Starting phenix.real_space_refine on Fri Feb 14 21:28:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a7f_6993/02_2025/6a7f_6993.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a7f_6993/02_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_6993/02_2025/6a7f_6993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a7f_6993/02_2025/6a7f_6993.map" model { file = "/net/cci-nas-00/data/ceres_data/6a7f_6993/02_2025/6a7f_6993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a7f_6993/02_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-5592/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: 2.69, per 1000 atoms: 0.25 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 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: 0.70 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: 3.16 Time building geometry restraints manager: 3.21 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: 0.11 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: 0.770 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 21.940 Find NCS groups from input model: 0.220 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- 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= 0.903 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 *********************** 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 : 1.419 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: 0.2457 time to fit residues: 276.8539 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 : 1.392 ------------------------------------------------------------------------------- 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: 0.6980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN 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 = 0.3492 r_free = 0.3492 target = 0.098869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086204 restraints weight = 19861.152| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.91 r_work: 0.3128 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10980 Z= 0.213 Angle : 0.577 7.471 14940 Z= 0.302 Chirality : 0.041 0.134 1980 Planarity : 0.005 0.032 1740 Dihedral : 4.260 11.770 1440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.41 % Allowed : 18.29 % Favored : 78.29 % 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: 0.42 (0.22), residues: 1350 helix: 0.36 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : 3.07 (0.42), 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 0.008 0.001 TYR D 9 ARG 0.002 0.001 ARG W 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 825 time to evaluate : 1.261 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 15 ASP cc_start: 0.8697 (m-30) cc_final: 0.8360 (m-30) REVERT: A 20 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8652 (mm-40) REVERT: A 27 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8863 (tp-100) REVERT: A 42 ILE cc_start: 0.9302 (tp) cc_final: 0.9060 (tt) REVERT: A 47 LYS cc_start: 0.9277 (tttt) cc_final: 0.8918 (tppt) REVERT: A 49 SER cc_start: 0.9475 (t) cc_final: 0.9029 (p) REVERT: B 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8479 (tt0) REVERT: B 42 ILE cc_start: 0.9628 (tt) cc_final: 0.9365 (tp) REVERT: B 51 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8797 (mtpt) REVERT: C 20 GLN cc_start: 0.8822 (tp40) cc_final: 0.8385 (mt0) REVERT: C 47 LYS cc_start: 0.9216 (tttt) cc_final: 0.8735 (tptt) REVERT: D 23 ASP cc_start: 0.8490 (m-30) cc_final: 0.8250 (m-30) REVERT: D 42 ILE cc_start: 0.9461 (tp) cc_final: 0.9244 (tt) REVERT: D 46 LYS cc_start: 0.9192 (mttm) cc_final: 0.8902 (mttp) REVERT: D 47 LYS cc_start: 0.9283 (tttt) cc_final: 0.9074 (tptt) REVERT: D 51 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8770 (mttt) REVERT: E 20 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8480 (mm-40) REVERT: E 42 ILE cc_start: 0.9431 (tp) cc_final: 0.9108 (tt) REVERT: F 8 ASN cc_start: 0.8027 (t0) cc_final: 0.7420 (t0) REVERT: F 9 TYR cc_start: 0.7117 (m-80) cc_final: 0.6894 (m-80) REVERT: G 9 TYR cc_start: 0.7127 (m-80) cc_final: 0.6898 (m-80) REVERT: G 12 GLU cc_start: 0.7932 (mp0) cc_final: 0.7730 (mp0) REVERT: G 20 GLN cc_start: 0.8987 (mm-40) cc_final: 0.7896 (mm-40) REVERT: G 40 LEU cc_start: 0.9582 (mt) cc_final: 0.9340 (mt) REVERT: H 9 TYR cc_start: 0.7727 (m-80) cc_final: 0.7296 (m-80) REVERT: H 19 THR cc_start: 0.8951 (p) cc_final: 0.8589 (p) REVERT: H 43 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8456 (ttm170) REVERT: I 19 THR cc_start: 0.9414 (t) cc_final: 0.9047 (p) REVERT: I 27 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8637 (tp-100) REVERT: I 50 SER cc_start: 0.8551 (t) cc_final: 0.8037 (p) REVERT: I 51 LYS cc_start: 0.9256 (mmtm) cc_final: 0.8865 (mtpp) REVERT: J 26 SER cc_start: 0.8982 (p) cc_final: 0.8732 (p) REVERT: J 27 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8759 (tp-100) REVERT: K 14 MET cc_start: 0.8793 (mmt) cc_final: 0.8291 (mmt) REVERT: L 20 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8852 (mm-40) REVERT: L 47 LYS cc_start: 0.8820 (tttt) cc_final: 0.8535 (ttmm) REVERT: L 51 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8751 (mmmm) REVERT: M 14 MET cc_start: 0.8740 (mmm) cc_final: 0.8178 (mmt) REVERT: M 15 ASP cc_start: 0.8611 (m-30) cc_final: 0.8381 (m-30) REVERT: M 27 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8812 (tp-100) REVERT: M 51 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8624 (mmmm) REVERT: N 8 ASN cc_start: 0.8049 (t0) cc_final: 0.7169 (m-40) REVERT: N 47 LYS cc_start: 0.8925 (tttt) cc_final: 0.8523 (ttmm) REVERT: N 50 SER cc_start: 0.8934 (t) cc_final: 0.8535 (p) REVERT: O 14 MET cc_start: 0.8739 (mmm) cc_final: 0.8423 (mmt) REVERT: O 27 GLN cc_start: 0.9066 (tp40) cc_final: 0.8686 (tp40) REVERT: P 15 ASP cc_start: 0.8265 (m-30) cc_final: 0.7946 (m-30) REVERT: P 27 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8598 (tp40) REVERT: Q 8 ASN cc_start: 0.8197 (t0) cc_final: 0.7742 (t0) REVERT: Q 9 TYR cc_start: 0.7263 (m-80) cc_final: 0.6930 (m-80) REVERT: Q 15 ASP cc_start: 0.8465 (m-30) cc_final: 0.8139 (m-30) REVERT: Q 27 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8269 (tp-100) REVERT: S 15 ASP cc_start: 0.8481 (m-30) cc_final: 0.8205 (m-30) REVERT: T 15 ASP cc_start: 0.8475 (m-30) cc_final: 0.8275 (m-30) REVERT: T 26 SER cc_start: 0.8761 (p) cc_final: 0.8557 (m) REVERT: T 27 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8751 (tp-100) REVERT: U 15 ASP cc_start: 0.8702 (m-30) cc_final: 0.8482 (m-30) REVERT: U 18 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8513 (ttmm) REVERT: U 40 LEU cc_start: 0.9283 (mp) cc_final: 0.8893 (mt) REVERT: V 8 ASN cc_start: 0.7381 (t0) cc_final: 0.6931 (t0) REVERT: V 47 LYS cc_start: 0.9120 (tttm) cc_final: 0.8859 (ttmm) REVERT: W 9 TYR cc_start: 0.7708 (m-80) cc_final: 0.7340 (m-80) REVERT: W 43 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8470 (ttp80) REVERT: X 51 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8740 (mttp) REVERT: Y 8 ASN cc_start: 0.7191 (t0) cc_final: 0.6205 (t0) REVERT: Y 18 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8696 (ttmm) REVERT: Y 47 LYS cc_start: 0.9055 (tttm) cc_final: 0.8812 (ttmm) REVERT: Z 18 LYS cc_start: 0.8791 (tttt) cc_final: 0.8402 (mptt) REVERT: Z 46 LYS cc_start: 0.8685 (mttt) cc_final: 0.8258 (mtmt) REVERT: Z 49 SER cc_start: 0.9126 (m) cc_final: 0.8776 (t) REVERT: a 9 TYR cc_start: 0.8098 (m-80) cc_final: 0.7431 (p90) REVERT: a 18 LYS cc_start: 0.8918 (tttt) cc_final: 0.8290 (mptt) REVERT: a 20 GLN cc_start: 0.9230 (mm110) cc_final: 0.9019 (mm-40) REVERT: b 15 ASP cc_start: 0.8862 (m-30) cc_final: 0.8570 (m-30) REVERT: b 18 LYS cc_start: 0.8817 (tttt) cc_final: 0.8392 (mptt) REVERT: b 24 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8976 (tp) REVERT: c 14 MET cc_start: 0.8415 (mmm) cc_final: 0.8213 (mmm) REVERT: c 15 ASP cc_start: 0.8604 (m-30) cc_final: 0.8322 (m-30) REVERT: c 18 LYS cc_start: 0.8878 (tttt) cc_final: 0.8417 (mptt) REVERT: c 25 ILE cc_start: 0.9382 (mt) cc_final: 0.9105 (mt) REVERT: d 15 ASP cc_start: 0.8545 (m-30) cc_final: 0.8227 (m-30) REVERT: d 18 LYS cc_start: 0.8786 (tttt) cc_final: 0.8087 (mmtt) outliers start: 42 outliers final: 28 residues processed: 829 average time/residue: 0.2351 time to fit residues: 268.4631 Evaluate side-chains 754 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 725 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083847 restraints weight = 20220.474| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.91 r_work: 0.3101 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10980 Z= 0.234 Angle : 0.589 6.232 14940 Z= 0.304 Chirality : 0.042 0.144 1980 Planarity : 0.004 0.029 1740 Dihedral : 4.048 11.529 1440 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.39 % Allowed : 22.36 % Favored : 73.25 % 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: 1.31 (0.23), residues: 1350 helix: 0.91 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.46 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 29 PHE 0.012 0.001 PHE Q 48 TYR 0.005 0.001 TYR L 9 ARG 0.003 0.000 ARG Q 43 *********************** 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 822 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 768 time to evaluate : 1.204 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 20 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8463 (mm-40) REVERT: A 27 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8760 (tp-100) REVERT: A 42 ILE cc_start: 0.9430 (tp) cc_final: 0.9154 (tt) REVERT: A 47 LYS cc_start: 0.9232 (tttt) cc_final: 0.8972 (mmtt) REVERT: A 49 SER cc_start: 0.9296 (t) cc_final: 0.9020 (m) REVERT: A 51 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8774 (mtpt) REVERT: B 20 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 42 ILE cc_start: 0.9638 (tt) cc_final: 0.9371 (tp) REVERT: B 45 PHE cc_start: 0.9388 (t80) cc_final: 0.9017 (t80) REVERT: B 51 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8822 (mttt) REVERT: C 47 LYS cc_start: 0.9207 (tttt) cc_final: 0.8718 (tptt) REVERT: D 23 ASP cc_start: 0.8523 (m-30) cc_final: 0.8266 (m-30) REVERT: D 51 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8804 (mttt) REVERT: E 14 MET cc_start: 0.8944 (mmt) cc_final: 0.8719 (tpp) REVERT: E 20 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8485 (mm-40) REVERT: E 42 ILE cc_start: 0.9385 (tp) cc_final: 0.9097 (tt) REVERT: F 8 ASN cc_start: 0.7957 (t0) cc_final: 0.7342 (m110) REVERT: F 9 TYR cc_start: 0.7184 (m-80) cc_final: 0.6854 (m-80) REVERT: G 12 GLU cc_start: 0.8115 (mp0) cc_final: 0.7798 (mp0) REVERT: G 49 SER cc_start: 0.9306 (m) cc_final: 0.9030 (t) REVERT: H 9 TYR cc_start: 0.7758 (m-80) cc_final: 0.7326 (m-80) REVERT: H 43 ARG cc_start: 0.8774 (mtp180) cc_final: 0.8398 (ttm170) REVERT: I 27 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8612 (tp-100) REVERT: I 50 SER cc_start: 0.8833 (t) cc_final: 0.8402 (p) REVERT: I 51 LYS cc_start: 0.9280 (mmtm) cc_final: 0.8886 (mtpp) REVERT: J 23 ASP cc_start: 0.8258 (p0) cc_final: 0.7917 (p0) REVERT: J 27 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8689 (tp-100) REVERT: J 48 PHE cc_start: 0.9463 (m-80) cc_final: 0.8858 (m-80) REVERT: J 51 LYS cc_start: 0.9418 (mtpp) cc_final: 0.9167 (mtpp) REVERT: K 12 GLU cc_start: 0.7842 (mp0) cc_final: 0.7600 (mp0) REVERT: K 14 MET cc_start: 0.8774 (mmt) cc_final: 0.8242 (mmt) REVERT: K 50 SER cc_start: 0.8945 (t) cc_final: 0.8436 (p) REVERT: K 51 LYS cc_start: 0.9295 (mmmm) cc_final: 0.9090 (mttp) REVERT: L 20 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8817 (mm-40) REVERT: L 47 LYS cc_start: 0.8838 (tttt) cc_final: 0.8320 (ttmm) REVERT: L 50 SER cc_start: 0.9045 (t) cc_final: 0.8643 (p) REVERT: M 14 MET cc_start: 0.8611 (mmm) cc_final: 0.8337 (mmt) REVERT: N 8 ASN cc_start: 0.7996 (t0) cc_final: 0.6937 (m-40) REVERT: N 47 LYS cc_start: 0.8885 (tttt) cc_final: 0.8439 (ttmm) REVERT: N 50 SER cc_start: 0.8979 (t) cc_final: 0.8538 (p) REVERT: N 51 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8778 (mtpp) REVERT: O 14 MET cc_start: 0.8761 (mmm) cc_final: 0.8451 (mmt) REVERT: O 27 GLN cc_start: 0.9069 (tp40) cc_final: 0.8686 (tp40) REVERT: P 15 ASP cc_start: 0.8268 (m-30) cc_final: 0.7991 (m-30) REVERT: P 27 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8736 (tp40) REVERT: Q 8 ASN cc_start: 0.8242 (t0) cc_final: 0.7914 (m110) REVERT: Q 15 ASP cc_start: 0.8464 (m-30) cc_final: 0.8126 (m-30) REVERT: S 15 ASP cc_start: 0.8411 (m-30) cc_final: 0.8082 (m-30) REVERT: T 27 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8712 (tp-100) REVERT: U 8 ASN cc_start: 0.7346 (t0) cc_final: 0.6630 (t0) REVERT: U 15 ASP cc_start: 0.8671 (m-30) cc_final: 0.8427 (m-30) REVERT: U 18 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8562 (ttmm) REVERT: U 40 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8882 (mt) REVERT: U 51 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8136 (mttm) REVERT: V 8 ASN cc_start: 0.7247 (t0) cc_final: 0.6530 (t0) REVERT: V 51 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8918 (mttm) REVERT: W 43 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8425 (ttp80) REVERT: X 51 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8835 (mttp) REVERT: Y 47 LYS cc_start: 0.9112 (tttm) cc_final: 0.8881 (ttmm) REVERT: Z 18 LYS cc_start: 0.8772 (tttt) cc_final: 0.8354 (mptt) REVERT: Z 44 LEU cc_start: 0.9448 (mt) cc_final: 0.9230 (mp) REVERT: Z 46 LYS cc_start: 0.8547 (mttt) cc_final: 0.8154 (mtmt) REVERT: Z 49 SER cc_start: 0.9321 (m) cc_final: 0.8936 (t) REVERT: a 18 LYS cc_start: 0.8792 (tttt) cc_final: 0.8222 (mptt) REVERT: b 15 ASP cc_start: 0.8710 (m-30) cc_final: 0.8500 (m-30) REVERT: b 18 LYS cc_start: 0.8860 (tttt) cc_final: 0.8282 (mptt) REVERT: c 15 ASP cc_start: 0.8647 (m-30) cc_final: 0.8417 (m-30) REVERT: c 18 LYS cc_start: 0.8902 (tttt) cc_final: 0.8366 (mptt) REVERT: d 18 LYS cc_start: 0.8740 (tttt) cc_final: 0.8019 (mmtt) outliers start: 54 outliers final: 40 residues processed: 775 average time/residue: 0.2221 time to fit residues: 239.3174 Evaluate side-chains 760 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 719 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 26 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 37 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 9 TYR 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: 0.9980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN O 8 ASN 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 = 0.3473 r_free = 0.3473 target = 0.088815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075436 restraints weight = 21005.833| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.07 r_work: 0.3110 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10980 Z= 0.221 Angle : 0.591 7.179 14940 Z= 0.303 Chirality : 0.043 0.151 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.942 11.177 1440 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.23 % Allowed : 25.53 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.23), residues: 1350 helix: 1.11 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.69 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 29 PHE 0.011 0.001 PHE U 48 TYR 0.007 0.001 TYR Y 9 ARG 0.002 0.000 ARG Q 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 760 time to evaluate : 1.229 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: 0.9132 (tp-100) cc_final: 0.8572 (mt0) REVERT: A 42 ILE cc_start: 0.9435 (tp) cc_final: 0.9179 (tt) REVERT: A 47 LYS cc_start: 0.9175 (tttt) cc_final: 0.8816 (tppt) REVERT: A 49 SER cc_start: 0.9307 (t) cc_final: 0.9021 (m) REVERT: A 51 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8755 (mtpt) REVERT: B 45 PHE cc_start: 0.9421 (t80) cc_final: 0.9099 (t80) REVERT: B 51 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8809 (mtpt) REVERT: C 45 PHE cc_start: 0.9487 (t80) cc_final: 0.9252 (t80) REVERT: C 47 LYS cc_start: 0.9176 (tttt) cc_final: 0.8688 (tptt) REVERT: D 23 ASP cc_start: 0.8525 (m-30) cc_final: 0.8284 (m-30) REVERT: D 51 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8883 (mttt) REVERT: E 42 ILE cc_start: 0.9334 (tp) cc_final: 0.9120 (tt) REVERT: F 8 ASN cc_start: 0.7777 (t0) cc_final: 0.7063 (m110) REVERT: G 27 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8636 (mm-40) REVERT: G 49 SER cc_start: 0.9327 (m) cc_final: 0.9029 (p) REVERT: H 9 TYR cc_start: 0.7647 (m-80) cc_final: 0.7273 (m-80) REVERT: H 43 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8372 (ttm170) REVERT: H 51 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9087 (mtpp) REVERT: I 27 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8492 (tp-100) REVERT: I 50 SER cc_start: 0.8875 (t) cc_final: 0.8408 (p) REVERT: I 51 LYS cc_start: 0.9324 (mmtm) cc_final: 0.8950 (mtpp) REVERT: J 23 ASP cc_start: 0.8306 (p0) cc_final: 0.7879 (p0) REVERT: J 27 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8811 (tp-100) REVERT: J 48 PHE cc_start: 0.9435 (m-80) cc_final: 0.8925 (m-80) REVERT: J 51 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9114 (mtpp) REVERT: K 14 MET cc_start: 0.8839 (mmt) cc_final: 0.8346 (mmt) REVERT: K 15 ASP cc_start: 0.8554 (m-30) cc_final: 0.8211 (m-30) REVERT: K 50 SER cc_start: 0.9028 (t) cc_final: 0.8496 (p) REVERT: L 14 MET cc_start: 0.8493 (mmt) cc_final: 0.8243 (mmt) REVERT: L 20 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8845 (mm-40) REVERT: L 47 LYS cc_start: 0.8683 (tttt) cc_final: 0.8386 (ttmm) REVERT: L 50 SER cc_start: 0.9083 (t) cc_final: 0.8643 (p) REVERT: L 51 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8804 (mtpp) REVERT: M 14 MET cc_start: 0.8691 (mmm) cc_final: 0.8459 (mmt) REVERT: M 15 ASP cc_start: 0.8624 (m-30) cc_final: 0.8409 (m-30) REVERT: M 27 GLN cc_start: 0.9048 (tp40) cc_final: 0.8810 (tp40) REVERT: N 8 ASN cc_start: 0.7607 (t0) cc_final: 0.7125 (m-40) REVERT: N 47 LYS cc_start: 0.8857 (tttt) cc_final: 0.8419 (ttmm) REVERT: N 50 SER cc_start: 0.8978 (t) cc_final: 0.8542 (p) REVERT: N 51 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8689 (mtpp) REVERT: O 14 MET cc_start: 0.8734 (mmm) cc_final: 0.8356 (mmt) REVERT: O 27 GLN cc_start: 0.9085 (tp40) cc_final: 0.8710 (tp40) REVERT: P 15 ASP cc_start: 0.8311 (m-30) cc_final: 0.8090 (m-30) REVERT: P 27 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8708 (tp40) REVERT: Q 8 ASN cc_start: 0.8186 (t0) cc_final: 0.7890 (m110) REVERT: Q 15 ASP cc_start: 0.8574 (m-30) cc_final: 0.8292 (m-30) REVERT: Q 27 GLN cc_start: 0.9077 (tp40) cc_final: 0.8587 (tp40) REVERT: S 15 ASP cc_start: 0.8450 (m-30) cc_final: 0.8219 (m-30) REVERT: T 27 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8716 (tp-100) REVERT: U 8 ASN cc_start: 0.6947 (t0) cc_final: 0.6308 (t0) REVERT: U 15 ASP cc_start: 0.8824 (m-30) cc_final: 0.8526 (m-30) REVERT: U 40 LEU cc_start: 0.9305 (mp) cc_final: 0.8927 (mt) REVERT: U 51 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8160 (mttp) REVERT: W 43 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8430 (ttp80) REVERT: Y 47 LYS cc_start: 0.9145 (tttm) cc_final: 0.8944 (ttmm) REVERT: Z 18 LYS cc_start: 0.8798 (tttt) cc_final: 0.8341 (mptt) REVERT: Z 44 LEU cc_start: 0.9441 (mt) cc_final: 0.9240 (mp) REVERT: Z 46 LYS cc_start: 0.8498 (mttt) cc_final: 0.8141 (mtmt) REVERT: Z 49 SER cc_start: 0.9299 (m) cc_final: 0.8977 (t) REVERT: a 18 LYS cc_start: 0.8719 (tttt) cc_final: 0.8223 (mptt) REVERT: b 18 LYS cc_start: 0.8896 (tttt) cc_final: 0.8260 (mptt) REVERT: c 11 THR cc_start: 0.9120 (p) cc_final: 0.8606 (p) REVERT: c 15 ASP cc_start: 0.8645 (m-30) cc_final: 0.8405 (m-30) REVERT: c 18 LYS cc_start: 0.8946 (tttt) cc_final: 0.8377 (mptt) REVERT: d 18 LYS cc_start: 0.8772 (tttt) cc_final: 0.8019 (mmtt) REVERT: d 23 ASP cc_start: 0.8538 (t0) cc_final: 0.8317 (t0) REVERT: d 26 SER cc_start: 0.9329 (m) cc_final: 0.9036 (p) outliers start: 52 outliers final: 41 residues processed: 769 average time/residue: 0.2203 time to fit residues: 236.5627 Evaluate side-chains 765 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 724 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 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 9 TYR Chi-restraints excluded: chain P residue 22 ILE 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 V residue 24 LEU Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain 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 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.097366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084364 restraints weight = 20173.426| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.93 r_work: 0.3106 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10980 Z= 0.229 Angle : 0.592 8.118 14940 Z= 0.303 Chirality : 0.043 0.170 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.934 11.521 1440 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.23 % Allowed : 27.32 % Favored : 68.46 % 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: 1.78 (0.23), residues: 1350 helix: 1.21 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.32 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 29 PHE 0.018 0.001 PHE U 48 TYR 0.009 0.001 TYR D 9 ARG 0.003 0.000 ARG S 43 *********************** 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 808 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 756 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.9455 (tp) cc_final: 0.9184 (tt) REVERT: A 47 LYS cc_start: 0.9176 (tttt) cc_final: 0.8951 (mmtt) REVERT: A 49 SER cc_start: 0.9202 (t) cc_final: 0.8949 (m) REVERT: B 51 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8789 (mtpt) REVERT: C 20 GLN cc_start: 0.8506 (mt0) cc_final: 0.8192 (mt0) REVERT: C 43 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8209 (ttp80) REVERT: C 45 PHE cc_start: 0.9467 (t80) cc_final: 0.9236 (t80) REVERT: C 47 LYS cc_start: 0.9178 (tttt) cc_final: 0.8682 (tptt) REVERT: D 12 GLU cc_start: 0.7915 (mp0) cc_final: 0.7629 (mp0) REVERT: D 23 ASP cc_start: 0.8508 (m-30) cc_final: 0.8279 (m-30) REVERT: D 25 ILE cc_start: 0.9405 (mt) cc_final: 0.9190 (mt) REVERT: D 51 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8863 (mttt) REVERT: E 8 ASN cc_start: 0.8516 (t0) cc_final: 0.8093 (t0) REVERT: E 19 THR cc_start: 0.8957 (p) cc_final: 0.8377 (p) REVERT: E 51 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8771 (mtpt) REVERT: F 8 ASN cc_start: 0.7438 (t0) cc_final: 0.6991 (m110) REVERT: F 27 GLN cc_start: 0.9047 (tp40) cc_final: 0.8836 (tp40) REVERT: G 27 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8666 (mm-40) REVERT: G 49 SER cc_start: 0.9331 (m) cc_final: 0.9030 (t) REVERT: H 9 TYR cc_start: 0.7469 (m-80) cc_final: 0.7245 (m-80) REVERT: H 43 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8313 (ttm170) REVERT: I 27 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8549 (tp-100) REVERT: I 50 SER cc_start: 0.8914 (t) cc_final: 0.8479 (p) REVERT: I 51 LYS cc_start: 0.9331 (mmtm) cc_final: 0.8988 (mtpp) REVERT: J 23 ASP cc_start: 0.8293 (p0) cc_final: 0.7944 (p0) REVERT: J 27 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8766 (tp-100) REVERT: J 48 PHE cc_start: 0.9397 (m-80) cc_final: 0.8927 (m-80) REVERT: K 12 GLU cc_start: 0.8032 (mp0) cc_final: 0.7720 (mp0) REVERT: K 14 MET cc_start: 0.8804 (mmt) cc_final: 0.8293 (mmt) REVERT: K 15 ASP cc_start: 0.8572 (m-30) cc_final: 0.8282 (m-30) REVERT: K 50 SER cc_start: 0.9123 (t) cc_final: 0.8545 (p) REVERT: K 51 LYS cc_start: 0.9400 (mtpp) cc_final: 0.8928 (mtpt) REVERT: L 14 MET cc_start: 0.8561 (mmt) cc_final: 0.8242 (mmt) REVERT: L 51 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8682 (mtpp) REVERT: M 14 MET cc_start: 0.8684 (mmm) cc_final: 0.8402 (mmt) REVERT: M 27 GLN cc_start: 0.9037 (tp40) cc_final: 0.8790 (tp40) REVERT: N 8 ASN cc_start: 0.7391 (t0) cc_final: 0.7018 (m-40) REVERT: N 47 LYS cc_start: 0.8833 (tttt) cc_final: 0.8418 (ttmm) REVERT: N 50 SER cc_start: 0.8964 (t) cc_final: 0.8522 (p) REVERT: N 51 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8705 (mtpp) REVERT: O 14 MET cc_start: 0.8771 (mmm) cc_final: 0.8437 (mmt) REVERT: P 15 ASP cc_start: 0.8352 (m-30) cc_final: 0.8119 (m-30) REVERT: P 27 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8711 (tp40) REVERT: Q 8 ASN cc_start: 0.8180 (t0) cc_final: 0.7900 (m110) REVERT: Q 15 ASP cc_start: 0.8602 (m-30) cc_final: 0.8306 (m-30) REVERT: Q 27 GLN cc_start: 0.9127 (tp40) cc_final: 0.8862 (tp40) REVERT: S 15 ASP cc_start: 0.8428 (m-30) cc_final: 0.8063 (m-30) REVERT: S 51 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8992 (ttmm) REVERT: T 27 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8726 (tp-100) REVERT: U 8 ASN cc_start: 0.6603 (t0) cc_final: 0.5762 (t0) REVERT: U 15 ASP cc_start: 0.8822 (m-30) cc_final: 0.8515 (m-30) REVERT: U 40 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8984 (mt) REVERT: U 51 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8210 (mttm) REVERT: W 18 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8640 (ttmm) REVERT: W 43 ARG cc_start: 0.8690 (ttm170) cc_final: 0.8389 (ttp80) REVERT: Y 18 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8555 (ttmm) REVERT: Z 18 LYS cc_start: 0.8791 (tttt) cc_final: 0.8351 (mptt) REVERT: Z 33 THR cc_start: 0.8821 (t) cc_final: 0.8520 (p) REVERT: Z 46 LYS cc_start: 0.8568 (mttt) cc_final: 0.8299 (mtmt) REVERT: Z 49 SER cc_start: 0.9297 (m) cc_final: 0.8989 (t) REVERT: a 18 LYS cc_start: 0.8743 (tttt) cc_final: 0.8199 (mptt) REVERT: b 15 ASP cc_start: 0.8548 (m-30) cc_final: 0.8346 (m-30) REVERT: b 18 LYS cc_start: 0.8912 (tttt) cc_final: 0.8211 (mptt) REVERT: c 11 THR cc_start: 0.9102 (p) cc_final: 0.8574 (p) REVERT: c 15 ASP cc_start: 0.8627 (m-30) cc_final: 0.8388 (m-30) REVERT: c 18 LYS cc_start: 0.8971 (tttt) cc_final: 0.8307 (mptt) REVERT: c 48 PHE cc_start: 0.9113 (m-80) cc_final: 0.8832 (m-80) REVERT: d 18 LYS cc_start: 0.8743 (tttt) cc_final: 0.7985 (mptt) REVERT: d 23 ASP cc_start: 0.8572 (t0) cc_final: 0.8328 (t0) REVERT: d 26 SER cc_start: 0.9268 (m) cc_final: 0.9034 (p) outliers start: 52 outliers final: 42 residues processed: 765 average time/residue: 0.2205 time to fit residues: 235.5533 Evaluate side-chains 770 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 726 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 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 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain a residue 49 SER 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 d residue 9 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN O 8 ASN R 27 GLN S 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076058 restraints weight = 21053.289| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.11 r_work: 0.3121 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10980 Z= 0.216 Angle : 0.606 7.369 14940 Z= 0.312 Chirality : 0.043 0.181 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.905 11.272 1440 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 4.47 % Allowed : 28.37 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1350 helix: 1.33 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.35 (0.43), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 29 PHE 0.021 0.001 PHE U 48 TYR 0.010 0.001 TYR L 9 ARG 0.002 0.000 ARG S 43 *********************** 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 795 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 740 time to evaluate : 1.207 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 27 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8605 (mt0) REVERT: A 42 ILE cc_start: 0.9466 (tp) cc_final: 0.9127 (tt) REVERT: A 47 LYS cc_start: 0.9149 (tttt) cc_final: 0.8895 (mmtt) REVERT: A 49 SER cc_start: 0.9138 (t) cc_final: 0.8909 (m) REVERT: B 51 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8816 (mtpt) REVERT: C 20 GLN cc_start: 0.8493 (mt0) cc_final: 0.8191 (mt0) REVERT: C 43 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8254 (ttp80) REVERT: C 45 PHE cc_start: 0.9418 (t80) cc_final: 0.9217 (t80) REVERT: C 47 LYS cc_start: 0.9156 (tttt) cc_final: 0.8637 (tptt) REVERT: D 12 GLU cc_start: 0.7953 (mp0) cc_final: 0.7660 (mp0) REVERT: D 23 ASP cc_start: 0.8522 (m-30) cc_final: 0.8288 (m-30) REVERT: D 37 VAL cc_start: 0.9244 (p) cc_final: 0.8966 (m) REVERT: D 51 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8809 (mttt) REVERT: E 8 ASN cc_start: 0.8712 (t0) cc_final: 0.8256 (t0) REVERT: E 51 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8733 (mtpt) REVERT: F 8 ASN cc_start: 0.7402 (t0) cc_final: 0.6956 (m110) REVERT: F 51 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8932 (mtpp) REVERT: G 27 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8654 (mm-40) REVERT: G 51 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8955 (mtpp) REVERT: H 9 TYR cc_start: 0.7623 (m-80) cc_final: 0.7099 (m-80) REVERT: H 43 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8437 (ttm170) REVERT: I 27 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8478 (tp-100) REVERT: I 50 SER cc_start: 0.8928 (t) cc_final: 0.8499 (p) REVERT: I 51 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9002 (mtpp) REVERT: J 23 ASP cc_start: 0.8268 (p0) cc_final: 0.7945 (p0) REVERT: J 27 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8640 (tp-100) REVERT: J 48 PHE cc_start: 0.9382 (m-80) cc_final: 0.8896 (m-80) REVERT: K 12 GLU cc_start: 0.8141 (mp0) cc_final: 0.7926 (mp0) REVERT: K 14 MET cc_start: 0.8809 (mmt) cc_final: 0.8267 (mmt) REVERT: K 15 ASP cc_start: 0.8618 (m-30) cc_final: 0.8326 (m-30) REVERT: K 50 SER cc_start: 0.9177 (t) cc_final: 0.8685 (p) REVERT: K 51 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9016 (mtpp) REVERT: L 14 MET cc_start: 0.8613 (mmt) cc_final: 0.8282 (mmt) REVERT: L 20 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8928 (mm-40) REVERT: L 50 SER cc_start: 0.9240 (t) cc_final: 0.8816 (p) REVERT: L 51 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8647 (mtpp) REVERT: M 27 GLN cc_start: 0.9083 (tp40) cc_final: 0.8843 (tp40) REVERT: N 8 ASN cc_start: 0.7472 (t0) cc_final: 0.6868 (m-40) REVERT: N 47 LYS cc_start: 0.8773 (tttt) cc_final: 0.8509 (ttmm) REVERT: O 14 MET cc_start: 0.8754 (mmm) cc_final: 0.8428 (mmt) REVERT: P 15 ASP cc_start: 0.8332 (m-30) cc_final: 0.8099 (m-30) REVERT: P 27 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8706 (tp40) REVERT: Q 8 ASN cc_start: 0.8125 (t0) cc_final: 0.7893 (m110) REVERT: Q 15 ASP cc_start: 0.8597 (m-30) cc_final: 0.8307 (m-30) REVERT: Q 27 GLN cc_start: 0.9133 (tp40) cc_final: 0.8816 (tp40) REVERT: S 15 ASP cc_start: 0.8435 (m-30) cc_final: 0.8193 (m-30) REVERT: S 51 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8967 (ttmm) REVERT: T 27 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8743 (tp-100) REVERT: U 8 ASN cc_start: 0.6176 (t0) cc_final: 0.5601 (t0) REVERT: U 15 ASP cc_start: 0.8894 (m-30) cc_final: 0.8540 (m-30) REVERT: U 40 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8973 (mt) REVERT: W 18 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8652 (ttmm) REVERT: W 43 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8419 (ttp80) REVERT: X 19 THR cc_start: 0.9213 (p) cc_final: 0.9007 (t) REVERT: Z 18 LYS cc_start: 0.8810 (tttt) cc_final: 0.8349 (mptt) REVERT: Z 46 LYS cc_start: 0.8585 (mttt) cc_final: 0.8277 (mtmt) REVERT: Z 49 SER cc_start: 0.9306 (m) cc_final: 0.9058 (t) REVERT: a 18 LYS cc_start: 0.8770 (tttt) cc_final: 0.8223 (mptt) REVERT: b 18 LYS cc_start: 0.8984 (tttt) cc_final: 0.8193 (mptt) REVERT: b 51 LYS cc_start: 0.8798 (mptt) cc_final: 0.8480 (mttm) REVERT: c 11 THR cc_start: 0.9101 (p) cc_final: 0.8554 (p) REVERT: c 15 ASP cc_start: 0.8629 (m-30) cc_final: 0.8403 (m-30) REVERT: c 18 LYS cc_start: 0.9006 (tttt) cc_final: 0.8262 (mptt) REVERT: d 18 LYS cc_start: 0.8673 (tttt) cc_final: 0.7937 (mptt) REVERT: d 23 ASP cc_start: 0.8645 (t0) cc_final: 0.8421 (t0) REVERT: d 26 SER cc_start: 0.9255 (m) cc_final: 0.8995 (p) REVERT: d 51 LYS cc_start: 0.9044 (mptt) cc_final: 0.8746 (mptt) outliers start: 55 outliers final: 41 residues processed: 750 average time/residue: 0.2191 time to fit residues: 228.5093 Evaluate side-chains 763 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 720 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 33 THR Chi-restraints excluded: chain F residue 34 THR 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 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 51 LYS 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 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 28 THR 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 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3519 r_free = 0.3519 target = 0.099214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085927 restraints weight = 20565.370| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3129 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.5684 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= 0.209 Angle : 0.609 8.095 14940 Z= 0.311 Chirality : 0.043 0.193 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.886 11.586 1440 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 3.98 % Allowed : 30.33 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.23), residues: 1350 helix: 1.40 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.53 (0.44), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 29 PHE 0.019 0.001 PHE U 48 TYR 0.008 0.001 TYR Y 9 ARG 0.004 0.000 ARG S 43 *********************** 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 806 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 757 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8563 (mt0) REVERT: A 42 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9072 (tt) REVERT: A 47 LYS cc_start: 0.9146 (tttt) cc_final: 0.8878 (mmtt) REVERT: A 49 SER cc_start: 0.9115 (t) cc_final: 0.8886 (m) REVERT: B 51 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8884 (mtpt) REVERT: C 9 TYR cc_start: 0.7570 (m-80) cc_final: 0.7341 (m-80) REVERT: C 20 GLN cc_start: 0.8462 (mt0) cc_final: 0.8161 (mt0) REVERT: C 43 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8154 (ttp80) REVERT: C 47 LYS cc_start: 0.9151 (tttt) cc_final: 0.8636 (tptt) REVERT: D 12 GLU cc_start: 0.7962 (mp0) cc_final: 0.7626 (mp0) REVERT: D 23 ASP cc_start: 0.8546 (m-30) cc_final: 0.8326 (m-30) REVERT: D 27 GLN cc_start: 0.9106 (tp40) cc_final: 0.8328 (tt0) REVERT: D 51 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8800 (mttt) REVERT: E 8 ASN cc_start: 0.8708 (t0) cc_final: 0.8242 (t0) REVERT: E 19 THR cc_start: 0.9200 (p) cc_final: 0.8575 (p) REVERT: E 51 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8728 (mtpt) REVERT: F 51 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8967 (mtpp) REVERT: H 9 TYR cc_start: 0.7385 (m-80) cc_final: 0.7057 (m-80) REVERT: H 43 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8354 (ttm170) REVERT: I 20 GLN cc_start: 0.8615 (tp40) cc_final: 0.8280 (mm-40) REVERT: I 27 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8389 (tp-100) REVERT: I 50 SER cc_start: 0.9004 (t) cc_final: 0.8544 (p) REVERT: I 51 LYS cc_start: 0.9328 (mmtm) cc_final: 0.9020 (mtpp) REVERT: J 23 ASP cc_start: 0.8317 (p0) cc_final: 0.8003 (p0) REVERT: J 27 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8633 (tp-100) REVERT: J 48 PHE cc_start: 0.9362 (m-80) cc_final: 0.8890 (m-80) REVERT: K 12 GLU cc_start: 0.8158 (mp0) cc_final: 0.7953 (mp0) REVERT: K 14 MET cc_start: 0.8777 (mmt) cc_final: 0.8254 (mmt) REVERT: K 15 ASP cc_start: 0.8618 (m-30) cc_final: 0.8353 (m-30) REVERT: K 18 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8456 (mttm) REVERT: K 50 SER cc_start: 0.9249 (t) cc_final: 0.8677 (p) REVERT: K 51 LYS cc_start: 0.9389 (mtpp) cc_final: 0.8927 (mtpp) REVERT: L 14 MET cc_start: 0.8618 (mmt) cc_final: 0.8251 (mmt) REVERT: L 20 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8863 (mm-40) REVERT: L 50 SER cc_start: 0.9238 (t) cc_final: 0.8807 (p) REVERT: L 51 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8609 (mtpp) REVERT: M 14 MET cc_start: 0.8666 (mmm) cc_final: 0.8126 (mmt) REVERT: M 27 GLN cc_start: 0.9068 (tp40) cc_final: 0.8806 (tp40) REVERT: N 8 ASN cc_start: 0.7506 (t0) cc_final: 0.7112 (m-40) REVERT: N 47 LYS cc_start: 0.8770 (tttt) cc_final: 0.8550 (ttmm) REVERT: N 51 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8718 (mtpp) REVERT: O 8 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7009 (m-40) REVERT: O 14 MET cc_start: 0.8741 (mmm) cc_final: 0.8322 (mmt) REVERT: P 15 ASP cc_start: 0.8305 (m-30) cc_final: 0.8062 (m-30) REVERT: P 23 ASP cc_start: 0.8843 (t0) cc_final: 0.8635 (t0) REVERT: P 27 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8718 (tp40) REVERT: Q 8 ASN cc_start: 0.8038 (t0) cc_final: 0.7792 (m110) REVERT: Q 15 ASP cc_start: 0.8591 (m-30) cc_final: 0.8254 (m-30) REVERT: Q 27 GLN cc_start: 0.9119 (tp40) cc_final: 0.8770 (tp40) REVERT: R 12 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8101 (tm-30) REVERT: S 15 ASP cc_start: 0.8403 (m-30) cc_final: 0.8106 (m-30) REVERT: S 51 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8974 (ttmm) REVERT: T 27 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8743 (tp-100) REVERT: U 8 ASN cc_start: 0.6350 (t0) cc_final: 0.5964 (t0) REVERT: U 11 THR cc_start: 0.8568 (p) cc_final: 0.8125 (p) REVERT: U 15 ASP cc_start: 0.8870 (m-30) cc_final: 0.8541 (m-30) REVERT: U 40 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8998 (mt) REVERT: W 18 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8646 (ttmm) REVERT: W 43 ARG cc_start: 0.8710 (ttm170) cc_final: 0.8395 (ttp80) REVERT: X 19 THR cc_start: 0.9195 (p) cc_final: 0.8993 (t) REVERT: Z 18 LYS cc_start: 0.8745 (tttt) cc_final: 0.8291 (mptt) REVERT: Z 33 THR cc_start: 0.8472 (p) cc_final: 0.8267 (p) REVERT: Z 46 LYS cc_start: 0.8602 (mttt) cc_final: 0.8326 (mtmt) REVERT: Z 49 SER cc_start: 0.9307 (m) cc_final: 0.9061 (t) REVERT: Z 51 LYS cc_start: 0.9052 (mptt) cc_final: 0.8808 (mttm) REVERT: a 18 LYS cc_start: 0.8752 (tttt) cc_final: 0.8207 (mptt) REVERT: b 18 LYS cc_start: 0.9012 (tttt) cc_final: 0.8133 (mptt) REVERT: b 51 LYS cc_start: 0.8645 (mptt) cc_final: 0.8315 (mttm) REVERT: c 11 THR cc_start: 0.9085 (p) cc_final: 0.8558 (p) REVERT: c 15 ASP cc_start: 0.8637 (m-30) cc_final: 0.8433 (m-30) REVERT: c 18 LYS cc_start: 0.8992 (tttt) cc_final: 0.8244 (mptt) REVERT: d 18 LYS cc_start: 0.8685 (tttt) cc_final: 0.7809 (mptt) REVERT: d 23 ASP cc_start: 0.8743 (t0) cc_final: 0.8540 (t0) REVERT: d 26 SER cc_start: 0.9254 (m) cc_final: 0.8988 (p) REVERT: d 51 LYS cc_start: 0.9004 (mptt) cc_final: 0.8733 (mptt) outliers start: 49 outliers final: 37 residues processed: 768 average time/residue: 0.2256 time to fit residues: 241.3997 Evaluate side-chains 779 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 738 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B 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 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain W residue 9 TYR Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 28 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.100419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087133 restraints weight = 19847.833| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.97 r_work: 0.3147 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10980 Z= 0.215 Angle : 0.623 8.110 14940 Z= 0.319 Chirality : 0.044 0.193 1980 Planarity : 0.004 0.036 1740 Dihedral : 3.926 12.095 1440 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 3.25 % Allowed : 31.95 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.19 (0.23), residues: 1350 helix: 1.45 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.94 (0.34), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 29 PHE 0.021 0.001 PHE c 48 TYR 0.008 0.001 TYR L 9 ARG 0.004 0.000 ARG c 43 *********************** 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 783 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 743 time to evaluate : 1.322 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: 0.9092 (tp-100) cc_final: 0.8580 (mt0) REVERT: A 42 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9131 (tt) REVERT: A 47 LYS cc_start: 0.9138 (tttt) cc_final: 0.8792 (tppt) REVERT: A 49 SER cc_start: 0.9108 (t) cc_final: 0.8893 (m) REVERT: B 27 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8312 (tt0) REVERT: B 45 PHE cc_start: 0.9336 (t80) cc_final: 0.9091 (t80) REVERT: C 9 TYR cc_start: 0.7567 (m-80) cc_final: 0.7345 (m-80) REVERT: C 43 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8052 (ttp80) REVERT: C 47 LYS cc_start: 0.9127 (tttt) cc_final: 0.8630 (tptt) REVERT: D 12 GLU cc_start: 0.8001 (mp0) cc_final: 0.7658 (mp0) REVERT: D 23 ASP cc_start: 0.8547 (m-30) cc_final: 0.8327 (m-30) REVERT: D 27 GLN cc_start: 0.9128 (tp40) cc_final: 0.8331 (tt0) REVERT: D 51 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8805 (mttt) REVERT: E 8 ASN cc_start: 0.8684 (t0) cc_final: 0.8228 (t0) REVERT: E 51 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8715 (mtpt) REVERT: H 9 TYR cc_start: 0.7246 (m-80) cc_final: 0.7028 (m-80) REVERT: H 43 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8342 (ttm170) REVERT: I 50 SER cc_start: 0.9014 (t) cc_final: 0.8553 (p) REVERT: I 51 LYS cc_start: 0.9327 (mmtm) cc_final: 0.9030 (mtpp) REVERT: J 23 ASP cc_start: 0.8276 (p0) cc_final: 0.7959 (p0) REVERT: J 27 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8626 (tp-100) REVERT: K 12 GLU cc_start: 0.8162 (mp0) cc_final: 0.7920 (mp0) REVERT: K 14 MET cc_start: 0.8772 (mmt) cc_final: 0.8259 (mmt) REVERT: K 15 ASP cc_start: 0.8642 (m-30) cc_final: 0.8387 (m-30) REVERT: K 18 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8451 (ttmm) REVERT: K 43 ARG cc_start: 0.8812 (mtp180) cc_final: 0.8456 (ttm170) REVERT: K 50 SER cc_start: 0.9196 (t) cc_final: 0.8629 (p) REVERT: K 51 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9190 (mtpp) REVERT: L 14 MET cc_start: 0.8591 (mmt) cc_final: 0.8268 (mmt) REVERT: L 20 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8924 (mm-40) REVERT: M 14 MET cc_start: 0.8755 (mmm) cc_final: 0.8169 (mmt) REVERT: N 8 ASN cc_start: 0.7554 (t0) cc_final: 0.7136 (m-40) REVERT: N 47 LYS cc_start: 0.8735 (tttt) cc_final: 0.8526 (ttmm) REVERT: N 51 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8693 (mtpp) REVERT: O 14 MET cc_start: 0.8747 (mmm) cc_final: 0.8419 (mmt) REVERT: P 15 ASP cc_start: 0.8326 (m-30) cc_final: 0.8092 (m-30) REVERT: P 27 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8709 (tp40) REVERT: Q 8 ASN cc_start: 0.8019 (t0) cc_final: 0.7778 (m110) REVERT: Q 15 ASP cc_start: 0.8543 (m-30) cc_final: 0.8228 (m-30) REVERT: Q 27 GLN cc_start: 0.9130 (tp40) cc_final: 0.8809 (tp40) REVERT: R 9 TYR cc_start: 0.7679 (m-80) cc_final: 0.7353 (m-80) REVERT: S 11 THR cc_start: 0.8664 (p) cc_final: 0.7968 (p) REVERT: S 15 ASP cc_start: 0.8357 (m-30) cc_final: 0.7964 (m-30) REVERT: S 51 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.9000 (ttmm) REVERT: T 27 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8802 (tp-100) REVERT: U 8 ASN cc_start: 0.6501 (t0) cc_final: 0.6062 (t0) REVERT: U 15 ASP cc_start: 0.8856 (m-30) cc_final: 0.8572 (m-30) REVERT: U 40 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8986 (mt) REVERT: W 18 LYS cc_start: 0.9016 (ttpt) cc_final: 0.8657 (ttmm) REVERT: W 43 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8390 (ttp80) REVERT: W 49 SER cc_start: 0.9248 (m) cc_final: 0.9035 (p) REVERT: Z 18 LYS cc_start: 0.8769 (tttt) cc_final: 0.8346 (mptt) REVERT: Z 46 LYS cc_start: 0.8630 (mttt) cc_final: 0.8349 (mtmt) REVERT: Z 49 SER cc_start: 0.9320 (m) cc_final: 0.9108 (t) REVERT: Z 51 LYS cc_start: 0.9046 (mptt) cc_final: 0.8811 (mttm) REVERT: a 18 LYS cc_start: 0.8713 (tttt) cc_final: 0.8187 (mptt) REVERT: b 18 LYS cc_start: 0.8981 (tttt) cc_final: 0.8127 (mptt) REVERT: b 46 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8620 (ttmt) REVERT: b 51 LYS cc_start: 0.8638 (mptt) cc_final: 0.8312 (mttm) REVERT: c 11 THR cc_start: 0.8983 (p) cc_final: 0.8498 (p) REVERT: c 18 LYS cc_start: 0.8973 (tttt) cc_final: 0.8253 (mptt) REVERT: d 18 LYS cc_start: 0.8743 (tttt) cc_final: 0.7853 (mptt) REVERT: d 23 ASP cc_start: 0.8713 (t0) cc_final: 0.8511 (t0) REVERT: d 26 SER cc_start: 0.9256 (m) cc_final: 0.8995 (p) REVERT: d 51 LYS cc_start: 0.9000 (mptt) cc_final: 0.8757 (mptt) outliers start: 40 outliers final: 32 residues processed: 751 average time/residue: 0.2260 time to fit residues: 235.4861 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 : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 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 W residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain a residue 49 SER 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 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: 0.8980 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.090864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076523 restraints weight = 21145.011| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.20 r_work: 0.3133 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5873 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= 0.234 Angle : 0.638 8.115 14940 Z= 0.328 Chirality : 0.045 0.208 1980 Planarity : 0.004 0.030 1740 Dihedral : 3.918 14.701 1440 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 3.17 % Allowed : 31.95 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.23), residues: 1350 helix: 1.48 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.86 (0.44), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 29 PHE 0.022 0.001 PHE c 48 TYR 0.007 0.001 TYR L 9 ARG 0.005 0.000 ARG F 43 *********************** 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 774 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 735 time to evaluate : 1.217 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: 0.9482 (OUTLIER) cc_final: 0.9196 (tt) REVERT: A 47 LYS cc_start: 0.9194 (tttt) cc_final: 0.8810 (tppt) REVERT: A 49 SER cc_start: 0.9099 (t) cc_final: 0.8882 (m) REVERT: B 45 PHE cc_start: 0.9345 (t80) cc_final: 0.9110 (t80) REVERT: C 9 TYR cc_start: 0.7630 (m-80) cc_final: 0.7354 (m-80) REVERT: C 43 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8053 (ttp80) REVERT: C 47 LYS cc_start: 0.9142 (tttt) cc_final: 0.8635 (tptt) REVERT: D 12 GLU cc_start: 0.8035 (mp0) cc_final: 0.7675 (mp0) REVERT: D 23 ASP cc_start: 0.8553 (m-30) cc_final: 0.8344 (m-30) REVERT: D 27 GLN cc_start: 0.9126 (tp40) cc_final: 0.8289 (tt0) REVERT: D 51 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8766 (mttt) REVERT: E 8 ASN cc_start: 0.8693 (t0) cc_final: 0.8231 (t0) REVERT: E 51 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8757 (mttt) REVERT: H 9 TYR cc_start: 0.7292 (m-80) cc_final: 0.7083 (m-80) REVERT: H 43 ARG cc_start: 0.8829 (mtp180) cc_final: 0.8321 (ttm170) REVERT: I 15 ASP cc_start: 0.8880 (m-30) cc_final: 0.8647 (m-30) REVERT: I 27 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8595 (mm-40) REVERT: I 50 SER cc_start: 0.9025 (t) cc_final: 0.8572 (p) REVERT: I 51 LYS cc_start: 0.9261 (mmtm) cc_final: 0.8991 (mtpp) REVERT: J 23 ASP cc_start: 0.8298 (p0) cc_final: 0.7997 (p0) REVERT: J 27 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8611 (tp-100) REVERT: K 12 GLU cc_start: 0.8236 (mp0) cc_final: 0.7928 (mp0) REVERT: K 14 MET cc_start: 0.8771 (mmt) cc_final: 0.8282 (mmt) REVERT: K 15 ASP cc_start: 0.8612 (m-30) cc_final: 0.8406 (m-30) REVERT: K 18 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8487 (ttmm) REVERT: K 43 ARG cc_start: 0.8812 (mtp180) cc_final: 0.8475 (ttm170) REVERT: K 50 SER cc_start: 0.9217 (t) cc_final: 0.8672 (p) REVERT: K 51 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9092 (mtpp) REVERT: L 14 MET cc_start: 0.8621 (mmt) cc_final: 0.8317 (mmt) REVERT: L 20 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8925 (mm-40) REVERT: M 14 MET cc_start: 0.8774 (mmm) cc_final: 0.8428 (mmt) REVERT: M 27 GLN cc_start: 0.9091 (tp40) cc_final: 0.8827 (tp40) REVERT: N 8 ASN cc_start: 0.7597 (t0) cc_final: 0.7054 (t0) REVERT: N 47 LYS cc_start: 0.8743 (tttt) cc_final: 0.8538 (ttmm) REVERT: N 51 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8823 (mtpp) REVERT: O 14 MET cc_start: 0.8837 (mmm) cc_final: 0.8403 (mmt) REVERT: P 15 ASP cc_start: 0.8315 (m-30) cc_final: 0.8088 (m-30) REVERT: Q 8 ASN cc_start: 0.8006 (t0) cc_final: 0.7764 (m110) REVERT: Q 15 ASP cc_start: 0.8545 (m-30) cc_final: 0.8183 (m-30) REVERT: Q 27 GLN cc_start: 0.9123 (tp40) cc_final: 0.8808 (tp40) REVERT: S 11 THR cc_start: 0.8569 (p) cc_final: 0.7866 (p) REVERT: S 15 ASP cc_start: 0.8336 (m-30) cc_final: 0.7973 (m-30) REVERT: S 51 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8902 (ttmm) REVERT: T 27 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8845 (tp-100) REVERT: U 11 THR cc_start: 0.8561 (p) cc_final: 0.8159 (p) REVERT: U 15 ASP cc_start: 0.8879 (m-30) cc_final: 0.8524 (m-30) REVERT: U 40 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8989 (mt) REVERT: V 49 SER cc_start: 0.9505 (t) cc_final: 0.9164 (p) REVERT: W 18 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8651 (ttmm) REVERT: W 43 ARG cc_start: 0.8721 (ttm170) cc_final: 0.8404 (ttp80) REVERT: X 23 ASP cc_start: 0.8754 (t70) cc_final: 0.8522 (t0) REVERT: Z 18 LYS cc_start: 0.8794 (tttt) cc_final: 0.8362 (mptt) REVERT: Z 46 LYS cc_start: 0.8602 (mttt) cc_final: 0.8318 (mtmt) REVERT: Z 47 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8823 (tttm) REVERT: Z 49 SER cc_start: 0.9323 (m) cc_final: 0.9111 (t) REVERT: Z 51 LYS cc_start: 0.9051 (mptt) cc_final: 0.8832 (mttm) REVERT: a 18 LYS cc_start: 0.8735 (tttt) cc_final: 0.8206 (mptt) REVERT: b 18 LYS cc_start: 0.8987 (tttt) cc_final: 0.8113 (mptt) REVERT: b 46 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8593 (ttmt) REVERT: b 51 LYS cc_start: 0.8645 (mptt) cc_final: 0.8320 (mttm) REVERT: c 14 MET cc_start: 0.6558 (mmm) cc_final: 0.6164 (tpp) REVERT: c 18 LYS cc_start: 0.8959 (tttt) cc_final: 0.8243 (mptt) REVERT: d 18 LYS cc_start: 0.8786 (tttt) cc_final: 0.7761 (mptt) REVERT: d 26 SER cc_start: 0.9283 (m) cc_final: 0.9018 (p) REVERT: d 51 LYS cc_start: 0.9000 (mptt) cc_final: 0.8724 (mptt) outliers start: 39 outliers final: 30 residues processed: 743 average time/residue: 0.2261 time to fit residues: 232.8561 Evaluate side-chains 760 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 726 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 51 LYS 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 40 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain a residue 49 SER 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 17 LEU Chi-restraints excluded: chain c residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 8 ASN S 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085344 restraints weight = 20372.285| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.01 r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.5906 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= 0.267 Angle : 0.677 7.284 14940 Z= 0.349 Chirality : 0.046 0.210 1980 Planarity : 0.004 0.027 1740 Dihedral : 3.981 14.860 1440 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 3.09 % Allowed : 33.33 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.23), residues: 1350 helix: 1.43 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.09 (0.48), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 29 PHE 0.018 0.002 PHE U 48 TYR 0.007 0.001 TYR N 9 ARG 0.006 0.000 ARG F 43 ********************** 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 758 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 720 time to evaluate : 1.233 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 42 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9165 (tt) REVERT: A 47 LYS cc_start: 0.9201 (tttt) cc_final: 0.8805 (tppt) REVERT: A 49 SER cc_start: 0.9110 (t) cc_final: 0.8890 (m) REVERT: C 9 TYR cc_start: 0.7650 (m-80) cc_final: 0.7165 (m-80) REVERT: C 43 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8103 (ttp80) REVERT: C 47 LYS cc_start: 0.9117 (tttt) cc_final: 0.8633 (tptt) REVERT: D 12 GLU cc_start: 0.8062 (mp0) cc_final: 0.7653 (mp0) REVERT: D 23 ASP cc_start: 0.8577 (m-30) cc_final: 0.8369 (m-30) REVERT: D 27 GLN cc_start: 0.9148 (tp40) cc_final: 0.8345 (tt0) REVERT: D 51 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8801 (mttt) REVERT: E 8 ASN cc_start: 0.8668 (t0) cc_final: 0.8238 (t0) REVERT: E 51 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8723 (mttt) REVERT: F 43 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8312 (ttp-110) REVERT: H 9 TYR cc_start: 0.7314 (m-80) cc_final: 0.7106 (m-80) REVERT: H 43 ARG cc_start: 0.8855 (mtp180) cc_final: 0.8383 (ttm170) REVERT: I 50 SER cc_start: 0.9062 (t) cc_final: 0.8632 (p) REVERT: I 51 LYS cc_start: 0.9264 (mmtm) cc_final: 0.9005 (mtpp) REVERT: J 23 ASP cc_start: 0.8308 (p0) cc_final: 0.7976 (p0) REVERT: J 27 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8617 (tp-100) REVERT: K 12 GLU cc_start: 0.8190 (mp0) cc_final: 0.7881 (mp0) REVERT: K 14 MET cc_start: 0.8811 (mmt) cc_final: 0.8363 (mmt) REVERT: K 18 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8509 (ttmm) REVERT: K 43 ARG cc_start: 0.8830 (mtp180) cc_final: 0.8433 (ttm170) REVERT: K 50 SER cc_start: 0.9243 (t) cc_final: 0.8645 (p) REVERT: K 51 LYS cc_start: 0.9382 (mtpp) cc_final: 0.8998 (mtpp) REVERT: L 14 MET cc_start: 0.8638 (mmt) cc_final: 0.8331 (mmt) REVERT: L 20 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8935 (mm-40) REVERT: M 14 MET cc_start: 0.8811 (mmm) cc_final: 0.8454 (mmt) REVERT: N 8 ASN cc_start: 0.7522 (t0) cc_final: 0.7271 (t0) REVERT: N 47 LYS cc_start: 0.8727 (tttt) cc_final: 0.8511 (ttmm) REVERT: O 14 MET cc_start: 0.8826 (mmm) cc_final: 0.8437 (mmt) REVERT: P 15 ASP cc_start: 0.8326 (m-30) cc_final: 0.8091 (m-30) REVERT: Q 8 ASN cc_start: 0.8119 (t0) cc_final: 0.7849 (m110) REVERT: Q 15 ASP cc_start: 0.8553 (m-30) cc_final: 0.8193 (m-30) REVERT: Q 27 GLN cc_start: 0.9143 (tp40) cc_final: 0.8834 (tp40) REVERT: S 11 THR cc_start: 0.8512 (p) cc_final: 0.7705 (p) REVERT: S 15 ASP cc_start: 0.8318 (m-30) cc_final: 0.7902 (m-30) REVERT: S 51 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8947 (ttmm) REVERT: T 27 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8836 (tp-100) REVERT: U 15 ASP cc_start: 0.8908 (m-30) cc_final: 0.8547 (m-30) REVERT: U 40 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8995 (mt) REVERT: V 49 SER cc_start: 0.9461 (t) cc_final: 0.9131 (p) REVERT: W 18 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8661 (ttmm) REVERT: X 23 ASP cc_start: 0.8759 (t70) cc_final: 0.8544 (t0) REVERT: X 49 SER cc_start: 0.9496 (OUTLIER) cc_final: 0.9237 (p) REVERT: Z 18 LYS cc_start: 0.8740 (tttt) cc_final: 0.8285 (mptt) REVERT: Z 46 LYS cc_start: 0.8614 (mttt) cc_final: 0.8326 (mtmt) REVERT: Z 49 SER cc_start: 0.9317 (m) cc_final: 0.9102 (t) REVERT: Z 51 LYS cc_start: 0.9061 (mptt) cc_final: 0.8821 (mttm) REVERT: a 18 LYS cc_start: 0.8736 (tttt) cc_final: 0.8175 (mptt) REVERT: b 18 LYS cc_start: 0.8982 (tttt) cc_final: 0.8114 (mptt) REVERT: b 46 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8579 (ttmt) REVERT: b 51 LYS cc_start: 0.8656 (mptt) cc_final: 0.8332 (mttm) REVERT: c 14 MET cc_start: 0.6410 (mmm) cc_final: 0.6025 (mmm) REVERT: c 18 LYS cc_start: 0.8953 (tttt) cc_final: 0.8208 (mptt) REVERT: d 18 LYS cc_start: 0.8769 (tttt) cc_final: 0.7647 (mmtt) REVERT: d 26 SER cc_start: 0.9283 (m) cc_final: 0.9035 (p) REVERT: d 51 LYS cc_start: 0.9002 (mptt) cc_final: 0.8727 (mptt) outliers start: 38 outliers final: 28 residues processed: 731 average time/residue: 0.2256 time to fit residues: 228.1518 Evaluate side-chains 741 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 708 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain S residue 51 LYS 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 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 X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain a residue 49 SER 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 17 LEU Chi-restraints excluded: chain c residue 37 VAL 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: 0.6980 chunk 13 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN O 8 ASN S 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086067 restraints weight = 20188.088| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.99 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10980 Z= 0.255 Angle : 0.678 7.427 14940 Z= 0.350 Chirality : 0.046 0.205 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.995 14.853 1440 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.85 % Allowed : 33.66 % Favored : 63.50 % 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: 2.09 (0.23), residues: 1350 helix: 1.39 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.00 (0.47), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 29 PHE 0.018 0.001 PHE b 48 TYR 0.010 0.001 TYR N 9 ARG 0.006 0.000 ARG F 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5156.31 seconds wall clock time: 92 minutes 37.15 seconds (5557.15 seconds total)