Starting phenix.real_space_refine on Mon Jul 28 20:35:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a7f_6993/07_2025/6a7f_6993.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a7f_6993/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6a7f_6993/07_2025/6a7f_6993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a7f_6993/07_2025/6a7f_6993.map" model { file = "/net/cci-nas-00/data/ceres_data/6a7f_6993/07_2025/6a7f_6993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a7f_6993/07_2025/6a7f_6993.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, d Time building chain proxies: 2.78, per 1000 atoms: 0.26 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: 3.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.72 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: 3.28 Time building geometry restraints manager: 3.60 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' 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: 0.820 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.190 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (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 TRP 0.003 0.001 TRP S 29 PHE 0.008 0.003 PHE Y 48 TYR 0.003 0.001 TYR G 9 ARG 0.006 0.002 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.06220 ( 960) hydrogen bonds : angle 5.11291 ( 2880) covalent geometry : bond 0.01424 (10980) covalent geometry : angle 1.17200 (14940) *********************** 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 : 1.281 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: 0.2430 time to fit residues: 277.6393 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 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 D 27 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085907 restraints weight = 19885.723| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.90 r_work: 0.3123 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10980 Z= 0.140 Angle : 0.577 7.393 14940 Z= 0.303 Chirality : 0.041 0.135 1980 Planarity : 0.005 0.032 1740 Dihedral : 4.262 11.706 1440 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1350 helix: 0.37 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 3.16 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 29 PHE 0.011 0.001 PHE Q 48 TYR 0.007 0.001 TYR D 9 ARG 0.002 0.001 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 960) hydrogen bonds : angle 3.76019 ( 2880) covalent geometry : bond 0.00329 (10980) covalent geometry : angle 0.57712 (14940) *********************** 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 866 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 823 time to evaluate : 1.206 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 9 TYR cc_start: 0.7650 (m-80) cc_final: 0.7438 (m-80) REVERT: A 15 ASP cc_start: 0.8704 (m-30) cc_final: 0.8371 (m-30) REVERT: A 20 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8664 (mm-40) REVERT: A 27 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8862 (tp-100) REVERT: A 42 ILE cc_start: 0.9270 (tp) cc_final: 0.9053 (tt) REVERT: A 47 LYS cc_start: 0.9274 (tttt) cc_final: 0.9002 (mmtt) REVERT: A 49 SER cc_start: 0.9276 (t) cc_final: 0.8839 (p) REVERT: B 27 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8478 (tt0) REVERT: B 42 ILE cc_start: 0.9629 (tt) cc_final: 0.9365 (tp) REVERT: B 47 LYS cc_start: 0.9090 (tttt) cc_final: 0.8886 (mmtt) REVERT: B 51 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8802 (mtpt) REVERT: C 9 TYR cc_start: 0.7573 (m-80) cc_final: 0.7331 (m-80) REVERT: C 20 GLN cc_start: 0.8830 (tp40) cc_final: 0.8395 (mt0) REVERT: C 47 LYS cc_start: 0.9216 (tttt) cc_final: 0.8719 (tptt) REVERT: D 23 ASP cc_start: 0.8494 (m-30) cc_final: 0.8255 (m-30) REVERT: D 42 ILE cc_start: 0.9462 (tp) cc_final: 0.9249 (tt) REVERT: D 46 LYS cc_start: 0.9195 (mttm) cc_final: 0.8915 (mttp) REVERT: D 51 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8775 (mttt) REVERT: E 20 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8441 (mm-40) REVERT: E 42 ILE cc_start: 0.9432 (tp) cc_final: 0.9104 (tt) REVERT: F 8 ASN cc_start: 0.8025 (t0) cc_final: 0.7469 (t0) REVERT: G 20 GLN cc_start: 0.8993 (mm-40) cc_final: 0.7908 (mm-40) REVERT: G 40 LEU cc_start: 0.9584 (mt) cc_final: 0.9345 (mt) REVERT: H 9 TYR cc_start: 0.7729 (m-80) cc_final: 0.7305 (m-80) REVERT: H 19 THR cc_start: 0.8952 (p) cc_final: 0.8596 (p) REVERT: H 43 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8455 (ttm170) REVERT: I 19 THR cc_start: 0.9415 (t) cc_final: 0.8927 (p) REVERT: I 27 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8638 (tp-100) REVERT: I 50 SER cc_start: 0.8582 (t) cc_final: 0.8073 (p) REVERT: I 51 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8869 (mtpp) REVERT: J 26 SER cc_start: 0.8988 (p) cc_final: 0.8736 (p) REVERT: J 27 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8752 (tp-100) REVERT: K 14 MET cc_start: 0.8801 (mmt) cc_final: 0.8299 (mmt) REVERT: L 20 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8856 (mm-40) REVERT: L 47 LYS cc_start: 0.8826 (tttt) cc_final: 0.8539 (ttmm) REVERT: L 51 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8754 (mmmm) REVERT: M 14 MET cc_start: 0.8734 (mmm) cc_final: 0.8121 (mmt) REVERT: M 15 ASP cc_start: 0.8626 (m-30) cc_final: 0.8389 (m-30) REVERT: M 27 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8805 (tp-100) REVERT: M 51 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8628 (mmmm) REVERT: N 8 ASN cc_start: 0.8059 (t0) cc_final: 0.7173 (m-40) REVERT: N 47 LYS cc_start: 0.8926 (tttt) cc_final: 0.8521 (ttmm) REVERT: N 50 SER cc_start: 0.8939 (t) cc_final: 0.8542 (p) REVERT: O 14 MET cc_start: 0.8747 (mmm) cc_final: 0.8425 (mmt) REVERT: O 27 GLN cc_start: 0.9064 (tp40) cc_final: 0.8685 (tp40) REVERT: P 15 ASP cc_start: 0.8270 (m-30) cc_final: 0.7954 (m-30) REVERT: P 27 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8714 (tp40) REVERT: P 51 LYS cc_start: 0.9269 (mmtp) cc_final: 0.9060 (mttm) REVERT: Q 8 ASN cc_start: 0.8199 (t0) cc_final: 0.7743 (t0) REVERT: Q 9 TYR cc_start: 0.7269 (m-80) cc_final: 0.6937 (m-80) REVERT: Q 15 ASP cc_start: 0.8472 (m-30) cc_final: 0.8146 (m-30) REVERT: Q 27 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8277 (tp-100) REVERT: Q 40 LEU cc_start: 0.9526 (mt) cc_final: 0.9301 (mt) REVERT: S 15 ASP cc_start: 0.8480 (m-30) cc_final: 0.8208 (m-30) REVERT: T 27 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8749 (tp-100) REVERT: U 15 ASP cc_start: 0.8704 (m-30) cc_final: 0.8498 (m-30) REVERT: U 18 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8510 (ttmm) REVERT: U 40 LEU cc_start: 0.9286 (mp) cc_final: 0.8901 (mt) REVERT: V 8 ASN cc_start: 0.7305 (t0) cc_final: 0.6873 (t0) REVERT: V 47 LYS cc_start: 0.9117 (tttm) cc_final: 0.8860 (ttmm) REVERT: W 9 TYR cc_start: 0.7711 (m-80) cc_final: 0.7318 (m-80) REVERT: W 43 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8471 (ttp80) REVERT: X 51 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8745 (mttp) REVERT: Y 8 ASN cc_start: 0.7196 (t0) cc_final: 0.6211 (t0) REVERT: Y 18 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8689 (ttmm) REVERT: Y 47 LYS cc_start: 0.9043 (tttm) cc_final: 0.8799 (ttmm) REVERT: Z 18 LYS cc_start: 0.8790 (tttt) cc_final: 0.8397 (mptt) REVERT: Z 46 LYS cc_start: 0.8681 (mttt) cc_final: 0.8258 (mtmt) REVERT: Z 49 SER cc_start: 0.9162 (m) cc_final: 0.8824 (t) REVERT: a 9 TYR cc_start: 0.8119 (m-80) cc_final: 0.7437 (p90) REVERT: a 18 LYS cc_start: 0.8913 (tttt) cc_final: 0.8286 (mptt) REVERT: a 20 GLN cc_start: 0.9218 (mm110) cc_final: 0.9007 (mm-40) REVERT: b 15 ASP cc_start: 0.8862 (m-30) cc_final: 0.8572 (m-30) REVERT: b 18 LYS cc_start: 0.8815 (tttt) cc_final: 0.8381 (mptt) REVERT: b 24 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8977 (tp) REVERT: c 15 ASP cc_start: 0.8609 (m-30) cc_final: 0.8330 (m-30) REVERT: c 18 LYS cc_start: 0.8878 (tttt) cc_final: 0.8410 (mptt) REVERT: c 25 ILE cc_start: 0.9381 (mt) cc_final: 0.9104 (mt) REVERT: d 15 ASP cc_start: 0.8552 (m-30) cc_final: 0.8232 (m-30) REVERT: d 18 LYS cc_start: 0.8782 (tttt) cc_final: 0.8076 (mmtt) outliers start: 43 outliers final: 30 residues processed: 827 average time/residue: 0.2273 time to fit residues: 259.8849 Evaluate side-chains 756 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 725 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 F residue 35 VAL 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 Q 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 24 LEU 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 48 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.095121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081953 restraints weight = 20380.335| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.90 r_work: 0.3066 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10980 Z= 0.183 Angle : 0.608 6.431 14940 Z= 0.316 Chirality : 0.043 0.139 1980 Planarity : 0.004 0.031 1740 Dihedral : 4.073 11.625 1440 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.04 % Allowed : 22.03 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1350 helix: 0.87 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 3.24 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 29 PHE 0.013 0.002 PHE Q 48 TYR 0.006 0.001 TYR K 9 ARG 0.003 0.000 ARG Q 43 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 960) hydrogen bonds : angle 3.75705 ( 2880) covalent geometry : bond 0.00442 (10980) covalent geometry : angle 0.60819 (14940) *********************** 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 815 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 753 time to evaluate : 1.181 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 20 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8483 (mm-40) REVERT: A 27 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8759 (tp-100) REVERT: A 42 ILE cc_start: 0.9425 (tp) cc_final: 0.9150 (tt) REVERT: A 47 LYS cc_start: 0.9234 (tttt) cc_final: 0.8964 (mmtt) REVERT: A 49 SER cc_start: 0.9291 (t) cc_final: 0.9020 (m) REVERT: A 51 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8768 (mtpt) REVERT: B 20 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 42 ILE cc_start: 0.9644 (tt) cc_final: 0.9400 (tp) REVERT: B 45 PHE cc_start: 0.9462 (t80) cc_final: 0.9106 (t80) REVERT: B 47 LYS cc_start: 0.9108 (tttt) cc_final: 0.8789 (mmtt) REVERT: B 51 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8834 (mttt) REVERT: C 20 GLN cc_start: 0.8793 (tp40) cc_final: 0.8565 (mt0) REVERT: C 47 LYS cc_start: 0.9211 (tttt) cc_final: 0.8713 (tptt) REVERT: D 23 ASP cc_start: 0.8529 (m-30) cc_final: 0.8280 (m-30) REVERT: D 51 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8810 (mttt) REVERT: E 14 MET cc_start: 0.8954 (mmt) cc_final: 0.8728 (tpp) REVERT: E 20 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8634 (mm-40) REVERT: E 42 ILE cc_start: 0.9415 (tp) cc_final: 0.9116 (tt) REVERT: F 8 ASN cc_start: 0.7918 (t0) cc_final: 0.7636 (t0) REVERT: F 20 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8561 (mm-40) REVERT: G 12 GLU cc_start: 0.8129 (mp0) cc_final: 0.7810 (mp0) REVERT: G 49 SER cc_start: 0.9310 (m) cc_final: 0.9040 (p) REVERT: H 9 TYR cc_start: 0.7781 (m-80) cc_final: 0.7508 (m-80) REVERT: H 43 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8492 (ttm170) REVERT: H 50 SER cc_start: 0.9150 (t) cc_final: 0.8738 (p) REVERT: H 51 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9140 (mtpp) REVERT: I 27 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8633 (tp-100) REVERT: I 50 SER cc_start: 0.8910 (t) cc_final: 0.8522 (p) REVERT: I 51 LYS cc_start: 0.9326 (mmtm) cc_final: 0.8944 (mtpp) REVERT: J 23 ASP cc_start: 0.8232 (p0) cc_final: 0.7867 (p0) REVERT: J 27 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8691 (tp-100) REVERT: J 48 PHE cc_start: 0.9481 (m-80) cc_final: 0.8878 (m-80) REVERT: J 51 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9203 (mtpp) REVERT: K 12 GLU cc_start: 0.7869 (mp0) cc_final: 0.7611 (mp0) REVERT: K 14 MET cc_start: 0.8757 (mmt) cc_final: 0.8232 (mmt) REVERT: K 50 SER cc_start: 0.8978 (t) cc_final: 0.8429 (p) REVERT: L 14 MET cc_start: 0.8842 (mmt) cc_final: 0.8529 (mmt) REVERT: L 47 LYS cc_start: 0.8878 (tttt) cc_final: 0.8375 (ttmm) REVERT: L 50 SER cc_start: 0.9075 (t) cc_final: 0.8675 (p) REVERT: M 14 MET cc_start: 0.8636 (mmm) cc_final: 0.8413 (mmt) REVERT: M 15 ASP cc_start: 0.8642 (m-30) cc_final: 0.8423 (m-30) REVERT: N 8 ASN cc_start: 0.8020 (t0) cc_final: 0.6937 (m-40) REVERT: N 18 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8500 (ttmt) REVERT: N 47 LYS cc_start: 0.8876 (tttt) cc_final: 0.8436 (ttmm) REVERT: N 50 SER cc_start: 0.9000 (t) cc_final: 0.8567 (p) REVERT: N 51 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8782 (mtpp) REVERT: O 12 GLU cc_start: 0.7547 (mp0) cc_final: 0.7332 (mp0) REVERT: O 14 MET cc_start: 0.8826 (mmm) cc_final: 0.8513 (mmt) REVERT: O 27 GLN cc_start: 0.9119 (tp40) cc_final: 0.8732 (tp40) REVERT: P 15 ASP cc_start: 0.8288 (m-30) cc_final: 0.7998 (m-30) REVERT: P 27 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8803 (tp40) REVERT: P 51 LYS cc_start: 0.9348 (mmtp) cc_final: 0.9128 (mttm) REVERT: Q 8 ASN cc_start: 0.8268 (t0) cc_final: 0.7925 (m110) REVERT: Q 15 ASP cc_start: 0.8500 (m-30) cc_final: 0.8221 (m-30) REVERT: Q 40 LEU cc_start: 0.9578 (mt) cc_final: 0.9361 (mt) REVERT: Q 42 ILE cc_start: 0.9637 (tp) cc_final: 0.9416 (tt) REVERT: S 15 ASP cc_start: 0.8440 (m-30) cc_final: 0.8123 (m-30) REVERT: T 27 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8743 (tp-100) REVERT: U 8 ASN cc_start: 0.7411 (t0) cc_final: 0.6742 (t0) REVERT: U 15 ASP cc_start: 0.8680 (m-30) cc_final: 0.8433 (m-30) REVERT: U 18 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8620 (ttmm) REVERT: U 40 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8907 (mt) REVERT: U 51 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8178 (mttp) REVERT: V 8 ASN cc_start: 0.7159 (t0) cc_final: 0.6474 (t0) REVERT: V 51 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8895 (mttm) REVERT: W 43 ARG cc_start: 0.8805 (ttm170) cc_final: 0.8526 (ttp80) REVERT: X 51 LYS cc_start: 0.9116 (mmtp) cc_final: 0.8878 (mttp) REVERT: Y 47 LYS cc_start: 0.9104 (tttm) cc_final: 0.8888 (ttmm) REVERT: Z 18 LYS cc_start: 0.8787 (tttt) cc_final: 0.8366 (mptt) REVERT: Z 44 LEU cc_start: 0.9466 (mt) cc_final: 0.9244 (mp) REVERT: Z 46 LYS cc_start: 0.8575 (mttt) cc_final: 0.8212 (mttt) REVERT: Z 49 SER cc_start: 0.9323 (m) cc_final: 0.8955 (t) REVERT: a 18 LYS cc_start: 0.8803 (tttt) cc_final: 0.8239 (mptt) REVERT: b 18 LYS cc_start: 0.8853 (tttt) cc_final: 0.8249 (mptt) REVERT: c 15 ASP cc_start: 0.8671 (m-30) cc_final: 0.8453 (m-30) REVERT: c 18 LYS cc_start: 0.8973 (tttt) cc_final: 0.8388 (mptt) REVERT: d 18 LYS cc_start: 0.8752 (tttt) cc_final: 0.8026 (mmtt) outliers start: 62 outliers final: 50 residues processed: 761 average time/residue: 0.2169 time to fit residues: 230.8877 Evaluate side-chains 765 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 714 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 35 VAL 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 26 SER Chi-restraints excluded: chain E residue 35 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 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 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 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 34 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 37 VAL 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 a residue 35 VAL Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 33 THR 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 24 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN Q 27 GLN R 27 GLN W 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074534 restraints weight = 21045.538| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.07 r_work: 0.3091 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10980 Z= 0.145 Angle : 0.588 6.912 14940 Z= 0.302 Chirality : 0.043 0.143 1980 Planarity : 0.004 0.031 1740 Dihedral : 3.944 11.332 1440 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.39 % Allowed : 24.96 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1350 helix: 1.08 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.58 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 29 PHE 0.011 0.001 PHE O 48 TYR 0.007 0.001 TYR H 9 ARG 0.003 0.000 ARG Q 43 Details of bonding type rmsd hydrogen bonds : bond 0.02645 ( 960) hydrogen bonds : angle 3.73633 ( 2880) covalent geometry : bond 0.00347 (10980) covalent geometry : angle 0.58806 (14940) *********************** 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 814 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 760 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8634 (mt0) REVERT: A 42 ILE cc_start: 0.9440 (tp) cc_final: 0.9178 (tt) REVERT: A 47 LYS cc_start: 0.9202 (tttt) cc_final: 0.8847 (tppt) REVERT: A 49 SER cc_start: 0.9274 (t) cc_final: 0.9025 (m) REVERT: A 51 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8750 (mtpt) REVERT: B 45 PHE cc_start: 0.9457 (t80) cc_final: 0.9154 (t80) REVERT: B 47 LYS cc_start: 0.9098 (tttt) cc_final: 0.8790 (mmtt) REVERT: B 51 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8809 (mtpt) REVERT: C 20 GLN cc_start: 0.8717 (tp40) cc_final: 0.8502 (mt0) REVERT: C 45 PHE cc_start: 0.9484 (t80) cc_final: 0.9228 (t80) REVERT: C 47 LYS cc_start: 0.9166 (tttt) cc_final: 0.8663 (tptt) REVERT: D 23 ASP cc_start: 0.8525 (m-30) cc_final: 0.8286 (m-30) REVERT: D 51 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8886 (mttt) REVERT: E 42 ILE cc_start: 0.9336 (tp) cc_final: 0.9052 (tt) REVERT: E 51 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8750 (mttt) REVERT: F 8 ASN cc_start: 0.7868 (t0) cc_final: 0.7082 (m110) REVERT: G 12 GLU cc_start: 0.8155 (mp0) cc_final: 0.7839 (mp0) REVERT: G 27 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8743 (mm-40) REVERT: G 49 SER cc_start: 0.9330 (m) cc_final: 0.9040 (p) REVERT: H 9 TYR cc_start: 0.7436 (m-80) cc_final: 0.7056 (m-80) REVERT: H 43 ARG cc_start: 0.8811 (mtp180) cc_final: 0.8388 (ttm170) REVERT: I 27 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8498 (tp-100) REVERT: I 50 SER cc_start: 0.8946 (t) cc_final: 0.8522 (p) REVERT: I 51 LYS cc_start: 0.9340 (mmtm) cc_final: 0.8991 (mtpp) REVERT: J 23 ASP cc_start: 0.8273 (p0) cc_final: 0.7873 (p0) REVERT: J 27 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8794 (tp-100) REVERT: K 14 MET cc_start: 0.8793 (mmt) cc_final: 0.8308 (mmt) REVERT: K 50 SER cc_start: 0.9038 (t) cc_final: 0.8537 (p) REVERT: K 51 LYS cc_start: 0.9359 (mtpp) cc_final: 0.8994 (mttp) REVERT: L 20 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8873 (mm-40) REVERT: L 47 LYS cc_start: 0.8733 (tttt) cc_final: 0.8325 (ttmm) REVERT: L 50 SER cc_start: 0.9066 (t) cc_final: 0.8624 (p) REVERT: L 51 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8997 (mtpp) REVERT: M 14 MET cc_start: 0.8710 (mmm) cc_final: 0.8494 (mmt) REVERT: M 15 ASP cc_start: 0.8576 (m-30) cc_final: 0.8341 (m-30) REVERT: M 27 GLN cc_start: 0.9022 (tp40) cc_final: 0.8770 (tp40) REVERT: N 8 ASN cc_start: 0.7627 (t0) cc_final: 0.7039 (m-40) REVERT: N 18 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8395 (ttmm) REVERT: N 47 LYS cc_start: 0.8836 (tttt) cc_final: 0.8409 (ttmm) REVERT: N 50 SER cc_start: 0.8983 (t) cc_final: 0.8554 (p) REVERT: N 51 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8776 (mtpp) REVERT: O 14 MET cc_start: 0.8772 (mmm) cc_final: 0.8414 (mmt) REVERT: O 27 GLN cc_start: 0.9089 (tp40) cc_final: 0.8712 (tp40) REVERT: P 15 ASP cc_start: 0.8327 (m-30) cc_final: 0.8124 (m-30) REVERT: P 27 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8691 (tp40) REVERT: Q 8 ASN cc_start: 0.8231 (t0) cc_final: 0.7918 (m110) REVERT: Q 15 ASP cc_start: 0.8523 (m-30) cc_final: 0.8180 (m-30) REVERT: Q 40 LEU cc_start: 0.9549 (mt) cc_final: 0.9327 (mt) REVERT: Q 42 ILE cc_start: 0.9629 (tp) cc_final: 0.9417 (tt) REVERT: S 15 ASP cc_start: 0.8449 (m-30) cc_final: 0.8213 (m-30) REVERT: T 27 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8728 (tp-100) REVERT: U 8 ASN cc_start: 0.6955 (t0) cc_final: 0.6327 (t0) REVERT: U 15 ASP cc_start: 0.8841 (m-30) cc_final: 0.8559 (m-30) REVERT: U 40 LEU cc_start: 0.9312 (mp) cc_final: 0.8934 (mt) REVERT: U 51 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8180 (mttp) REVERT: V 51 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8786 (mttm) REVERT: W 15 ASP cc_start: 0.8625 (m-30) cc_final: 0.8378 (m-30) REVERT: W 43 ARG cc_start: 0.8726 (ttm170) cc_final: 0.8436 (ttp80) REVERT: X 19 THR cc_start: 0.9183 (p) cc_final: 0.8950 (t) REVERT: Z 18 LYS cc_start: 0.8799 (tttt) cc_final: 0.8342 (mptt) REVERT: Z 46 LYS cc_start: 0.8506 (mttt) cc_final: 0.8210 (mtmt) REVERT: Z 49 SER cc_start: 0.9299 (m) cc_final: 0.8983 (t) REVERT: a 18 LYS cc_start: 0.8715 (tttt) cc_final: 0.8217 (mptt) REVERT: b 15 ASP cc_start: 0.8653 (m-30) cc_final: 0.8365 (m-30) REVERT: b 18 LYS cc_start: 0.8922 (tttt) cc_final: 0.8240 (mptt) REVERT: c 11 THR cc_start: 0.9015 (p) cc_final: 0.8544 (p) REVERT: c 15 ASP cc_start: 0.8658 (m-30) cc_final: 0.8435 (m-30) REVERT: c 18 LYS cc_start: 0.8973 (tttt) cc_final: 0.8278 (mptt) REVERT: d 18 LYS cc_start: 0.8771 (tttt) cc_final: 0.8019 (mmtt) REVERT: d 23 ASP cc_start: 0.8558 (t0) cc_final: 0.8341 (t0) REVERT: d 26 SER cc_start: 0.9340 (m) cc_final: 0.9045 (p) outliers start: 54 outliers final: 40 residues processed: 771 average time/residue: 0.2175 time to fit residues: 235.8500 Evaluate side-chains 761 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 721 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 J residue 44 LEU 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 9 TYR Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S 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 37 VAL Chi-restraints excluded: chain V residue 9 TYR 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 37 VAL Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR 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 70 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 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 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 = 0.3462 r_free = 0.3462 target = 0.088254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074815 restraints weight = 21087.290| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.03 r_work: 0.3096 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.5224 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= 0.145 Angle : 0.580 6.511 14940 Z= 0.299 Chirality : 0.043 0.163 1980 Planarity : 0.004 0.030 1740 Dihedral : 3.898 11.375 1440 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.63 % Allowed : 26.34 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1350 helix: 1.23 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.53 (0.45), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 29 PHE 0.013 0.001 PHE O 48 TYR 0.006 0.001 TYR Y 9 ARG 0.003 0.000 ARG S 43 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 960) hydrogen bonds : angle 3.76159 ( 2880) covalent geometry : bond 0.00350 (10980) covalent geometry : angle 0.57955 (14940) *********************** 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 809 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 752 time to evaluate : 1.126 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: 0.9101 (tp-100) cc_final: 0.8586 (mt0) REVERT: A 42 ILE cc_start: 0.9451 (tp) cc_final: 0.9188 (tt) REVERT: A 47 LYS cc_start: 0.9138 (tttt) cc_final: 0.8918 (mmtt) REVERT: A 49 SER cc_start: 0.9199 (t) cc_final: 0.8949 (m) REVERT: B 47 LYS cc_start: 0.9085 (tttt) cc_final: 0.8804 (mmtt) REVERT: B 51 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8793 (mtpt) REVERT: C 43 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8269 (ttp80) REVERT: C 45 PHE cc_start: 0.9444 (t80) cc_final: 0.9226 (t80) REVERT: C 47 LYS cc_start: 0.9163 (tttt) cc_final: 0.8661 (tptt) REVERT: D 23 ASP cc_start: 0.8516 (m-30) cc_final: 0.8290 (m-30) REVERT: D 25 ILE cc_start: 0.9407 (mt) cc_final: 0.9177 (mt) REVERT: D 51 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8878 (mttt) REVERT: E 8 ASN cc_start: 0.8561 (t0) cc_final: 0.8086 (t0) REVERT: E 19 THR cc_start: 0.8958 (p) cc_final: 0.8366 (p) REVERT: E 51 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8722 (mtpt) REVERT: F 8 ASN cc_start: 0.7567 (t0) cc_final: 0.7068 (m110) REVERT: G 27 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8651 (mm-40) REVERT: G 43 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8761 (mtp180) REVERT: G 49 SER cc_start: 0.9347 (m) cc_final: 0.9052 (p) REVERT: H 43 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8340 (ttm170) REVERT: H 50 SER cc_start: 0.9019 (t) cc_final: 0.8607 (p) REVERT: I 19 THR cc_start: 0.9248 (t) cc_final: 0.8975 (p) REVERT: I 20 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8451 (tp40) REVERT: I 27 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8513 (tp-100) REVERT: I 50 SER cc_start: 0.8960 (t) cc_final: 0.8531 (p) REVERT: I 51 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9041 (mtpp) REVERT: J 20 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8875 (mm-40) REVERT: J 23 ASP cc_start: 0.8258 (p0) cc_final: 0.7949 (p0) REVERT: J 27 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8782 (tp-100) REVERT: K 12 GLU cc_start: 0.8041 (mp0) cc_final: 0.7733 (mp0) REVERT: K 14 MET cc_start: 0.8768 (mmt) cc_final: 0.8243 (mmt) REVERT: K 15 ASP cc_start: 0.8637 (m-30) cc_final: 0.8327 (m-30) REVERT: K 50 SER cc_start: 0.9093 (t) cc_final: 0.8628 (p) REVERT: K 51 LYS cc_start: 0.9340 (mtpp) cc_final: 0.8993 (mttp) REVERT: L 20 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8863 (mm-40) REVERT: L 47 LYS cc_start: 0.8689 (tttt) cc_final: 0.8312 (ttmm) REVERT: L 50 SER cc_start: 0.9158 (t) cc_final: 0.8707 (p) REVERT: L 51 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8874 (mtpp) REVERT: M 15 ASP cc_start: 0.8552 (m-30) cc_final: 0.8336 (m-30) REVERT: M 27 GLN cc_start: 0.9036 (tp40) cc_final: 0.8792 (tp40) REVERT: N 8 ASN cc_start: 0.7420 (t0) cc_final: 0.7004 (m-40) REVERT: N 18 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8359 (ttmm) REVERT: N 47 LYS cc_start: 0.8838 (tttt) cc_final: 0.8554 (ttmm) REVERT: O 14 MET cc_start: 0.8801 (mmm) cc_final: 0.8470 (mmt) REVERT: P 15 ASP cc_start: 0.8345 (m-30) cc_final: 0.8115 (m-30) REVERT: P 27 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8709 (tp40) REVERT: Q 8 ASN cc_start: 0.8174 (t0) cc_final: 0.7894 (m110) REVERT: Q 15 ASP cc_start: 0.8592 (m-30) cc_final: 0.8319 (m-30) REVERT: R 9 TYR cc_start: 0.7814 (m-80) cc_final: 0.7529 (m-80) REVERT: S 15 ASP cc_start: 0.8419 (m-30) cc_final: 0.8032 (m-30) REVERT: T 27 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8732 (tp-100) REVERT: U 8 ASN cc_start: 0.6740 (t0) cc_final: 0.5775 (t0) REVERT: U 15 ASP cc_start: 0.8712 (m-30) cc_final: 0.8387 (m-30) REVERT: U 40 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9034 (mt) REVERT: W 9 TYR cc_start: 0.7394 (m-80) cc_final: 0.6892 (m-80) REVERT: W 11 THR cc_start: 0.8761 (p) cc_final: 0.8246 (p) REVERT: W 15 ASP cc_start: 0.8724 (m-30) cc_final: 0.8410 (m-30) REVERT: W 43 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8401 (ttp80) REVERT: X 19 THR cc_start: 0.9151 (p) cc_final: 0.8914 (t) REVERT: Z 18 LYS cc_start: 0.8830 (tttt) cc_final: 0.8386 (mptt) REVERT: Z 33 THR cc_start: 0.8859 (t) cc_final: 0.8635 (p) REVERT: Z 46 LYS cc_start: 0.8572 (mttt) cc_final: 0.8297 (mtmt) REVERT: Z 49 SER cc_start: 0.9303 (m) cc_final: 0.9002 (t) REVERT: a 18 LYS cc_start: 0.8789 (tttt) cc_final: 0.8249 (mptt) REVERT: b 18 LYS cc_start: 0.8941 (tttt) cc_final: 0.8143 (mptt) REVERT: c 11 THR cc_start: 0.8999 (p) cc_final: 0.8507 (p) REVERT: c 18 LYS cc_start: 0.9003 (tttt) cc_final: 0.8240 (mptt) REVERT: c 48 PHE cc_start: 0.9069 (m-80) cc_final: 0.8803 (m-80) REVERT: d 18 LYS cc_start: 0.8783 (tttt) cc_final: 0.7970 (mmtt) REVERT: d 23 ASP cc_start: 0.8583 (t0) cc_final: 0.8338 (t0) REVERT: d 26 SER cc_start: 0.9271 (m) cc_final: 0.9001 (p) outliers start: 57 outliers final: 48 residues processed: 761 average time/residue: 0.2890 time to fit residues: 312.0354 Evaluate side-chains 774 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 725 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 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 J residue 49 SER 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 M residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 9 TYR 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 37 VAL 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 32 VAL Chi-restraints excluded: chain X residue 37 VAL 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 17 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS 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 42 ILE Chi-restraints excluded: chain d residue 9 TYR Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3456 r_free = 0.3456 target = 0.088012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074308 restraints weight = 21347.615| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.12 r_work: 0.3080 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10980 Z= 0.166 Angle : 0.624 7.531 14940 Z= 0.320 Chirality : 0.044 0.179 1980 Planarity : 0.004 0.032 1740 Dihedral : 3.911 11.793 1440 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.28 % Allowed : 26.83 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1350 helix: 1.28 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.59 (0.42), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 29 PHE 0.013 0.002 PHE O 48 TYR 0.007 0.001 TYR N 9 ARG 0.002 0.000 ARG S 43 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 960) hydrogen bonds : angle 3.84329 ( 2880) covalent geometry : bond 0.00402 (10980) covalent geometry : angle 0.62373 (14940) *********************** 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 800 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 735 time to evaluate : 1.501 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 42 ILE cc_start: 0.9465 (tp) cc_final: 0.9166 (tt) REVERT: A 47 LYS cc_start: 0.9146 (tttt) cc_final: 0.8905 (mmtt) REVERT: A 49 SER cc_start: 0.9171 (t) cc_final: 0.8930 (m) REVERT: B 47 LYS cc_start: 0.9098 (tttt) cc_final: 0.8802 (mmtt) REVERT: B 51 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8828 (mtpt) REVERT: C 9 TYR cc_start: 0.7662 (m-80) cc_final: 0.7223 (m-80) REVERT: C 43 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8269 (ttp80) REVERT: C 47 LYS cc_start: 0.9142 (tttt) cc_final: 0.8629 (tptt) REVERT: D 23 ASP cc_start: 0.8562 (m-30) cc_final: 0.8346 (m-30) REVERT: D 25 ILE cc_start: 0.9373 (mt) cc_final: 0.9132 (mt) REVERT: D 37 VAL cc_start: 0.9266 (p) cc_final: 0.8992 (m) REVERT: D 51 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8828 (mttt) REVERT: E 8 ASN cc_start: 0.8555 (t0) cc_final: 0.8156 (t0) REVERT: E 51 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8724 (mtpt) REVERT: F 8 ASN cc_start: 0.7663 (t0) cc_final: 0.7059 (m110) REVERT: F 51 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8942 (mtpp) REVERT: G 12 GLU cc_start: 0.8314 (mp0) cc_final: 0.8046 (mp0) REVERT: G 27 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8773 (mm-40) REVERT: G 43 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8787 (mtp180) REVERT: H 43 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8415 (ttm170) REVERT: I 27 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8457 (tp-100) REVERT: I 50 SER cc_start: 0.9028 (t) cc_final: 0.8574 (p) REVERT: I 51 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9031 (mtpp) REVERT: J 23 ASP cc_start: 0.8246 (p0) cc_final: 0.7935 (p0) REVERT: J 27 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8723 (tp-100) REVERT: K 7 THR cc_start: 0.8397 (p) cc_final: 0.8174 (t) REVERT: K 12 GLU cc_start: 0.8146 (mp0) cc_final: 0.7778 (mp0) REVERT: K 14 MET cc_start: 0.8811 (mmt) cc_final: 0.8324 (mmt) REVERT: K 15 ASP cc_start: 0.8663 (m-30) cc_final: 0.8359 (m-30) REVERT: K 50 SER cc_start: 0.9026 (t) cc_final: 0.8642 (p) REVERT: K 51 LYS cc_start: 0.9341 (mtpp) cc_final: 0.8984 (mtpp) REVERT: L 14 MET cc_start: 0.8762 (mmt) cc_final: 0.8200 (mmt) REVERT: L 47 LYS cc_start: 0.8671 (tttt) cc_final: 0.8328 (ttmm) REVERT: L 50 SER cc_start: 0.9209 (t) cc_final: 0.8759 (p) REVERT: L 51 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8782 (mtpp) REVERT: M 27 GLN cc_start: 0.9089 (tp40) cc_final: 0.8835 (tp40) REVERT: N 8 ASN cc_start: 0.7527 (t0) cc_final: 0.6913 (m-40) REVERT: N 18 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8344 (ttmm) REVERT: N 47 LYS cc_start: 0.8706 (tttt) cc_final: 0.8502 (ttmm) REVERT: O 14 MET cc_start: 0.8782 (mmm) cc_final: 0.8501 (mmt) REVERT: P 15 ASP cc_start: 0.8348 (m-30) cc_final: 0.8115 (m-30) REVERT: P 27 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8721 (tp40) REVERT: Q 8 ASN cc_start: 0.8146 (t0) cc_final: 0.7889 (m110) REVERT: Q 15 ASP cc_start: 0.8570 (m-30) cc_final: 0.8278 (m-30) REVERT: Q 27 GLN cc_start: 0.9108 (tp40) cc_final: 0.8839 (tp40) REVERT: S 15 ASP cc_start: 0.8456 (m-30) cc_final: 0.8207 (m-30) REVERT: T 27 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8836 (tp-100) REVERT: U 8 ASN cc_start: 0.6424 (t0) cc_final: 0.5914 (t0) REVERT: U 40 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9001 (mt) REVERT: W 11 THR cc_start: 0.8863 (p) cc_final: 0.8315 (p) REVERT: W 15 ASP cc_start: 0.8781 (m-30) cc_final: 0.8532 (m-30) REVERT: X 19 THR cc_start: 0.9140 (p) cc_final: 0.8909 (t) REVERT: Y 14 MET cc_start: 0.8573 (mtt) cc_final: 0.8123 (mtm) REVERT: Z 18 LYS cc_start: 0.8846 (tttt) cc_final: 0.8423 (mptt) REVERT: Z 46 LYS cc_start: 0.8596 (mttt) cc_final: 0.8320 (mtmt) REVERT: Z 49 SER cc_start: 0.9309 (m) cc_final: 0.9076 (t) REVERT: a 18 LYS cc_start: 0.8762 (tttt) cc_final: 0.8224 (mptt) REVERT: b 18 LYS cc_start: 0.9022 (tttt) cc_final: 0.8159 (mptt) REVERT: b 51 LYS cc_start: 0.8837 (mptt) cc_final: 0.8463 (mttm) REVERT: c 11 THR cc_start: 0.8945 (p) cc_final: 0.8578 (p) REVERT: c 14 MET cc_start: 0.7200 (mmm) cc_final: 0.6833 (tpp) REVERT: c 15 ASP cc_start: 0.8620 (m-30) cc_final: 0.8358 (m-30) REVERT: c 18 LYS cc_start: 0.8991 (tttt) cc_final: 0.8253 (mptt) REVERT: d 18 LYS cc_start: 0.8700 (tttt) cc_final: 0.7816 (mmtt) REVERT: d 26 SER cc_start: 0.9326 (m) cc_final: 0.9043 (p) outliers start: 65 outliers final: 51 residues processed: 746 average time/residue: 0.3291 time to fit residues: 346.1914 Evaluate side-chains 767 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 715 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 26 SER 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 H residue 9 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 49 SER 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 M residue 42 ILE Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 9 TYR 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 37 VAL 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 a residue 17 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS 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 42 ILE Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.099346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086326 restraints weight = 20624.840| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.97 r_work: 0.3134 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.5636 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= 0.135 Angle : 0.617 6.976 14940 Z= 0.314 Chirality : 0.044 0.183 1980 Planarity : 0.004 0.030 1740 Dihedral : 3.923 11.176 1440 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 4.23 % Allowed : 29.76 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.23), residues: 1350 helix: 1.37 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.72 (0.38), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 29 PHE 0.016 0.001 PHE c 48 TYR 0.007 0.001 TYR N 9 ARG 0.002 0.000 ARG S 43 Details of bonding type rmsd hydrogen bonds : bond 0.02633 ( 960) hydrogen bonds : angle 3.86022 ( 2880) covalent geometry : bond 0.00322 (10980) covalent geometry : angle 0.61660 (14940) *********************** 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 805 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 753 time to evaluate : 1.455 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: 0.9073 (tp-100) cc_final: 0.8558 (mt0) REVERT: A 42 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9190 (tt) REVERT: A 47 LYS cc_start: 0.9148 (tttt) cc_final: 0.8898 (mmtt) REVERT: A 49 SER cc_start: 0.9123 (t) cc_final: 0.8893 (m) REVERT: B 47 LYS cc_start: 0.9072 (tttt) cc_final: 0.8774 (ttpp) REVERT: C 9 TYR cc_start: 0.7587 (m-80) cc_final: 0.7175 (m-80) REVERT: C 20 GLN cc_start: 0.8418 (mt0) cc_final: 0.8160 (mt0) REVERT: C 43 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8208 (ttp80) REVERT: C 47 LYS cc_start: 0.9123 (tttt) cc_final: 0.8627 (tptt) REVERT: D 23 ASP cc_start: 0.8499 (m-30) cc_final: 0.8276 (m-30) REVERT: D 25 ILE cc_start: 0.9389 (mt) cc_final: 0.9185 (mt) REVERT: D 27 GLN cc_start: 0.9143 (tp40) cc_final: 0.8336 (tt0) REVERT: D 37 VAL cc_start: 0.9187 (p) cc_final: 0.8985 (m) REVERT: D 51 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8800 (mttt) REVERT: E 8 ASN cc_start: 0.8712 (t0) cc_final: 0.8262 (t0) REVERT: E 19 THR cc_start: 0.9220 (p) cc_final: 0.8590 (p) REVERT: E 51 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8720 (mtpt) REVERT: F 8 ASN cc_start: 0.7621 (t0) cc_final: 0.6972 (m110) REVERT: F 51 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8981 (mtpp) REVERT: G 12 GLU cc_start: 0.8250 (mp0) cc_final: 0.8010 (mp0) REVERT: G 27 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8590 (mm-40) REVERT: G 49 SER cc_start: 0.9277 (m) cc_final: 0.9073 (p) REVERT: G 51 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8895 (mtmm) REVERT: H 43 ARG cc_start: 0.8787 (mtp180) cc_final: 0.8349 (ttm170) REVERT: I 26 SER cc_start: 0.9147 (m) cc_final: 0.8855 (m) REVERT: I 27 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8411 (tp-100) REVERT: I 50 SER cc_start: 0.9023 (t) cc_final: 0.8568 (p) REVERT: I 51 LYS cc_start: 0.9259 (mmtm) cc_final: 0.8978 (mtpp) REVERT: J 20 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8880 (mm-40) REVERT: J 23 ASP cc_start: 0.8264 (p0) cc_final: 0.7974 (p0) REVERT: J 27 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8672 (tp-100) REVERT: K 14 MET cc_start: 0.8775 (mmt) cc_final: 0.8313 (mmt) REVERT: K 15 ASP cc_start: 0.8603 (m-30) cc_final: 0.8324 (m-30) REVERT: K 50 SER cc_start: 0.9029 (t) cc_final: 0.8551 (p) REVERT: K 51 LYS cc_start: 0.9309 (mtpp) cc_final: 0.8978 (mtpp) REVERT: L 14 MET cc_start: 0.8687 (mmt) cc_final: 0.8292 (mmt) REVERT: L 20 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8969 (mm-40) REVERT: L 51 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8820 (mtpp) REVERT: M 15 ASP cc_start: 0.8611 (m-30) cc_final: 0.8354 (m-30) REVERT: M 27 GLN cc_start: 0.9058 (tp40) cc_final: 0.8781 (tp40) REVERT: N 8 ASN cc_start: 0.7527 (t0) cc_final: 0.7142 (m-40) REVERT: N 18 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8352 (ttmm) REVERT: N 47 LYS cc_start: 0.8771 (tttt) cc_final: 0.8541 (ttmm) REVERT: O 14 MET cc_start: 0.8770 (mmm) cc_final: 0.8519 (mmt) REVERT: P 15 ASP cc_start: 0.8291 (m-30) cc_final: 0.8052 (m-30) REVERT: P 27 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8698 (tp40) REVERT: Q 8 ASN cc_start: 0.8108 (t0) cc_final: 0.7870 (m110) REVERT: Q 15 ASP cc_start: 0.8579 (m-30) cc_final: 0.8272 (m-30) REVERT: R 9 TYR cc_start: 0.7690 (m-80) cc_final: 0.7346 (m-80) REVERT: S 15 ASP cc_start: 0.8434 (m-30) cc_final: 0.8136 (m-30) REVERT: T 27 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8815 (tp-100) REVERT: U 8 ASN cc_start: 0.6404 (t0) cc_final: 0.5796 (t0) REVERT: U 40 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9036 (mt) REVERT: W 11 THR cc_start: 0.8842 (p) cc_final: 0.8228 (p) REVERT: W 15 ASP cc_start: 0.8774 (m-30) cc_final: 0.8447 (m-30) REVERT: W 18 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8648 (ttmm) REVERT: X 19 THR cc_start: 0.9112 (p) cc_final: 0.8891 (t) REVERT: Z 18 LYS cc_start: 0.8850 (tttt) cc_final: 0.8420 (mptt) REVERT: Z 46 LYS cc_start: 0.8585 (mttt) cc_final: 0.8309 (mtmt) REVERT: Z 51 LYS cc_start: 0.9076 (mptt) cc_final: 0.8798 (mttm) REVERT: a 18 LYS cc_start: 0.8749 (tttt) cc_final: 0.8217 (mptt) REVERT: a 43 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8850 (ttp80) REVERT: b 18 LYS cc_start: 0.8997 (tttt) cc_final: 0.8126 (mptt) REVERT: b 46 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8621 (ttmt) REVERT: b 51 LYS cc_start: 0.8661 (mptt) cc_final: 0.8331 (mttm) REVERT: c 14 MET cc_start: 0.6676 (mmm) cc_final: 0.6230 (tpp) REVERT: c 18 LYS cc_start: 0.8916 (tttt) cc_final: 0.8175 (mptt) REVERT: d 18 LYS cc_start: 0.8690 (tttt) cc_final: 0.7780 (mmtt) REVERT: d 26 SER cc_start: 0.9213 (m) cc_final: 0.8974 (p) outliers start: 52 outliers final: 40 residues processed: 760 average time/residue: 0.2245 time to fit residues: 238.7229 Evaluate side-chains 770 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 727 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 J residue 49 SER 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 18 LYS Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 34 THR 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 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 44 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 46 LYS 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 32 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 107 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.089562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075682 restraints weight = 20886.253| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.11 r_work: 0.3116 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10980 Z= 0.168 Angle : 0.653 6.989 14940 Z= 0.336 Chirality : 0.045 0.197 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.994 11.610 1440 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 4.07 % Allowed : 31.87 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1350 helix: 1.34 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.69 (0.37), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 29 PHE 0.022 0.002 PHE c 48 TYR 0.006 0.001 TYR K 9 ARG 0.003 0.000 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 960) hydrogen bonds : angle 4.00518 ( 2880) covalent geometry : bond 0.00405 (10980) covalent geometry : angle 0.65348 (14940) *********************** 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 773 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 723 time to evaluate : 1.881 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 42 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9148 (tt) REVERT: A 47 LYS cc_start: 0.9138 (tttt) cc_final: 0.8880 (mmtt) REVERT: A 49 SER cc_start: 0.9097 (t) cc_final: 0.8883 (m) REVERT: B 45 PHE cc_start: 0.9386 (t80) cc_final: 0.9131 (t80) REVERT: B 47 LYS cc_start: 0.9085 (tttt) cc_final: 0.8783 (ttpp) REVERT: C 9 TYR cc_start: 0.7587 (m-80) cc_final: 0.7263 (m-80) REVERT: C 43 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8169 (ttp80) REVERT: C 47 LYS cc_start: 0.9141 (tttt) cc_final: 0.8652 (tptt) REVERT: D 23 ASP cc_start: 0.8511 (m-30) cc_final: 0.8310 (m-30) REVERT: D 37 VAL cc_start: 0.9261 (p) cc_final: 0.9057 (m) REVERT: D 51 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8816 (mttt) REVERT: E 8 ASN cc_start: 0.8709 (t0) cc_final: 0.8253 (t0) REVERT: F 8 ASN cc_start: 0.7658 (t0) cc_final: 0.7060 (m110) REVERT: F 51 LYS cc_start: 0.9227 (mtpp) cc_final: 0.9013 (mtpp) REVERT: H 12 GLU cc_start: 0.8271 (mp0) cc_final: 0.8063 (mp0) REVERT: H 43 ARG cc_start: 0.8837 (mtp180) cc_final: 0.8373 (ttm170) REVERT: I 26 SER cc_start: 0.9190 (m) cc_final: 0.8951 (m) REVERT: I 27 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8415 (tp-100) REVERT: I 50 SER cc_start: 0.9033 (t) cc_final: 0.8587 (p) REVERT: I 51 LYS cc_start: 0.9270 (mmtm) cc_final: 0.8990 (mtpp) REVERT: J 20 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8898 (mm-40) REVERT: J 23 ASP cc_start: 0.8267 (p0) cc_final: 0.7974 (p0) REVERT: J 27 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8683 (tp-100) REVERT: K 15 ASP cc_start: 0.8624 (m-30) cc_final: 0.8375 (m-30) REVERT: K 50 SER cc_start: 0.9105 (t) cc_final: 0.8706 (p) REVERT: K 51 LYS cc_start: 0.9326 (mtpp) cc_final: 0.9066 (mtpp) REVERT: L 14 MET cc_start: 0.8710 (mmt) cc_final: 0.8280 (mmt) REVERT: M 15 ASP cc_start: 0.8657 (m-30) cc_final: 0.8365 (m-30) REVERT: M 27 GLN cc_start: 0.9081 (tp40) cc_final: 0.8805 (tp40) REVERT: N 8 ASN cc_start: 0.7596 (t0) cc_final: 0.7044 (t0) REVERT: N 18 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8377 (ttmm) REVERT: N 47 LYS cc_start: 0.8745 (tttt) cc_final: 0.8533 (ttmm) REVERT: O 14 MET cc_start: 0.8756 (mmm) cc_final: 0.8511 (mmt) REVERT: P 15 ASP cc_start: 0.8322 (m-30) cc_final: 0.8073 (m-30) REVERT: Q 8 ASN cc_start: 0.8104 (t0) cc_final: 0.7874 (m110) REVERT: Q 15 ASP cc_start: 0.8598 (m-30) cc_final: 0.8303 (m-30) REVERT: S 15 ASP cc_start: 0.8357 (m-30) cc_final: 0.7915 (m-30) REVERT: T 27 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8845 (tp-100) REVERT: W 11 THR cc_start: 0.8843 (p) cc_final: 0.8203 (p) REVERT: W 15 ASP cc_start: 0.8788 (m-30) cc_final: 0.8446 (m-30) REVERT: W 18 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8688 (ttmm) REVERT: X 19 THR cc_start: 0.9139 (p) cc_final: 0.8917 (t) REVERT: Z 18 LYS cc_start: 0.8849 (tttt) cc_final: 0.8393 (mptt) REVERT: Z 46 LYS cc_start: 0.8574 (mttt) cc_final: 0.8291 (mtmt) REVERT: Z 51 LYS cc_start: 0.9094 (mptt) cc_final: 0.8825 (mttm) REVERT: a 18 LYS cc_start: 0.8718 (tttt) cc_final: 0.8191 (mptt) REVERT: b 18 LYS cc_start: 0.8996 (tttt) cc_final: 0.8010 (mmtt) REVERT: b 46 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8654 (ttmt) REVERT: b 51 LYS cc_start: 0.8657 (mptt) cc_final: 0.8345 (mttm) REVERT: c 18 LYS cc_start: 0.8988 (tttt) cc_final: 0.8172 (mptt) REVERT: d 18 LYS cc_start: 0.8793 (tttt) cc_final: 0.7890 (mmtt) REVERT: d 26 SER cc_start: 0.9217 (m) cc_final: 0.9006 (p) outliers start: 50 outliers final: 40 residues processed: 733 average time/residue: 0.2487 time to fit residues: 253.4722 Evaluate side-chains 751 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 709 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 15 ASP 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 J residue 49 SER 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 L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 18 LYS Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 37 VAL 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 37 VAL 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 17 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 17 LEU 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 80 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3487 r_free = 0.3487 target = 0.097428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084257 restraints weight = 20684.797| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.95 r_work: 0.3096 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10980 Z= 0.189 Angle : 0.675 6.846 14940 Z= 0.348 Chirality : 0.046 0.203 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.009 12.658 1440 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 3.50 % Allowed : 33.17 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1350 helix: 1.32 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.50 (0.42), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 29 PHE 0.023 0.002 PHE c 48 TYR 0.007 0.001 TYR N 9 ARG 0.005 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 960) hydrogen bonds : angle 4.07948 ( 2880) covalent geometry : bond 0.00457 (10980) covalent geometry : angle 0.67452 (14940) *********************** 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 759 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 716 time to evaluate : 1.352 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: A 42 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9146 (tt) REVERT: A 47 LYS cc_start: 0.9138 (tttt) cc_final: 0.8873 (mmtt) REVERT: A 49 SER cc_start: 0.9059 (t) cc_final: 0.8846 (m) REVERT: B 45 PHE cc_start: 0.9404 (t80) cc_final: 0.9166 (t80) REVERT: B 47 LYS cc_start: 0.9069 (tttt) cc_final: 0.8762 (ttpp) REVERT: C 9 TYR cc_start: 0.7681 (m-80) cc_final: 0.7375 (m-80) REVERT: C 43 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8192 (ttp80) REVERT: C 47 LYS cc_start: 0.9140 (tttt) cc_final: 0.8630 (tptt) REVERT: D 37 VAL cc_start: 0.9297 (p) cc_final: 0.9074 (m) REVERT: D 51 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8808 (mttt) REVERT: E 8 ASN cc_start: 0.8712 (t0) cc_final: 0.7553 (t0) REVERT: E 19 THR cc_start: 0.9194 (p) cc_final: 0.8587 (p) REVERT: G 49 SER cc_start: 0.9291 (m) cc_final: 0.9042 (p) REVERT: H 12 GLU cc_start: 0.8306 (mp0) cc_final: 0.8086 (mp0) REVERT: H 43 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8457 (ttm170) REVERT: I 26 SER cc_start: 0.9144 (m) cc_final: 0.8881 (m) REVERT: I 27 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8405 (tp-100) REVERT: I 50 SER cc_start: 0.9061 (t) cc_final: 0.8619 (p) REVERT: I 51 LYS cc_start: 0.9275 (mmtm) cc_final: 0.9015 (mtpp) REVERT: J 20 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8957 (mm-40) REVERT: J 23 ASP cc_start: 0.8280 (p0) cc_final: 0.7991 (p0) REVERT: J 27 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8689 (tp-100) REVERT: K 15 ASP cc_start: 0.8641 (m-30) cc_final: 0.8402 (m-30) REVERT: K 50 SER cc_start: 0.9153 (t) cc_final: 0.8732 (p) REVERT: K 51 LYS cc_start: 0.9352 (mtpp) cc_final: 0.9000 (mtpp) REVERT: L 14 MET cc_start: 0.8726 (mmt) cc_final: 0.8289 (mmt) REVERT: L 51 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8869 (mtpp) REVERT: M 15 ASP cc_start: 0.8656 (m-30) cc_final: 0.8335 (m-30) REVERT: M 27 GLN cc_start: 0.9083 (tp40) cc_final: 0.8788 (tp40) REVERT: M 50 SER cc_start: 0.9197 (t) cc_final: 0.8876 (p) REVERT: N 8 ASN cc_start: 0.7556 (t0) cc_final: 0.6928 (t0) REVERT: N 18 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8391 (ttmm) REVERT: O 14 MET cc_start: 0.8793 (mmm) cc_final: 0.8534 (mmt) REVERT: P 15 ASP cc_start: 0.8327 (m-30) cc_final: 0.8074 (m-30) REVERT: Q 8 ASN cc_start: 0.8062 (t0) cc_final: 0.7797 (m110) REVERT: Q 15 ASP cc_start: 0.8551 (m-30) cc_final: 0.8248 (m-30) REVERT: S 15 ASP cc_start: 0.8311 (m-30) cc_final: 0.7919 (m-30) REVERT: T 27 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8883 (tp-100) REVERT: W 11 THR cc_start: 0.8856 (p) cc_final: 0.8190 (p) REVERT: W 15 ASP cc_start: 0.8710 (m-30) cc_final: 0.8371 (m-30) REVERT: W 18 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8696 (ttmm) REVERT: X 19 THR cc_start: 0.9138 (p) cc_final: 0.8931 (t) REVERT: X 23 ASP cc_start: 0.8744 (t70) cc_final: 0.8532 (t0) REVERT: X 49 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9209 (p) REVERT: X 51 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8806 (ttmm) REVERT: Z 18 LYS cc_start: 0.8861 (tttt) cc_final: 0.8448 (mptt) REVERT: Z 46 LYS cc_start: 0.8587 (mttt) cc_final: 0.8350 (mtmt) REVERT: Z 47 LYS cc_start: 0.9189 (ttmm) cc_final: 0.8958 (ttmm) REVERT: Z 51 LYS cc_start: 0.9103 (mptt) cc_final: 0.8862 (mttm) REVERT: a 18 LYS cc_start: 0.8708 (tttt) cc_final: 0.8232 (mptt) REVERT: b 18 LYS cc_start: 0.8990 (tttt) cc_final: 0.8119 (mptt) REVERT: b 46 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8590 (ttmt) REVERT: b 51 LYS cc_start: 0.8673 (mptt) cc_final: 0.8337 (mttm) REVERT: c 18 LYS cc_start: 0.8975 (tttt) cc_final: 0.8167 (mptt) REVERT: d 18 LYS cc_start: 0.8780 (tttt) cc_final: 0.7897 (mmtt) REVERT: d 26 SER cc_start: 0.9228 (m) cc_final: 0.8998 (p) outliers start: 43 outliers final: 36 residues processed: 724 average time/residue: 0.2219 time to fit residues: 223.5088 Evaluate side-chains 747 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 708 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain I residue 35 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 J residue 49 SER 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 L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 18 LYS Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS 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 37 VAL 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 17 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 32 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 115 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 54 optimal weight: 0.0070 chunk 68 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.3532 r_free = 0.3532 target = 0.100266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087042 restraints weight = 20211.117| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.97 r_work: 0.3141 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10980 Z= 0.146 Angle : 0.679 7.996 14940 Z= 0.350 Chirality : 0.045 0.194 1980 Planarity : 0.004 0.031 1740 Dihedral : 4.005 13.249 1440 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.93 % Allowed : 34.96 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.23), residues: 1350 helix: 1.33 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.60 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 29 PHE 0.022 0.001 PHE c 48 TYR 0.009 0.001 TYR N 9 ARG 0.003 0.000 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 960) hydrogen bonds : angle 4.06031 ( 2880) covalent geometry : bond 0.00348 (10980) covalent geometry : angle 0.67929 (14940) ********************** 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 771 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 735 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8549 (mt0) REVERT: A 42 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 47 LYS cc_start: 0.9108 (tttt) cc_final: 0.8867 (mmtt) REVERT: A 49 SER cc_start: 0.9068 (t) cc_final: 0.8857 (m) REVERT: B 27 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8322 (tt0) REVERT: B 45 PHE cc_start: 0.9416 (t80) cc_final: 0.9193 (t80) REVERT: B 47 LYS cc_start: 0.9062 (tttt) cc_final: 0.8756 (ttpp) REVERT: C 9 TYR cc_start: 0.7541 (m-80) cc_final: 0.7247 (m-80) REVERT: C 43 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8154 (ttp80) REVERT: C 47 LYS cc_start: 0.9131 (tttt) cc_final: 0.8630 (tptt) REVERT: D 27 GLN cc_start: 0.9111 (tp40) cc_final: 0.8316 (tt0) REVERT: D 37 VAL cc_start: 0.9265 (p) cc_final: 0.9044 (m) REVERT: D 51 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8787 (mttt) REVERT: E 8 ASN cc_start: 0.8475 (t0) cc_final: 0.8144 (t0) REVERT: E 15 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: E 43 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8417 (mtm110) REVERT: F 8 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6711 (m110) REVERT: G 49 SER cc_start: 0.9268 (m) cc_final: 0.8962 (p) REVERT: G 51 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8848 (mtpp) REVERT: I 26 SER cc_start: 0.9192 (m) cc_final: 0.8967 (m) REVERT: I 27 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8365 (tp-100) REVERT: I 50 SER cc_start: 0.9045 (t) cc_final: 0.8597 (p) REVERT: I 51 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8978 (mtpp) REVERT: J 23 ASP cc_start: 0.8288 (p0) cc_final: 0.7982 (p0) REVERT: J 27 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8663 (tp-100) REVERT: K 15 ASP cc_start: 0.8576 (m-30) cc_final: 0.8335 (m-30) REVERT: K 43 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8447 (ttm170) REVERT: K 50 SER cc_start: 0.9111 (t) cc_final: 0.8598 (p) REVERT: K 51 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8982 (mtpp) REVERT: L 14 MET cc_start: 0.8701 (mmt) cc_final: 0.8253 (mmt) REVERT: L 51 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8800 (mtpp) REVERT: M 15 ASP cc_start: 0.8654 (m-30) cc_final: 0.8413 (m-30) REVERT: M 27 GLN cc_start: 0.9089 (tp40) cc_final: 0.8796 (tp40) REVERT: M 50 SER cc_start: 0.9180 (t) cc_final: 0.8908 (p) REVERT: N 8 ASN cc_start: 0.7333 (t0) cc_final: 0.7100 (t0) REVERT: N 18 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8347 (ttmm) REVERT: O 14 MET cc_start: 0.8624 (mmm) cc_final: 0.8345 (mmt) REVERT: P 15 ASP cc_start: 0.8295 (m-30) cc_final: 0.8044 (m-30) REVERT: Q 8 ASN cc_start: 0.7998 (t0) cc_final: 0.7763 (m110) REVERT: Q 15 ASP cc_start: 0.8516 (m-30) cc_final: 0.8197 (m-30) REVERT: S 15 ASP cc_start: 0.8306 (m-30) cc_final: 0.7881 (m-30) REVERT: T 27 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8867 (tp-100) REVERT: V 9 TYR cc_start: 0.7404 (m-80) cc_final: 0.6465 (p90) REVERT: V 50 SER cc_start: 0.9380 (t) cc_final: 0.9121 (p) REVERT: W 11 THR cc_start: 0.8837 (p) cc_final: 0.8170 (p) REVERT: W 15 ASP cc_start: 0.8778 (m-30) cc_final: 0.8485 (m-30) REVERT: W 18 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8717 (ttmt) REVERT: X 19 THR cc_start: 0.9146 (p) cc_final: 0.8905 (t) REVERT: X 23 ASP cc_start: 0.8657 (t70) cc_final: 0.8442 (t0) REVERT: X 49 SER cc_start: 0.9478 (OUTLIER) cc_final: 0.9215 (p) REVERT: Z 18 LYS cc_start: 0.8802 (tttt) cc_final: 0.8384 (mptt) REVERT: Z 46 LYS cc_start: 0.8680 (mttt) cc_final: 0.8404 (mtmt) REVERT: a 18 LYS cc_start: 0.8699 (tttt) cc_final: 0.8144 (mmtt) REVERT: b 18 LYS cc_start: 0.8999 (tttt) cc_final: 0.8125 (mptt) REVERT: b 46 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8669 (ttmt) REVERT: b 51 LYS cc_start: 0.8620 (mptt) cc_final: 0.8258 (mttm) REVERT: c 18 LYS cc_start: 0.8968 (tttt) cc_final: 0.8160 (mptt) REVERT: d 9 TYR cc_start: 0.8667 (m-80) cc_final: 0.8251 (m-80) REVERT: d 18 LYS cc_start: 0.8769 (tttt) cc_final: 0.7767 (mptt) REVERT: d 26 SER cc_start: 0.9200 (m) cc_final: 0.8990 (p) outliers start: 36 outliers final: 27 residues processed: 742 average time/residue: 0.2727 time to fit residues: 289.7182 Evaluate side-chains 754 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 722 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 8 ASN 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 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 M residue 18 LYS Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 37 VAL 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 17 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 46 LYS 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 64 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN F 8 ASN I 8 ASN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.086338 restraints weight = 20268.496| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10980 Z= 0.164 Angle : 0.698 7.871 14940 Z= 0.359 Chirality : 0.046 0.206 1980 Planarity : 0.004 0.030 1740 Dihedral : 4.046 13.503 1440 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.68 % Allowed : 36.34 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1350 helix: 1.29 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.71 (0.44), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 29 PHE 0.016 0.001 PHE b 48 TYR 0.017 0.001 TYR F 9 ARG 0.005 0.000 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 960) hydrogen bonds : angle 4.08216 ( 2880) covalent geometry : bond 0.00397 (10980) covalent geometry : angle 0.69781 (14940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5869.12 seconds wall clock time: 106 minutes 20.97 seconds (6380.97 seconds total)