) cc_final: 0.8082 (t70) REVERT: G 27 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8531 (tp-100) REVERT: G 40 LEU cc_start: 0.9460 (mt) cc_final: 0.9216 (mt) REVERT: G 44 LEU cc_start: 0.9175 (mt) cc_final: 0.8916 (mm) REVERT: G 51 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8630 (mtpp) REVERT: H 9 TYR cc_start: 0.7680 (m-80) cc_final: 0.7168 (m-80) REVERT: H 19 THR cc_start: 0.8734 (p) cc_final: 0.8234 (p) REVERT: H 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8570 (tp-100) REVERT: H 51 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8522 (mtpp) REVERT: I 9 TYR cc_start: 0.8034 (m-80) cc_final: 0.7647 (m-80) REVERT: I 22 ILE cc_start: 0.8599 (mt) cc_final: 0.8280 (mm) REVERT: I 27 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8468 (tp40) REVERT: I 42 ILE cc_start: 0.9383 (tt) cc_final: 0.9075 (tt) REVERT: I 48 PHE cc_start: 0.8802 (m-80) cc_final: 0.8492 (m-80) REVERT: J 9 TYR cc_start: 0.7627 (m-80) cc_final: 0.7395 (m-80) REVERT: J 27 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8704 (tp-100) REVERT: J 51 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8733 (mtpp) REVERT: K 14 MET cc_start: 0.8519 (mmt) cc_final: 0.8016 (mmm) REVERT: K 47 LYS cc_start: 0.8333 (tttt) cc_final: 0.8028 (ttmm) REVERT: K 51 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8393 (mmmm) REVERT: L 14 MET cc_start: 0.8784 (mmt) cc_final: 0.8200 (mmm) REVERT: L 27 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8958 (tp-100) REVERT: L 47 LYS cc_start: 0.8460 (tttt) cc_final: 0.8066 (ttmm) REVERT: L 48 PHE cc_start: 0.9030 (m-80) cc_final: 0.8697 (m-80) REVERT: L 51 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8415 (mmmm) REVERT: M 27 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8517 (tp-100) REVERT: M 44 LEU cc_start: 0.9220 (mt) cc_final: 0.8966 (mm) REVERT: M 47 LYS cc_start: 0.8423 (tttt) cc_final: 0.7859 (ttmm) REVERT: M 50 SER cc_start: 0.8485 (t) cc_final: 0.7994 (p) REVERT: M 51 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8200 (mmmm) REVERT: N 8 ASN cc_start: 0.7876 (t0) cc_final: 0.7366 (m-40) REVERT: N 27 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8518 (tp40) REVERT: N 47 LYS cc_start: 0.8508 (tttt) cc_final: 0.8168 (ttmm) REVERT: O 47 LYS cc_start: 0.8522 (tttt) cc_final: 0.8077 (ttmm) REVERT: P 15 ASP cc_start: 0.8433 (m-30) cc_final: 0.8038 (m-30) REVERT: P 47 LYS cc_start: 0.8756 (tttt) cc_final: 0.8391 (ttmm) REVERT: Q 8 ASN cc_start: 0.8056 (t0) cc_final: 0.7833 (m110) REVERT: Q 11 THR cc_start: 0.8462 (p) cc_final: 0.8228 (p) REVERT: Q 15 ASP cc_start: 0.8497 (m-30) cc_final: 0.8270 (m-30) REVERT: Q 40 LEU cc_start: 0.9270 (mt) cc_final: 0.9030 (mt) REVERT: Q 42 ILE cc_start: 0.9294 (tt) cc_final: 0.8998 (tp) REVERT: Q 47 LYS cc_start: 0.8444 (tttt) cc_final: 0.8166 (ttmm) REVERT: Q 50 SER cc_start: 0.8939 (t) cc_final: 0.8725 (t) REVERT: R 14 MET cc_start: 0.8904 (mmt) cc_final: 0.8633 (mmt) REVERT: R 40 LEU cc_start: 0.9348 (mt) cc_final: 0.9098 (mp) REVERT: S 15 ASP cc_start: 0.8499 (m-30) cc_final: 0.8092 (m-30) REVERT: S 40 LEU cc_start: 0.9190 (mt) cc_final: 0.8906 (mp) REVERT: S 43 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7925 (ttt180) REVERT: T 22 ILE cc_start: 0.8345 (mt) cc_final: 0.7996 (mm) REVERT: T 47 LYS cc_start: 0.8481 (tttt) cc_final: 0.8178 (ttmm) REVERT: U 8 ASN cc_start: 0.7409 (t0) cc_final: 0.6156 (t0) REVERT: U 9 TYR cc_start: 0.7665 (m-80) cc_final: 0.7396 (m-80) REVERT: U 20 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8920 (mm-40) REVERT: U 47 LYS cc_start: 0.8692 (tttt) cc_final: 0.8239 (ttpt) REVERT: U 51 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7837 (mptp) REVERT: V 8 ASN cc_start: 0.7551 (t0) cc_final: 0.6269 (t0) REVERT: V 9 TYR cc_start: 0.7745 (m-80) cc_final: 0.7266 (m-80) REVERT: V 15 ASP cc_start: 0.8903 (m-30) cc_final: 0.8701 (m-30) REVERT: W 8 ASN cc_start: 0.7522 (t0) cc_final: 0.6374 (t0) REVERT: W 15 ASP cc_start: 0.8820 (m-30) cc_final: 0.8591 (m-30) REVERT: W 47 LYS cc_start: 0.8618 (tttt) cc_final: 0.8379 (ttmm) REVERT: X 15 ASP cc_start: 0.8859 (m-30) cc_final: 0.8638 (m-30) REVERT: Y 8 ASN cc_start: 0.7577 (t0) cc_final: 0.5856 (t0) REVERT: Y 9 TYR cc_start: 0.7655 (m-80) cc_final: 0.7452 (m-80) REVERT: Y 15 ASP cc_start: 0.8931 (m-30) cc_final: 0.8615 (m-30) REVERT: Z 18 LYS cc_start: 0.8464 (tttt) cc_final: 0.7960 (mptt) REVERT: Z 20 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8999 (mm-40) REVERT: Z 23 ASP cc_start: 0.8326 (m-30) cc_final: 0.8062 (t0) REVERT: Z 40 LEU cc_start: 0.9048 (mt) cc_final: 0.8789 (mt) REVERT: a 18 LYS cc_start: 0.8443 (tttt) cc_final: 0.7740 (mptt) REVERT: b 15 ASP cc_start: 0.8733 (m-30) cc_final: 0.8400 (m-30) REVERT: b 18 LYS cc_start: 0.8297 (tttt) cc_final: 0.8021 (mptt) REVERT: c 15 ASP cc_start: 0.8716 (m-30) cc_final: 0.8418 (m-30) REVERT: c 18 LYS cc_start: 0.8306 (tttt) cc_final: 0.8041 (mptt) REVERT: c 25 ILE cc_start: 0.8552 (mt) cc_final: 0.8294 (mt) REVERT: d 18 LYS cc_start: 0.8472 (tttt) cc_final: 0.7821 (mmtt) REVERT: d 22 ILE cc_start: 0.8606 (mt) cc_final: 0.8373 (mm) outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 0.1074 time to fit residues: 123.0971 Evaluate side-chains 662 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086260 restraints weight = 19918.091| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3129 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10980 Z= 0.141 Angle : 0.576 7.466 14940 Z= 0.303 Chirality : 0.041 0.136 1980 Planarity : 0.005 0.031 1740 Dihedral : 4.276 11.415 1440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.50 % Allowed : 18.29 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.22), residues: 1350 helix: 0.36 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 2.95 (0.42), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 43 TYR 0.007 0.001 TYR D 9 PHE 0.011 0.001 PHE b 48 TRP 0.010 0.001 TRP L 29 Details of bonding type rmsd covalent geometry : bond 0.00327 (10980) covalent geometry : angle 0.57631 (14940) hydrogen bonds : bond 0.02774 ( 960) hydrogen bonds : angle 3.76217 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 824 time to evaluate : 0.314 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: A 20 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8659 (mm-40) REVERT: A 27 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8867 (tp-100) REVERT: A 42 ILE cc_start: 0.9267 (tp) cc_final: 0.9040 (tt) REVERT: A 47 LYS cc_start: 0.9275 (tttt) cc_final: 0.8915 (tppt) REVERT: A 49 SER cc_start: 0.9472 (t) cc_final: 0.9024 (p) REVERT: B 20 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8648 (mm-40) REVERT: B 27 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8483 (tt0) REVERT: B 42 ILE cc_start: 0.9628 (tt) cc_final: 0.9369 (tp) REVERT: B 47 LYS cc_start: 0.9090 (tttt) cc_final: 0.8887 (mmtt) REVERT: B 51 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8799 (mtpt) REVERT: C 20 GLN cc_start: 0.8828 (tp40) cc_final: 0.8385 (mt0) REVERT: C 47 LYS cc_start: 0.9215 (tttt) cc_final: 0.8728 (tptt) REVERT: D 23 ASP cc_start: 0.8497 (m-30) cc_final: 0.8256 (m-30) REVERT: D 42 ILE cc_start: 0.9463 (tp) cc_final: 0.9244 (tt) REVERT: D 46 LYS cc_start: 0.9191 (mttm) cc_final: 0.8902 (mttp) REVERT: D 47 LYS cc_start: 0.9285 (tttt) cc_final: 0.9075 (tptt) REVERT: D 51 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8764 (mttt) REVERT: E 20 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8490 (mm-40) REVERT: E 42 ILE cc_start: 0.9429 (tp) cc_final: 0.9104 (tt) REVERT: F 8 ASN cc_start: 0.8016 (t0) cc_final: 0.7460 (t0) REVERT: G 20 GLN cc_start: 0.8991 (mm-40) cc_final: 0.7902 (mm-40) REVERT: G 40 LEU cc_start: 0.9614 (mt) cc_final: 0.9361 (mt) REVERT: H 9 TYR cc_start: 0.7730 (m-80) cc_final: 0.7296 (m-80) REVERT: H 19 THR cc_start: 0.8945 (p) cc_final: 0.8590 (p) REVERT: H 43 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8452 (ttm170) REVERT: I 19 THR cc_start: 0.9413 (t) cc_final: 0.9047 (p) REVERT: I 27 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8637 (tp-100) REVERT: I 50 SER cc_start: 0.8461 (t) cc_final: 0.7974 (p) REVERT: I 51 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8858 (mtpp) REVERT: J 26 SER cc_start: 0.8985 (p) cc_final: 0.8729 (p) REVERT: J 27 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8758 (tp-100) REVERT: J 48 PHE cc_start: 0.9447 (m-80) cc_final: 0.9103 (m-80) REVERT: K 14 MET cc_start: 0.8780 (mmt) cc_final: 0.8270 (mmt) REVERT: L 20 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8852 (mm-40) REVERT: L 47 LYS cc_start: 0.8820 (tttt) cc_final: 0.8538 (ttmm) REVERT: L 51 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8754 (mmmm) REVERT: M 14 MET cc_start: 0.8734 (mmm) cc_final: 0.8184 (mmt) REVERT: M 15 ASP cc_start: 0.8616 (m-30) cc_final: 0.8388 (m-30) REVERT: M 27 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8801 (tp40) REVERT: M 51 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8620 (mmmm) REVERT: N 8 ASN cc_start: 0.8049 (t0) cc_final: 0.7163 (m-40) REVERT: N 47 LYS cc_start: 0.8925 (tttt) cc_final: 0.8524 (ttmm) REVERT: N 50 SER cc_start: 0.8930 (t) cc_final: 0.8534 (p) REVERT: O 14 MET cc_start: 0.8757 (mmm) cc_final: 0.8412 (mmt) REVERT: O 27 GLN cc_start: 0.9062 (tp40) cc_final: 0.8676 (tp40) REVERT: P 15 ASP cc_start: 0.8275 (m-30) cc_final: 0.7940 (m-30) REVERT: P 27 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8716 (tp40) REVERT: Q 8 ASN cc_start: 0.8254 (t0) cc_final: 0.7811 (t0) REVERT: Q 9 TYR cc_start: 0.7259 (m-80) cc_final: 0.6919 (m-80) REVERT: Q 15 ASP cc_start: 0.8473 (m-30) cc_final: 0.8142 (m-30) REVERT: Q 27 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8781 (tp40) REVERT: S 15 ASP cc_start: 0.8485 (m-30) cc_final: 0.8205 (m-30) REVERT: T 15 ASP cc_start: 0.8487 (m-30) cc_final: 0.8287 (m-30) REVERT: T 26 SER cc_start: 0.8756 (p) cc_final: 0.8551 (m) REVERT: T 27 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8749 (tp-100) REVERT: U 15 ASP cc_start: 0.8710 (m-30) cc_final: 0.8482 (m-30) REVERT: U 18 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8497 (ttmm) REVERT: U 40 LEU cc_start: 0.9284 (mp) cc_final: 0.8895 (mt) REVERT: V 8 ASN cc_start: 0.7366 (t0) cc_final: 0.6928 (t0) REVERT: V 47 LYS cc_start: 0.9108 (tttm) cc_final: 0.8851 (ttmm) REVERT: W 9 TYR cc_start: 0.7712 (m-80) cc_final: 0.7343 (m-80) REVERT: W 43 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8447 (ttp80) REVERT: X 51 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8735 (mttp) REVERT: Y 8 ASN cc_start: 0.7171 (t0) cc_final: 0.6206 (t0) REVERT: Y 18 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8687 (ttmm) REVERT: Y 47 LYS cc_start: 0.9036 (tttm) cc_final: 0.8787 (ttmm) REVERT: Z 18 LYS cc_start: 0.8783 (tttt) cc_final: 0.8388 (mptt) REVERT: Z 46 LYS cc_start: 0.8683 (mttt) cc_final: 0.8256 (mtmt) REVERT: Z 49 SER cc_start: 0.9125 (m) cc_final: 0.8766 (t) REVERT: a 9 TYR cc_start: 0.8129 (m-80) cc_final: 0.7436 (p90) REVERT: a 18 LYS cc_start: 0.8914 (tttt) cc_final: 0.8283 (mptt) REVERT: a 20 GLN cc_start: 0.9235 (mm110) cc_final: 0.9016 (mm-40) REVERT: b 15 ASP cc_start: 0.8880 (m-30) cc_final: 0.8567 (m-30) REVERT: b 18 LYS cc_start: 0.8749 (tttt) cc_final: 0.8340 (mptt) REVERT: b 24 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8980 (tp) REVERT: c 14 MET cc_start: 0.8408 (mmm) cc_final: 0.8202 (mmm) REVERT: c 15 ASP cc_start: 0.8611 (m-30) cc_final: 0.8328 (m-30) REVERT: c 18 LYS cc_start: 0.8869 (tttt) cc_final: 0.8411 (mptt) REVERT: c 25 ILE cc_start: 0.9380 (mt) cc_final: 0.9100 (mt) REVERT: d 15 ASP cc_start: 0.8558 (m-30) cc_final: 0.8233 (m-30) REVERT: d 18 LYS cc_start: 0.8782 (tttt) cc_final: 0.8081 (mmtt) outliers start: 43 outliers final: 27 residues processed: 828 average time/residue: 0.0994 time to fit residues: 115.3215 Evaluate side-chains 752 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 724 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083655 restraints weight = 20396.743| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.89 r_work: 0.3096 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10980 Z= 0.154 Angle : 0.591 6.185 14940 Z= 0.305 Chirality : 0.042 0.141 1980 Planarity : 0.004 0.030 1740 Dihedral : 4.052 11.340 1440 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.31 % Allowed : 22.93 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.23), residues: 1350 helix: 0.90 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.16 (0.42), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 43 TYR 0.005 0.001 TYR K 9 PHE 0.012 0.001 PHE Q 48 TRP 0.011 0.002 TRP b 29 Details of bonding type rmsd covalent geometry : bond 0.00374 (10980) covalent geometry : angle 0.59068 (14940) hydrogen bonds : bond 0.02680 ( 960) hydrogen bonds : angle 3.70439 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 767 time to evaluate : 0.475 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: A 20 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8461 (mm-40) REVERT: A 27 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8767 (tp-100) REVERT: A 42 ILE cc_start: 0.9300 (tp) cc_final: 0.9004 (tt) REVERT: A 47 LYS cc_start: 0.9233 (tttt) cc_final: 0.8978 (mmtt) REVERT: A 49 SER cc_start: 0.9294 (t) cc_final: 0.9021 (m) REVERT: A 51 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8785 (mtpt) REVERT: B 20 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8391 (mm-40) REVERT: B 42 ILE cc_start: 0.9633 (tt) cc_final: 0.9366 (tp) REVERT: B 45 PHE cc_start: 0.9438 (t80) cc_final: 0.9062 (t80) REVERT: B 47 LYS cc_start: 0.9105 (tttt) cc_final: 0.8801 (mmtt) REVERT: B 51 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8825 (mttt) REVERT: C 47 LYS cc_start: 0.9217 (tttt) cc_final: 0.8719 (tptt) REVERT: D 23 ASP cc_start: 0.8523 (m-30) cc_final: 0.8271 (m-30) REVERT: D 51 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8785 (mttt) REVERT: E 14 MET cc_start: 0.8948 (mmt) cc_final: 0.8720 (tpp) REVERT: E 20 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8494 (mm-40) REVERT: E 42 ILE cc_start: 0.9380 (tp) cc_final: 0.9095 (tt) REVERT: F 8 ASN cc_start: 0.7985 (t0) cc_final: 0.7363 (m110) REVERT: F 9 TYR cc_start: 0.6925 (m-80) cc_final: 0.6692 (m-80) REVERT: F 20 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8598 (mm-40) REVERT: G 12 GLU cc_start: 0.8089 (mp0) cc_final: 0.7825 (mp0) REVERT: G 40 LEU cc_start: 0.9622 (mt) cc_final: 0.9422 (mt) REVERT: G 49 SER cc_start: 0.9306 (m) cc_final: 0.9036 (t) REVERT: G 51 LYS cc_start: 0.9363 (mtpp) cc_final: 0.9156 (mtpp) REVERT: H 9 TYR cc_start: 0.7775 (m-80) cc_final: 0.7215 (m-80) REVERT: H 43 ARG cc_start: 0.8784 (mtp180) cc_final: 0.8399 (ttm170) REVERT: I 27 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8635 (tp-100) REVERT: I 50 SER cc_start: 0.8826 (t) cc_final: 0.8403 (p) REVERT: I 51 LYS cc_start: 0.9274 (mmtm) cc_final: 0.8878 (mtpp) REVERT: J 23 ASP cc_start: 0.8275 (p0) cc_final: 0.7925 (p0) REVERT: J 27 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8684 (tp-100) REVERT: J 48 PHE cc_start: 0.9454 (m-80) cc_final: 0.8892 (m-80) REVERT: K 14 MET cc_start: 0.8769 (mmt) cc_final: 0.8238 (mmt) REVERT: K 50 SER cc_start: 0.8976 (t) cc_final: 0.8455 (p) REVERT: L 14 MET cc_start: 0.8819 (mmt) cc_final: 0.8534 (mmt) REVERT: L 20 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8769 (mm-40) REVERT: L 47 LYS cc_start: 0.8851 (tttt) cc_final: 0.8324 (ttmm) REVERT: L 50 SER cc_start: 0.9049 (t) cc_final: 0.8645 (p) REVERT: M 14 MET cc_start: 0.8631 (mmm) cc_final: 0.8402 (mmt) REVERT: M 27 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8807 (tp40) REVERT: N 8 ASN cc_start: 0.7981 (t0) cc_final: 0.6957 (m-40) REVERT: N 18 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8450 (ttmt) REVERT: N 47 LYS cc_start: 0.8893 (tttt) cc_final: 0.8443 (ttmm) REVERT: N 50 SER cc_start: 0.8966 (t) cc_final: 0.8527 (p) REVERT: N 51 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8774 (mtpp) REVERT: O 14 MET cc_start: 0.8772 (mmm) cc_final: 0.8399 (mmt) REVERT: O 27 GLN cc_start: 0.9077 (tp40) cc_final: 0.8687 (tp40) REVERT: P 15 ASP cc_start: 0.8278 (m-30) cc_final: 0.8004 (m-30) REVERT: P 27 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8684 (tp40) REVERT: Q 8 ASN cc_start: 0.8246 (t0) cc_final: 0.7913 (m110) REVERT: Q 15 ASP cc_start: 0.8474 (m-30) cc_final: 0.8139 (m-30) REVERT: Q 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8669 (tp40) REVERT: S 15 ASP cc_start: 0.8420 (m-30) cc_final: 0.8096 (m-30) REVERT: T 27 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8715 (tp-100) REVERT: U 8 ASN cc_start: 0.7375 (t0) cc_final: 0.6705 (t0) REVERT: U 15 ASP cc_start: 0.8668 (m-30) cc_final: 0.8403 (m-30) REVERT: U 18 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8558 (ttmm) REVERT: U 40 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8881 (mt) REVERT: U 51 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8149 (mttp) REVERT: V 8 ASN cc_start: 0.7150 (t0) cc_final: 0.6187 (t0) REVERT: V 32 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8683 (p) REVERT: V 51 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8901 (mttm) REVERT: W 43 ARG cc_start: 0.8737 (ttm170) cc_final: 0.8422 (ttp80) REVERT: X 51 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8834 (mttp) REVERT: Y 47 LYS cc_start: 0.9120 (tttm) cc_final: 0.8881 (ttmm) REVERT: Z 18 LYS cc_start: 0.8772 (tttt) cc_final: 0.8359 (mptt) REVERT: Z 46 LYS cc_start: 0.8552 (mttt) cc_final: 0.8198 (mtmt) REVERT: Z 49 SER cc_start: 0.9313 (m) cc_final: 0.8924 (t) REVERT: a 18 LYS cc_start: 0.8847 (tttt) cc_final: 0.8238 (mptt) REVERT: b 15 ASP cc_start: 0.8698 (m-30) cc_final: 0.8486 (m-30) REVERT: b 18 LYS cc_start: 0.8856 (tttt) cc_final: 0.8295 (mptt) REVERT: c 15 ASP cc_start: 0.8620 (m-30) cc_final: 0.8393 (m-30) REVERT: c 18 LYS cc_start: 0.8901 (tttt) cc_final: 0.8370 (mptt) REVERT: c 48 PHE cc_start: 0.9091 (m-80) cc_final: 0.8813 (m-80) REVERT: d 18 LYS cc_start: 0.8759 (tttt) cc_final: 0.8051 (mmtt) outliers start: 53 outliers final: 39 residues processed: 772 average time/residue: 0.1048 time to fit residues: 114.3413 Evaluate side-chains 763 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 722 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN I 8 ASN O 8 ASN R 27 GLN S 27 GLN W 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075272 restraints weight = 21239.525| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.09 r_work: 0.3106 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10980 Z= 0.140 Angle : 0.579 6.964 14940 Z= 0.298 Chirality : 0.042 0.142 1980 Planarity : 0.004 0.030 1740 Dihedral : 3.926 11.536 1440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.07 % Allowed : 25.12 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1350 helix: 1.13 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.48 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 43 TYR 0.005 0.001 TYR F 9 PHE 0.011 0.001 PHE Q 48 TRP 0.015 0.001 TRP Z 29 Details of bonding type rmsd covalent geometry : bond 0.00335 (10980) covalent geometry : angle 0.57947 (14940) hydrogen bonds : bond 0.02603 ( 960) hydrogen bonds : angle 3.72068 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 762 time to evaluate : 0.471 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: A 27 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8604 (mt0) REVERT: A 42 ILE cc_start: 0.9410 (tp) cc_final: 0.9113 (tt) REVERT: A 47 LYS cc_start: 0.9203 (tttt) cc_final: 0.8823 (tppt) REVERT: A 49 SER cc_start: 0.9295 (t) cc_final: 0.9009 (m) REVERT: A 51 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8750 (mtpt) REVERT: B 45 PHE cc_start: 0.9445 (t80) cc_final: 0.9134 (t80) REVERT: B 47 LYS cc_start: 0.9076 (tttt) cc_final: 0.8790 (mmtt) REVERT: B 51 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8795 (mtpt) REVERT: C 45 PHE cc_start: 0.9493 (t80) cc_final: 0.9245 (t80) REVERT: C 47 LYS cc_start: 0.9184 (tttt) cc_final: 0.8679 (tptt) REVERT: D 23 ASP cc_start: 0.8549 (m-30) cc_final: 0.8299 (m-30) REVERT: D 51 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8901 (mttt) REVERT: E 42 ILE cc_start: 0.9312 (tp) cc_final: 0.9102 (tt) REVERT: F 8 ASN cc_start: 0.7794 (t0) cc_final: 0.7075 (m110) REVERT: F 43 ARG cc_start: 0.8879 (ttp80) cc_final: 0.8664 (ttp-110) REVERT: G 12 GLU cc_start: 0.8169 (mp0) cc_final: 0.7865 (mp0) REVERT: G 27 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8663 (mm-40) REVERT: G 49 SER cc_start: 0.9325 (m) cc_final: 0.9016 (p) REVERT: G 51 LYS cc_start: 0.9298 (mtpp) cc_final: 0.9022 (mtpp) REVERT: H 9 TYR cc_start: 0.7476 (m-80) cc_final: 0.7084 (m-80) REVERT: H 43 ARG cc_start: 0.8751 (mtp180) cc_final: 0.8349 (ttm170) REVERT: H 51 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9070 (mtpp) REVERT: I 27 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8638 (tp-100) REVERT: I 50 SER cc_start: 0.8875 (t) cc_final: 0.8414 (p) REVERT: I 51 LYS cc_start: 0.9322 (mmtm) cc_final: 0.8952 (mtpp) REVERT: J 23 ASP cc_start: 0.8302 (p0) cc_final: 0.7886 (p0) REVERT: J 27 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8650 (tp-100) REVERT: J 48 PHE cc_start: 0.9412 (m-80) cc_final: 0.8877 (m-80) REVERT: K 12 GLU cc_start: 0.8001 (mp0) cc_final: 0.7738 (mp0) REVERT: K 14 MET cc_start: 0.8817 (mmt) cc_final: 0.8293 (mmt) REVERT: K 15 ASP cc_start: 0.8577 (m-30) cc_final: 0.8217 (m-30) REVERT: K 50 SER cc_start: 0.8987 (t) cc_final: 0.8419 (p) REVERT: L 47 LYS cc_start: 0.8723 (tttt) cc_final: 0.8376 (ttmm) REVERT: L 50 SER cc_start: 0.9068 (t) cc_final: 0.8635 (p) REVERT: L 51 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8740 (mtpp) REVERT: M 15 ASP cc_start: 0.8655 (m-30) cc_final: 0.8453 (m-30) REVERT: M 27 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8823 (tp40) REVERT: N 8 ASN cc_start: 0.7642 (t0) cc_final: 0.6957 (m-40) REVERT: N 47 LYS cc_start: 0.8858 (tttt) cc_final: 0.8413 (ttmm) REVERT: N 50 SER cc_start: 0.8966 (t) cc_final: 0.8534 (p) REVERT: N 51 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8711 (mtpp) REVERT: O 14 MET cc_start: 0.8698 (mmm) cc_final: 0.8287 (mmt) REVERT: O 27 GLN cc_start: 0.9070 (tp40) cc_final: 0.8693 (tp40) REVERT: P 15 ASP cc_start: 0.8322 (m-30) cc_final: 0.8102 (m-30) REVERT: P 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8705 (tp40) REVERT: Q 8 ASN cc_start: 0.8208 (t0) cc_final: 0.7899 (m110) REVERT: Q 15 ASP cc_start: 0.8582 (m-30) cc_final: 0.8286 (m-30) REVERT: Q 27 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8556 (tp40) REVERT: R 34 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9138 (m) REVERT: S 15 ASP cc_start: 0.8441 (m-30) cc_final: 0.8170 (m-30) REVERT: T 27 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8739 (tp-100) REVERT: T 47 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8664 (ttmt) REVERT: U 8 ASN cc_start: 0.6955 (t0) cc_final: 0.6330 (t0) REVERT: U 15 ASP cc_start: 0.8802 (m-30) cc_final: 0.8502 (m-30) REVERT: U 40 LEU cc_start: 0.9294 (mp) cc_final: 0.8913 (mt) REVERT: U 51 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8183 (mttp) REVERT: V 51 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8781 (mttm) REVERT: W 43 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8425 (ttp80) REVERT: Y 47 LYS cc_start: 0.9146 (tttm) cc_final: 0.8921 (ttmm) REVERT: Z 18 LYS cc_start: 0.8784 (tttt) cc_final: 0.8322 (mptt) REVERT: Z 46 LYS cc_start: 0.8503 (mttt) cc_final: 0.8140 (mtmt) REVERT: Z 49 SER cc_start: 0.9331 (m) cc_final: 0.8976 (t) REVERT: a 9 TYR cc_start: 0.8199 (m-80) cc_final: 0.7491 (p90) REVERT: a 18 LYS cc_start: 0.8718 (tttt) cc_final: 0.8222 (mptt) REVERT: b 18 LYS cc_start: 0.8888 (tttt) cc_final: 0.8256 (mptt) REVERT: c 11 THR cc_start: 0.9118 (p) cc_final: 0.8614 (p) REVERT: c 15 ASP cc_start: 0.8663 (m-30) cc_final: 0.8421 (m-30) REVERT: c 18 LYS cc_start: 0.8936 (tttt) cc_final: 0.8375 (mptt) REVERT: d 15 ASP cc_start: 0.8790 (t0) cc_final: 0.8568 (m-30) REVERT: d 18 LYS cc_start: 0.8730 (tttt) cc_final: 0.8003 (mmtt) outliers start: 50 outliers final: 35 residues processed: 771 average time/residue: 0.1044 time to fit residues: 114.0608 Evaluate side-chains 762 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 726 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075158 restraints weight = 21161.536| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.07 r_work: 0.3106 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10980 Z= 0.146 Angle : 0.590 7.971 14940 Z= 0.301 Chirality : 0.043 0.176 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.892 11.076 1440 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.31 % Allowed : 27.64 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.23), residues: 1350 helix: 1.26 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.37 (0.45), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 43 TYR 0.005 0.001 TYR O 9 PHE 0.018 0.001 PHE U 48 TRP 0.014 0.001 TRP c 29 Details of bonding type rmsd covalent geometry : bond 0.00349 (10980) covalent geometry : angle 0.58969 (14940) hydrogen bonds : bond 0.02626 ( 960) hydrogen bonds : angle 3.77941 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 751 time to evaluate : 0.464 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: A 27 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8609 (mt0) REVERT: A 42 ILE cc_start: 0.9395 (tp) cc_final: 0.9071 (tt) REVERT: A 47 LYS cc_start: 0.9173 (tttt) cc_final: 0.8956 (mmtt) REVERT: A 49 SER cc_start: 0.9200 (t) cc_final: 0.8950 (m) REVERT: B 47 LYS cc_start: 0.9077 (tttt) cc_final: 0.8801 (mmtt) REVERT: B 51 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8791 (mtpt) REVERT: C 20 GLN cc_start: 0.8520 (mt0) cc_final: 0.8103 (mt0) REVERT: C 43 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8251 (ttp80) REVERT: C 45 PHE cc_start: 0.9472 (t80) cc_final: 0.9240 (t80) REVERT: C 47 LYS cc_start: 0.9176 (tttt) cc_final: 0.8687 (tptt) REVERT: D 23 ASP cc_start: 0.8508 (m-30) cc_final: 0.8267 (m-30) REVERT: D 25 ILE cc_start: 0.9394 (mt) cc_final: 0.9171 (mt) REVERT: D 51 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8823 (mttt) REVERT: E 8 ASN cc_start: 0.8504 (t0) cc_final: 0.8090 (t0) REVERT: E 19 THR cc_start: 0.8962 (p) cc_final: 0.8367 (p) REVERT: E 51 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8779 (mtpt) REVERT: F 8 ASN cc_start: 0.7519 (t0) cc_final: 0.7008 (m110) REVERT: F 51 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8934 (mtpp) REVERT: G 27 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8606 (mm-40) REVERT: G 49 SER cc_start: 0.9334 (m) cc_final: 0.9052 (p) REVERT: G 51 LYS cc_start: 0.9270 (mtpp) cc_final: 0.9067 (mtpp) REVERT: H 9 TYR cc_start: 0.7678 (m-80) cc_final: 0.7259 (m-80) REVERT: H 43 ARG cc_start: 0.8730 (mtp180) cc_final: 0.8336 (ttm170) REVERT: I 27 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8572 (tp40) REVERT: I 50 SER cc_start: 0.8909 (t) cc_final: 0.8476 (p) REVERT: I 51 LYS cc_start: 0.9333 (mmtm) cc_final: 0.8990 (mtpp) REVERT: J 23 ASP cc_start: 0.8292 (p0) cc_final: 0.7957 (p0) REVERT: J 27 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8755 (tp-100) REVERT: J 48 PHE cc_start: 0.9400 (m-80) cc_final: 0.8936 (m-80) REVERT: K 12 GLU cc_start: 0.8035 (mp0) cc_final: 0.7734 (mp0) REVERT: K 14 MET cc_start: 0.8805 (mmt) cc_final: 0.8292 (mmt) REVERT: K 15 ASP cc_start: 0.8580 (m-30) cc_final: 0.8245 (m-30) REVERT: K 50 SER cc_start: 0.9103 (t) cc_final: 0.8542 (p) REVERT: K 51 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9112 (mtpp) REVERT: L 14 MET cc_start: 0.8752 (mmt) cc_final: 0.8269 (mmt) REVERT: L 20 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8874 (mm-40) REVERT: L 47 LYS cc_start: 0.8727 (tttt) cc_final: 0.8422 (ttmm) REVERT: L 50 SER cc_start: 0.9238 (t) cc_final: 0.8802 (p) REVERT: L 51 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8634 (mtpp) REVERT: M 14 MET cc_start: 0.8651 (mmm) cc_final: 0.8135 (mmt) REVERT: M 27 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8867 (tp40) REVERT: M 51 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8868 (mtpp) REVERT: N 8 ASN cc_start: 0.7391 (t0) cc_final: 0.7004 (m-40) REVERT: N 47 LYS cc_start: 0.8845 (tttt) cc_final: 0.8426 (ttmm) REVERT: N 50 SER cc_start: 0.8963 (t) cc_final: 0.8524 (p) REVERT: N 51 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8708 (mtpp) REVERT: O 14 MET cc_start: 0.8784 (mmm) cc_final: 0.8424 (mmt) REVERT: P 15 ASP cc_start: 0.8299 (m-30) cc_final: 0.8062 (m-30) REVERT: P 27 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8687 (tp40) REVERT: Q 8 ASN cc_start: 0.8166 (t0) cc_final: 0.7898 (m110) REVERT: Q 15 ASP cc_start: 0.8594 (m-30) cc_final: 0.8292 (m-30) REVERT: S 15 ASP cc_start: 0.8400 (m-30) cc_final: 0.8049 (m-30) REVERT: S 51 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8960 (ttmm) REVERT: T 27 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8726 (tp-100) REVERT: U 8 ASN cc_start: 0.6767 (t0) cc_final: 0.5964 (t0) REVERT: U 40 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8984 (mt) REVERT: U 51 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8230 (mttm) REVERT: W 43 ARG cc_start: 0.8662 (ttm170) cc_final: 0.8378 (ttp80) REVERT: W 51 LYS cc_start: 0.8955 (mttp) cc_final: 0.8752 (mttp) REVERT: Y 18 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8614 (tttp) REVERT: Y 47 LYS cc_start: 0.9111 (tttm) cc_final: 0.8889 (ttmm) REVERT: Z 18 LYS cc_start: 0.8827 (tttt) cc_final: 0.8376 (mptt) REVERT: Z 33 THR cc_start: 0.8834 (t) cc_final: 0.8561 (p) REVERT: Z 46 LYS cc_start: 0.8608 (mttt) cc_final: 0.8341 (mtmt) REVERT: Z 49 SER cc_start: 0.9306 (m) cc_final: 0.9009 (t) REVERT: a 18 LYS cc_start: 0.8754 (tttt) cc_final: 0.8215 (mptt) REVERT: b 15 ASP cc_start: 0.8559 (m-30) cc_final: 0.8330 (m-30) REVERT: b 18 LYS cc_start: 0.8912 (tttt) cc_final: 0.8123 (mptt) REVERT: c 11 THR cc_start: 0.9116 (p) cc_final: 0.8589 (p) REVERT: c 15 ASP cc_start: 0.8635 (m-30) cc_final: 0.8398 (m-30) REVERT: c 18 LYS cc_start: 0.8985 (tttt) cc_final: 0.8322 (mptt) REVERT: c 48 PHE cc_start: 0.9117 (m-80) cc_final: 0.8833 (m-80) REVERT: d 18 LYS cc_start: 0.8767 (tttt) cc_final: 0.8006 (mptt) REVERT: d 51 LYS cc_start: 0.9087 (mptt) cc_final: 0.8778 (mptt) outliers start: 53 outliers final: 39 residues processed: 761 average time/residue: 0.1031 time to fit residues: 111.0183 Evaluate side-chains 766 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 725 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain Q residue 9 TYR Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085670 restraints weight = 20428.190| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.95 r_work: 0.3115 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10980 Z= 0.143 Angle : 0.610 7.027 14940 Z= 0.311 Chirality : 0.043 0.182 1980 Planarity : 0.004 0.027 1740 Dihedral : 3.887 10.897 1440 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.47 % Allowed : 28.78 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.23), residues: 1350 helix: 1.36 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.30 (0.39), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 43 TYR 0.008 0.001 TYR N 9 PHE 0.021 0.001 PHE U 48 TRP 0.010 0.001 TRP O 29 Details of bonding type rmsd covalent geometry : bond 0.00343 (10980) covalent geometry : angle 0.60955 (14940) hydrogen bonds : bond 0.02605 ( 960) hydrogen bonds : angle 3.81680 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 743 time to evaluate : 0.443 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: A 27 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8628 (mt0) REVERT: A 42 ILE cc_start: 0.9388 (tp) cc_final: 0.9035 (tt) REVERT: A 47 LYS cc_start: 0.9154 (tttt) cc_final: 0.8891 (mmtt) REVERT: A 49 SER cc_start: 0.9174 (t) cc_final: 0.8937 (m) REVERT: B 47 LYS cc_start: 0.9085 (tttt) cc_final: 0.8787 (mmtt) REVERT: B 51 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8854 (mtpt) REVERT: C 43 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8248 (ttp80) REVERT: C 47 LYS cc_start: 0.9146 (tttt) cc_final: 0.8649 (tptt) REVERT: D 23 ASP cc_start: 0.8493 (m-30) cc_final: 0.8267 (m-30) REVERT: D 27 GLN cc_start: 0.9162 (tp40) cc_final: 0.8357 (tt0) REVERT: D 37 VAL cc_start: 0.9194 (p) cc_final: 0.8991 (m) REVERT: D 51 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8821 (mttt) REVERT: E 8 ASN cc_start: 0.8693 (t0) cc_final: 0.8234 (t0) REVERT: E 51 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8734 (mtpt) REVERT: F 51 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8968 (mtpp) REVERT: G 27 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8748 (mm-40) REVERT: H 9 TYR cc_start: 0.7642 (m-80) cc_final: 0.7294 (m-80) REVERT: H 43 ARG cc_start: 0.8766 (mtp180) cc_final: 0.8429 (ttm170) REVERT: I 27 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8657 (tp40) REVERT: I 50 SER cc_start: 0.8921 (t) cc_final: 0.8491 (p) REVERT: I 51 LYS cc_start: 0.9314 (mmtm) cc_final: 0.9003 (mtpp) REVERT: J 23 ASP cc_start: 0.8242 (p0) cc_final: 0.7918 (p0) REVERT: J 27 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8688 (tp-100) REVERT: J 48 PHE cc_start: 0.9350 (m-80) cc_final: 0.8835 (m-80) REVERT: K 12 GLU cc_start: 0.8104 (mp0) cc_final: 0.7768 (mp0) REVERT: K 14 MET cc_start: 0.8815 (mmt) cc_final: 0.8294 (mmt) REVERT: K 15 ASP cc_start: 0.8606 (m-30) cc_final: 0.8311 (m-30) REVERT: K 18 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8432 (ttmm) REVERT: K 50 SER cc_start: 0.9054 (t) cc_final: 0.8602 (p) REVERT: K 51 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9160 (mtpp) REVERT: L 14 MET cc_start: 0.8821 (mmt) cc_final: 0.8338 (mmt) REVERT: L 20 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8850 (mm-40) REVERT: L 47 LYS cc_start: 0.8702 (tttt) cc_final: 0.8403 (ttmm) REVERT: L 50 SER cc_start: 0.9312 (t) cc_final: 0.8910 (p) REVERT: L 51 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8630 (mtpp) REVERT: M 27 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8845 (tp40) REVERT: N 8 ASN cc_start: 0.7530 (t0) cc_final: 0.6957 (m-40) REVERT: N 15 ASP cc_start: 0.8550 (m-30) cc_final: 0.8318 (m-30) REVERT: N 47 LYS cc_start: 0.8780 (tttt) cc_final: 0.8512 (ttmm) REVERT: O 14 MET cc_start: 0.8739 (mmm) cc_final: 0.8427 (mmt) REVERT: P 15 ASP cc_start: 0.8329 (m-30) cc_final: 0.8082 (m-30) REVERT: P 27 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8698 (tp40) REVERT: Q 8 ASN cc_start: 0.8133 (t0) cc_final: 0.7874 (m110) REVERT: Q 15 ASP cc_start: 0.8592 (m-30) cc_final: 0.8282 (m-30) REVERT: S 15 ASP cc_start: 0.8427 (m-30) cc_final: 0.8046 (m-30) REVERT: S 51 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9000 (ttmm) REVERT: T 27 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8760 (tp-100) REVERT: U 40 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8951 (mt) REVERT: W 43 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8397 (ttp80) REVERT: Z 18 LYS cc_start: 0.8828 (tttt) cc_final: 0.8370 (mptt) REVERT: Z 46 LYS cc_start: 0.8584 (mttt) cc_final: 0.8279 (mtmt) REVERT: Z 49 SER cc_start: 0.9306 (m) cc_final: 0.9064 (t) REVERT: a 18 LYS cc_start: 0.8755 (tttt) cc_final: 0.8214 (mptt) REVERT: b 18 LYS cc_start: 0.8867 (tttt) cc_final: 0.8078 (mptt) REVERT: b 51 LYS cc_start: 0.8823 (mptt) cc_final: 0.8483 (mttm) REVERT: c 11 THR cc_start: 0.8986 (p) cc_final: 0.8492 (p) REVERT: c 15 ASP cc_start: 0.8636 (m-30) cc_final: 0.8404 (m-30) REVERT: c 18 LYS cc_start: 0.8998 (tttt) cc_final: 0.8261 (mptt) REVERT: d 18 LYS cc_start: 0.8673 (tttt) cc_final: 0.7942 (mptt) REVERT: d 51 LYS cc_start: 0.9049 (mptt) cc_final: 0.8736 (mptt) outliers start: 55 outliers final: 38 residues processed: 752 average time/residue: 0.1077 time to fit residues: 113.7147 Evaluate side-chains 754 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 714 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 ASN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085648 restraints weight = 20499.333| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.97 r_work: 0.3121 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10980 Z= 0.147 Angle : 0.620 7.698 14940 Z= 0.318 Chirality : 0.043 0.198 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.909 12.821 1440 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 3.82 % Allowed : 30.89 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.23), residues: 1350 helix: 1.40 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.39 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 43 TYR 0.007 0.001 TYR N 9 PHE 0.020 0.001 PHE U 48 TRP 0.012 0.001 TRP K 29 Details of bonding type rmsd covalent geometry : bond 0.00353 (10980) covalent geometry : angle 0.62025 (14940) hydrogen bonds : bond 0.02685 ( 960) hydrogen bonds : angle 3.82815 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 744 time to evaluate : 0.526 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: A 27 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8585 (mt0) REVERT: A 42 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9080 (tt) REVERT: A 47 LYS cc_start: 0.9148 (tttt) cc_final: 0.8890 (mmtt) REVERT: A 49 SER cc_start: 0.9150 (t) cc_final: 0.8915 (m) REVERT: B 47 LYS cc_start: 0.9067 (tttt) cc_final: 0.8812 (mmtt) REVERT: C 9 TYR cc_start: 0.7572 (m-80) cc_final: 0.7351 (m-80) REVERT: C 20 GLN cc_start: 0.8523 (mt0) cc_final: 0.8048 (mt0) REVERT: C 43 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8157 (ttp80) REVERT: C 47 LYS cc_start: 0.9145 (tttt) cc_final: 0.8642 (tptt) REVERT: D 23 ASP cc_start: 0.8513 (m-30) cc_final: 0.8294 (m-30) REVERT: D 27 GLN cc_start: 0.9136 (tp40) cc_final: 0.8342 (tt0) REVERT: D 37 VAL cc_start: 0.9258 (p) cc_final: 0.9033 (m) REVERT: D 51 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8816 (mttt) REVERT: E 8 ASN cc_start: 0.8695 (t0) cc_final: 0.8227 (t0) REVERT: E 19 THR cc_start: 0.9231 (p) cc_final: 0.8607 (p) REVERT: E 51 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8742 (mtpt) REVERT: F 51 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8991 (mtpp) REVERT: G 27 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8694 (mm-40) REVERT: H 9 TYR cc_start: 0.7656 (m-80) cc_final: 0.7269 (m-80) REVERT: H 43 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8350 (ttm170) REVERT: I 27 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8617 (tp40) REVERT: I 50 SER cc_start: 0.8966 (t) cc_final: 0.8529 (p) REVERT: I 51 LYS cc_start: 0.9308 (mmtm) cc_final: 0.9008 (mtpp) REVERT: J 23 ASP cc_start: 0.8308 (p0) cc_final: 0.7990 (p0) REVERT: J 27 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8645 (tp-100) REVERT: J 48 PHE cc_start: 0.9336 (m-80) cc_final: 0.8872 (m-80) REVERT: K 14 MET cc_start: 0.8764 (mmt) cc_final: 0.8286 (mmt) REVERT: K 15 ASP cc_start: 0.8601 (m-30) cc_final: 0.8342 (m-30) REVERT: K 18 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8478 (ttmm) REVERT: K 50 SER cc_start: 0.9093 (t) cc_final: 0.8596 (p) REVERT: K 51 LYS cc_start: 0.9405 (mtpp) cc_final: 0.9181 (mtpp) REVERT: L 14 MET cc_start: 0.8797 (mmt) cc_final: 0.8254 (mmt) REVERT: L 20 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8850 (mm-40) REVERT: L 47 LYS cc_start: 0.8679 (tttt) cc_final: 0.8399 (ttmm) REVERT: L 50 SER cc_start: 0.9338 (t) cc_final: 0.8934 (p) REVERT: L 51 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8641 (mtpp) REVERT: M 27 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8887 (tp40) REVERT: N 8 ASN cc_start: 0.7389 (t0) cc_final: 0.6976 (m-40) REVERT: N 47 LYS cc_start: 0.8754 (tttt) cc_final: 0.8551 (ttmm) REVERT: N 51 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8737 (mtpp) REVERT: O 8 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.6878 (m-40) REVERT: O 14 MET cc_start: 0.8715 (mmm) cc_final: 0.8298 (mmt) REVERT: P 15 ASP cc_start: 0.8301 (m-30) cc_final: 0.8075 (m-30) REVERT: P 27 GLN cc_start: 0.9092 (tp-100) cc_final: 0.8720 (tp40) REVERT: Q 15 ASP cc_start: 0.8599 (m-30) cc_final: 0.8302 (m-30) REVERT: R 12 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8077 (tm-30) REVERT: S 15 ASP cc_start: 0.8396 (m-30) cc_final: 0.8011 (m-30) REVERT: S 51 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8984 (ttmm) REVERT: T 27 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8722 (tp-100) REVERT: U 8 ASN cc_start: 0.6133 (t0) cc_final: 0.5569 (t0) REVERT: U 40 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9004 (mt) REVERT: W 18 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8663 (ttmm) REVERT: W 43 ARG cc_start: 0.8694 (ttm170) cc_final: 0.8362 (ttp80) REVERT: X 18 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8729 (tttp) REVERT: Z 18 LYS cc_start: 0.8845 (tttt) cc_final: 0.8406 (mptt) REVERT: Z 33 THR cc_start: 0.8531 (p) cc_final: 0.8316 (p) REVERT: Z 46 LYS cc_start: 0.8601 (mttt) cc_final: 0.8328 (mtmt) REVERT: Z 49 SER cc_start: 0.9314 (m) cc_final: 0.9065 (t) REVERT: Z 51 LYS cc_start: 0.9069 (mptt) cc_final: 0.8799 (mttm) REVERT: a 18 LYS cc_start: 0.8799 (tttt) cc_final: 0.8226 (mptt) REVERT: b 18 LYS cc_start: 0.9023 (tttt) cc_final: 0.8195 (mptt) REVERT: b 51 LYS cc_start: 0.8679 (mptt) cc_final: 0.8318 (mttm) REVERT: c 11 THR cc_start: 0.8999 (p) cc_final: 0.8501 (p) REVERT: c 15 ASP cc_start: 0.8629 (m-30) cc_final: 0.8428 (m-30) REVERT: c 18 LYS cc_start: 0.9012 (tttt) cc_final: 0.8269 (mptt) REVERT: d 18 LYS cc_start: 0.8704 (tttt) cc_final: 0.7835 (mptt) REVERT: d 51 LYS cc_start: 0.8981 (mptt) cc_final: 0.8706 (mptt) outliers start: 47 outliers final: 36 residues processed: 752 average time/residue: 0.1059 time to fit residues: 112.1203 Evaluate side-chains 765 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 725 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 8 ASN S 27 GLN V 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086667 restraints weight = 20273.466| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.97 r_work: 0.3136 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10980 Z= 0.143 Angle : 0.631 7.471 14940 Z= 0.323 Chirality : 0.044 0.203 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.954 13.210 1440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 3.25 % Allowed : 31.95 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.23), residues: 1350 helix: 1.43 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.96 (0.33), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 43 TYR 0.008 0.001 TYR L 9 PHE 0.020 0.001 PHE c 48 TRP 0.011 0.001 TRP O 29 Details of bonding type rmsd covalent geometry : bond 0.00341 (10980) covalent geometry : angle 0.63077 (14940) hydrogen bonds : bond 0.02698 ( 960) hydrogen bonds : angle 3.89675 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 737 time to evaluate : 0.464 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: A 27 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8564 (mt0) REVERT: A 42 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9130 (tt) REVERT: A 47 LYS cc_start: 0.9135 (tttt) cc_final: 0.8763 (tppt) REVERT: A 49 SER cc_start: 0.9195 (t) cc_final: 0.8979 (m) REVERT: B 27 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8310 (tt0) REVERT: B 47 LYS cc_start: 0.9070 (tttt) cc_final: 0.8774 (ttpp) REVERT: C 9 TYR cc_start: 0.7584 (m-80) cc_final: 0.7171 (m-80) REVERT: C 20 GLN cc_start: 0.8457 (mt0) cc_final: 0.8127 (mt0) REVERT: C 43 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8108 (ttp80) REVERT: C 47 LYS cc_start: 0.9125 (tttt) cc_final: 0.8632 (tptt) REVERT: D 23 ASP cc_start: 0.8518 (m-30) cc_final: 0.8298 (m-30) REVERT: D 27 GLN cc_start: 0.9115 (tp40) cc_final: 0.8283 (tt0) REVERT: D 37 VAL cc_start: 0.9249 (p) cc_final: 0.9021 (m) REVERT: D 51 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8805 (mttt) REVERT: E 8 ASN cc_start: 0.8687 (t0) cc_final: 0.8221 (t0) REVERT: E 47 LYS cc_start: 0.8265 (mmtt) cc_final: 0.8058 (ttpt) REVERT: E 51 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8731 (mtpt) REVERT: F 43 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8294 (ttp-110) REVERT: G 27 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8687 (mm-40) REVERT: H 9 TYR cc_start: 0.7629 (m-80) cc_final: 0.7291 (m-80) REVERT: H 43 ARG cc_start: 0.8767 (mtp180) cc_final: 0.8324 (ttm170) REVERT: I 27 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8510 (tp40) REVERT: I 50 SER cc_start: 0.8977 (t) cc_final: 0.8550 (p) REVERT: I 51 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8962 (mtpp) REVERT: J 23 ASP cc_start: 0.8310 (p0) cc_final: 0.8003 (p0) REVERT: J 27 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8676 (tp-100) REVERT: K 15 ASP cc_start: 0.8616 (m-30) cc_final: 0.8382 (m-30) REVERT: K 18 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8459 (ttmm) REVERT: K 43 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8435 (ttm170) REVERT: K 50 SER cc_start: 0.9117 (t) cc_final: 0.8583 (p) REVERT: K 51 LYS cc_start: 0.9343 (mtpp) cc_final: 0.9137 (mtpp) REVERT: L 14 MET cc_start: 0.8730 (mmt) cc_final: 0.8316 (mmt) REVERT: L 20 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8870 (mm-40) REVERT: L 47 LYS cc_start: 0.8664 (tttt) cc_final: 0.8409 (ttmm) REVERT: L 50 SER cc_start: 0.9326 (t) cc_final: 0.8932 (p) REVERT: L 51 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8622 (mtpp) REVERT: M 27 GLN cc_start: 0.9157 (tp-100) cc_final: 0.8844 (tp-100) REVERT: N 8 ASN cc_start: 0.7583 (t0) cc_final: 0.7184 (m-40) REVERT: N 15 ASP cc_start: 0.8499 (m-30) cc_final: 0.8291 (m-30) REVERT: N 51 LYS cc_start: 0.9132 (mtpp) cc_final: 0.8709 (mtpp) REVERT: O 14 MET cc_start: 0.8717 (mmm) cc_final: 0.8437 (mmt) REVERT: P 15 ASP cc_start: 0.8311 (m-30) cc_final: 0.8080 (m-30) REVERT: Q 15 ASP cc_start: 0.8604 (m-30) cc_final: 0.8284 (m-30) REVERT: R 9 TYR cc_start: 0.7681 (m-80) cc_final: 0.7342 (m-80) REVERT: S 15 ASP cc_start: 0.8409 (m-30) cc_final: 0.8032 (m-30) REVERT: S 51 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (ttmm) REVERT: T 27 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8813 (tp-100) REVERT: U 40 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8998 (mt) REVERT: W 18 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8662 (ttmm) REVERT: W 43 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8390 (ttp80) REVERT: X 23 ASP cc_start: 0.8733 (t70) cc_final: 0.8515 (t0) REVERT: X 51 LYS cc_start: 0.9328 (ttmm) cc_final: 0.9124 (ttmm) REVERT: Z 18 LYS cc_start: 0.8854 (tttt) cc_final: 0.8397 (mptt) REVERT: Z 46 LYS cc_start: 0.8618 (mttt) cc_final: 0.8337 (mtmt) REVERT: Z 49 SER cc_start: 0.9317 (m) cc_final: 0.9110 (t) REVERT: Z 51 LYS cc_start: 0.9038 (mptt) cc_final: 0.8794 (mttm) REVERT: a 18 LYS cc_start: 0.8713 (tttt) cc_final: 0.8200 (mptt) REVERT: b 18 LYS cc_start: 0.9014 (tttt) cc_final: 0.8137 (mptt) REVERT: b 51 LYS cc_start: 0.8668 (mptt) cc_final: 0.8334 (mttp) REVERT: c 18 LYS cc_start: 0.8983 (tttt) cc_final: 0.8246 (mptt) REVERT: d 18 LYS cc_start: 0.8781 (tttt) cc_final: 0.7924 (mptt) REVERT: d 51 LYS cc_start: 0.8955 (mptt) cc_final: 0.8731 (mptt) outliers start: 40 outliers final: 32 residues processed: 744 average time/residue: 0.1061 time to fit residues: 110.5011 Evaluate side-chains 761 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 726 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087250 restraints weight = 20074.141| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.96 r_work: 0.3151 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10980 Z= 0.145 Angle : 0.650 8.366 14940 Z= 0.333 Chirality : 0.044 0.206 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.920 12.766 1440 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 3.33 % Allowed : 32.93 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.23), residues: 1350 helix: 1.46 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.13 (0.44), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 43 TYR 0.006 0.001 TYR L 9 PHE 0.020 0.001 PHE c 48 TRP 0.008 0.001 TRP O 29 Details of bonding type rmsd covalent geometry : bond 0.00347 (10980) covalent geometry : angle 0.65049 (14940) hydrogen bonds : bond 0.02687 ( 960) hydrogen bonds : angle 3.90476 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 735 time to evaluate : 0.428 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: A 27 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8574 (mt0) REVERT: A 42 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9081 (tt) REVERT: A 47 LYS cc_start: 0.9179 (tttt) cc_final: 0.8801 (tppt) REVERT: A 49 SER cc_start: 0.9186 (t) cc_final: 0.8969 (m) REVERT: B 45 PHE cc_start: 0.9391 (t80) cc_final: 0.9170 (t80) REVERT: B 47 LYS cc_start: 0.9057 (tttt) cc_final: 0.8756 (ttpp) REVERT: C 9 TYR cc_start: 0.7588 (m-80) cc_final: 0.7357 (m-80) REVERT: C 20 GLN cc_start: 0.8456 (mt0) cc_final: 0.8146 (mt0) REVERT: C 43 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8091 (ttp80) REVERT: C 47 LYS cc_start: 0.9110 (tttt) cc_final: 0.8625 (tptt) REVERT: D 14 MET cc_start: 0.9061 (tpp) cc_final: 0.8841 (mmt) REVERT: D 23 ASP cc_start: 0.8488 (m-30) cc_final: 0.8271 (m-30) REVERT: D 27 GLN cc_start: 0.9123 (tp40) cc_final: 0.8290 (tt0) REVERT: D 37 VAL cc_start: 0.9248 (p) cc_final: 0.9017 (m) REVERT: D 51 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8774 (mttt) REVERT: E 8 ASN cc_start: 0.8659 (t0) cc_final: 0.8204 (t0) REVERT: E 19 THR cc_start: 0.9170 (p) cc_final: 0.8546 (p) REVERT: E 43 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8396 (mtm110) REVERT: E 47 LYS cc_start: 0.8256 (mmtt) cc_final: 0.8055 (ttpt) REVERT: E 51 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8731 (mtpt) REVERT: G 27 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8668 (mm-40) REVERT: H 9 TYR cc_start: 0.7579 (m-80) cc_final: 0.7286 (m-80) REVERT: H 43 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8330 (ttm170) REVERT: I 15 ASP cc_start: 0.8764 (m-30) cc_final: 0.8548 (m-30) REVERT: I 27 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8493 (tp40) REVERT: I 50 SER cc_start: 0.8988 (t) cc_final: 0.8571 (p) REVERT: I 51 LYS cc_start: 0.9233 (mmtm) cc_final: 0.8976 (mtpp) REVERT: J 20 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8727 (mt0) REVERT: J 23 ASP cc_start: 0.8256 (p0) cc_final: 0.7967 (p0) REVERT: J 27 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8632 (tp-100) REVERT: K 15 ASP cc_start: 0.8600 (m-30) cc_final: 0.8382 (m-30) REVERT: K 18 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8485 (ttmm) REVERT: K 43 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8465 (ttm170) REVERT: K 50 SER cc_start: 0.9126 (t) cc_final: 0.8620 (p) REVERT: K 51 LYS cc_start: 0.9349 (mtpp) cc_final: 0.9143 (mtpp) REVERT: L 14 MET cc_start: 0.8714 (mmt) cc_final: 0.8299 (mmt) REVERT: L 20 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8861 (mm-40) REVERT: L 47 LYS cc_start: 0.8641 (tttt) cc_final: 0.8379 (ttmm) REVERT: L 50 SER cc_start: 0.9249 (t) cc_final: 0.8848 (p) REVERT: L 51 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8622 (mtpp) REVERT: M 27 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8845 (tp-100) REVERT: N 8 ASN cc_start: 0.7635 (t0) cc_final: 0.7084 (t0) REVERT: N 51 LYS cc_start: 0.9095 (mtpp) cc_final: 0.8815 (mtpp) REVERT: O 14 MET cc_start: 0.8849 (mmm) cc_final: 0.8394 (mmt) REVERT: P 15 ASP cc_start: 0.8290 (m-30) cc_final: 0.8040 (m-30) REVERT: Q 15 ASP cc_start: 0.8526 (m-30) cc_final: 0.8179 (m-30) REVERT: S 15 ASP cc_start: 0.8393 (m-30) cc_final: 0.7976 (m-30) REVERT: S 51 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8997 (ttmm) REVERT: T 27 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8822 (tp-100) REVERT: U 8 ASN cc_start: 0.6342 (t0) cc_final: 0.6006 (t0) REVERT: U 40 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8993 (mt) REVERT: W 18 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8640 (ttmm) REVERT: W 43 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8407 (ttp80) REVERT: X 23 ASP cc_start: 0.8724 (t70) cc_final: 0.8513 (t0) REVERT: X 51 LYS cc_start: 0.9315 (ttmm) cc_final: 0.8873 (ttmm) REVERT: Y 47 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8744 (tttt) REVERT: Z 18 LYS cc_start: 0.8835 (tttt) cc_final: 0.8375 (mptt) REVERT: Z 28 THR cc_start: 0.9463 (m) cc_final: 0.9035 (p) REVERT: Z 46 LYS cc_start: 0.8593 (mttt) cc_final: 0.8302 (mtmt) REVERT: Z 47 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8837 (tttm) REVERT: Z 49 SER cc_start: 0.9320 (m) cc_final: 0.9111 (t) REVERT: Z 51 LYS cc_start: 0.9036 (mptt) cc_final: 0.8816 (mttm) REVERT: a 18 LYS cc_start: 0.8695 (tttt) cc_final: 0.8184 (mptt) REVERT: b 18 LYS cc_start: 0.8968 (tttt) cc_final: 0.8005 (mmtt) REVERT: b 46 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8528 (ttmm) REVERT: b 51 LYS cc_start: 0.8617 (mptt) cc_final: 0.8256 (mttp) REVERT: c 14 MET cc_start: 0.6560 (mmm) cc_final: 0.6161 (tpp) REVERT: c 18 LYS cc_start: 0.8956 (tttt) cc_final: 0.8241 (mptt) REVERT: d 18 LYS cc_start: 0.8781 (tttt) cc_final: 0.7937 (mptt) REVERT: d 51 LYS cc_start: 0.8957 (mptt) cc_final: 0.8685 (mptt) outliers start: 41 outliers final: 32 residues processed: 743 average time/residue: 0.1059 time to fit residues: 109.8293 Evaluate side-chains 760 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 725 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088006 restraints weight = 20104.886| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.99 r_work: 0.3164 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10980 Z= 0.145 Angle : 0.670 8.036 14940 Z= 0.344 Chirality : 0.045 0.205 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.946 14.615 1440 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.85 % Allowed : 34.47 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.23), residues: 1350 helix: 1.43 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.23 (0.48), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 43 TYR 0.014 0.001 TYR G 9 PHE 0.019 0.001 PHE c 48 TRP 0.010 0.001 TRP K 29 Details of bonding type rmsd covalent geometry : bond 0.00347 (10980) covalent geometry : angle 0.66994 (14940) hydrogen bonds : bond 0.02724 ( 960) hydrogen bonds : angle 3.99739 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 730 time to evaluate : 0.470 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: A 27 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8587 (mt0) REVERT: A 42 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9182 (tt) REVERT: A 47 LYS cc_start: 0.9173 (tttt) cc_final: 0.8789 (tppt) REVERT: A 49 SER cc_start: 0.9171 (t) cc_final: 0.8953 (m) REVERT: B 27 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8332 (tt0) REVERT: B 45 PHE cc_start: 0.9379 (t80) cc_final: 0.9166 (t80) REVERT: B 47 LYS cc_start: 0.9044 (tttt) cc_final: 0.8739 (ttpp) REVERT: C 9 TYR cc_start: 0.7568 (m-80) cc_final: 0.7354 (m-80) REVERT: C 43 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8059 (ttp80) REVERT: C 47 LYS cc_start: 0.9093 (tttt) cc_final: 0.8623 (tptt) REVERT: D 23 ASP cc_start: 0.8505 (m-30) cc_final: 0.8285 (m-30) REVERT: D 27 GLN cc_start: 0.9113 (tp40) cc_final: 0.8275 (tt0) REVERT: D 37 VAL cc_start: 0.9246 (p) cc_final: 0.9013 (m) REVERT: D 51 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8780 (mttt) REVERT: E 8 ASN cc_start: 0.8656 (t0) cc_final: 0.8226 (t0) REVERT: E 43 ARG cc_start: 0.8580 (mtp180) cc_final: 0.8367 (mtm110) REVERT: E 51 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8743 (mttt) REVERT: G 27 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8566 (mm-40) REVERT: G 49 SER cc_start: 0.9391 (m) cc_final: 0.9120 (p) REVERT: H 43 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8398 (ttm170) REVERT: I 27 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8477 (tp40) REVERT: I 50 SER cc_start: 0.8990 (t) cc_final: 0.8575 (p) REVERT: I 51 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8966 (mtpp) REVERT: J 20 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8727 (mt0) REVERT: J 23 ASP cc_start: 0.8288 (p0) cc_final: 0.7986 (p0) REVERT: J 27 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8617 (tp-100) REVERT: K 15 ASP cc_start: 0.8617 (m-30) cc_final: 0.8328 (m-30) REVERT: K 18 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8484 (ttmm) REVERT: K 43 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8406 (ttm170) REVERT: K 50 SER cc_start: 0.9123 (t) cc_final: 0.8591 (p) REVERT: K 51 LYS cc_start: 0.9341 (mtpp) cc_final: 0.9140 (mtpp) REVERT: L 14 MET cc_start: 0.8663 (mmt) cc_final: 0.8268 (mmt) REVERT: L 20 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8868 (mm-40) REVERT: M 27 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8844 (tp-100) REVERT: N 8 ASN cc_start: 0.7507 (t0) cc_final: 0.6859 (t0) REVERT: O 14 MET cc_start: 0.8822 (mmm) cc_final: 0.8409 (mmt) REVERT: P 15 ASP cc_start: 0.8391 (m-30) cc_final: 0.8139 (m-30) REVERT: P 27 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8840 (tp40) REVERT: Q 15 ASP cc_start: 0.8504 (m-30) cc_final: 0.8207 (m-30) REVERT: R 9 TYR cc_start: 0.7537 (m-80) cc_final: 0.7313 (m-80) REVERT: S 15 ASP cc_start: 0.8341 (m-30) cc_final: 0.7932 (m-30) REVERT: S 51 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8981 (ttmm) REVERT: T 14 MET cc_start: 0.8900 (tpp) cc_final: 0.8693 (tpp) REVERT: T 27 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8818 (tp-100) REVERT: T 47 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8893 (ttmm) REVERT: U 40 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8988 (mt) REVERT: W 18 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8649 (ttmm) REVERT: W 43 ARG cc_start: 0.8710 (ttm170) cc_final: 0.8411 (ttp80) REVERT: X 23 ASP cc_start: 0.8703 (t70) cc_final: 0.8495 (t0) REVERT: X 51 LYS cc_start: 0.9305 (ttmm) cc_final: 0.8904 (ttmm) REVERT: Z 18 LYS cc_start: 0.8796 (tttt) cc_final: 0.8335 (mptt) REVERT: Z 28 THR cc_start: 0.9447 (m) cc_final: 0.9000 (p) REVERT: Z 46 LYS cc_start: 0.8603 (mttt) cc_final: 0.8267 (mtmt) REVERT: Z 47 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8853 (tttm) REVERT: Z 49 SER cc_start: 0.9315 (m) cc_final: 0.9103 (t) REVERT: Z 51 LYS cc_start: 0.9016 (mptt) cc_final: 0.8711 (mttm) REVERT: a 18 LYS cc_start: 0.8679 (tttt) cc_final: 0.8169 (mptt) REVERT: b 18 LYS cc_start: 0.8974 (tttt) cc_final: 0.8127 (mptt) REVERT: b 46 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8491 (ttmm) REVERT: b 51 LYS cc_start: 0.8610 (mptt) cc_final: 0.8269 (mttm) REVERT: c 14 MET cc_start: 0.6349 (mmm) cc_final: 0.6004 (mmm) REVERT: c 18 LYS cc_start: 0.8952 (tttt) cc_final: 0.8253 (mptt) REVERT: d 18 LYS cc_start: 0.8775 (tttt) cc_final: 0.7932 (mptt) REVERT: d 51 LYS cc_start: 0.8944 (mptt) cc_final: 0.8680 (mptt) outliers start: 35 outliers final: 29 residues processed: 737 average time/residue: 0.1086 time to fit residues: 111.1827 Evaluate side-chains 749 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 717 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 98 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 20 GLN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078346 restraints weight = 21002.310| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.20 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10980 Z= 0.143 Angle : 0.666 7.994 14940 Z= 0.343 Chirality : 0.044 0.204 1980 Planarity : 0.004 0.030 1740 Dihedral : 3.947 15.045 1440 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.93 % Allowed : 34.88 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.23), residues: 1350 helix: 1.43 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.07 (0.46), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 43 TYR 0.010 0.001 TYR G 9 PHE 0.017 0.001 PHE U 48 TRP 0.011 0.001 TRP I 29 Details of bonding type rmsd covalent geometry : bond 0.00341 (10980) covalent geometry : angle 0.66606 (14940) hydrogen bonds : bond 0.02705 ( 960) hydrogen bonds : angle 3.97682 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.33 seconds wall clock time: 45 minutes 53.39 seconds (2753.39 seconds total)