Starting phenix.real_space_refine on Wed Sep 25 15:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_6993.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_6993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_6993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_6993.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a7f_6993/09_2024/6a7f_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-5461/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: 2.80, per 1000 atoms: 0.26 Number of scatterers: 10830 At special positions: 0 Unit cell: (76.7, 76.7, 165.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2010 8.00 N 1740 7.00 C 7050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 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: 0.69 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: 2.77 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 21.530 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 1.432 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: 0.2572 time to fit residues: 293.6047 Evaluate side-chains 662 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 fitting. rotamer outliers: 42 poor density : 825 time to evaluate : 1.329 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 9 TYR cc_start: 0.7519 (m-80) cc_final: 0.7270 (m-80) REVERT: A 15 ASP cc_start: 0.8577 (m-30) cc_final: 0.8299 (m-30) REVERT: A 20 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8568 (mm-40) REVERT: A 27 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8732 (tp-100) REVERT: A 42 ILE cc_start: 0.8974 (tp) cc_final: 0.8635 (tt) REVERT: A 47 LYS cc_start: 0.9210 (tttt) cc_final: 0.8735 (tppt) REVERT: A 49 SER cc_start: 0.9228 (t) cc_final: 0.8733 (p) REVERT: B 27 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8325 (tt0) REVERT: B 42 ILE cc_start: 0.9423 (tt) cc_final: 0.9042 (tp) REVERT: B 47 LYS cc_start: 0.8925 (tttt) cc_final: 0.8575 (mmtt) REVERT: B 51 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8719 (mtpt) REVERT: C 20 GLN cc_start: 0.9035 (tp40) cc_final: 0.8412 (mt0) REVERT: C 23 ASP cc_start: 0.8379 (t0) cc_final: 0.8028 (p0) REVERT: C 47 LYS cc_start: 0.9089 (tttt) cc_final: 0.8507 (tptt) REVERT: D 23 ASP cc_start: 0.8391 (m-30) cc_final: 0.8100 (m-30) REVERT: D 42 ILE cc_start: 0.9110 (tp) cc_final: 0.8828 (tt) REVERT: D 46 LYS cc_start: 0.8915 (mttm) cc_final: 0.8640 (mttp) REVERT: D 47 LYS cc_start: 0.9157 (tttt) cc_final: 0.8826 (tptt) REVERT: D 51 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8670 (mttt) REVERT: E 20 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8443 (mm-40) REVERT: E 42 ILE cc_start: 0.9090 (tp) cc_final: 0.8706 (tt) REVERT: F 8 ASN cc_start: 0.7781 (t0) cc_final: 0.7200 (t0) REVERT: F 9 TYR cc_start: 0.6888 (m-80) cc_final: 0.6642 (m-80) REVERT: F 12 GLU cc_start: 0.7787 (mp0) cc_final: 0.7572 (mp0) REVERT: F 27 GLN cc_start: 0.8806 (tp40) cc_final: 0.8603 (tp40) REVERT: F 51 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8568 (mtpp) REVERT: G 9 TYR cc_start: 0.7057 (m-80) cc_final: 0.6736 (m-80) REVERT: G 12 GLU cc_start: 0.7664 (mp0) cc_final: 0.7413 (mp0) REVERT: G 20 GLN cc_start: 0.9137 (mm-40) cc_final: 0.7869 (mm-40) REVERT: G 40 LEU cc_start: 0.9412 (mt) cc_final: 0.9207 (mt) REVERT: G 51 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8674 (mtpp) REVERT: H 9 TYR cc_start: 0.7580 (m-80) cc_final: 0.7051 (m-80) REVERT: H 19 THR cc_start: 0.8551 (p) cc_final: 0.8154 (p) REVERT: H 27 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8824 (tp40) REVERT: H 43 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8223 (ttm170) REVERT: H 51 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8587 (mtpp) REVERT: I 19 THR cc_start: 0.9348 (t) cc_final: 0.8844 (p) REVERT: I 23 ASP cc_start: 0.8337 (t70) cc_final: 0.8111 (p0) REVERT: I 27 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8378 (tp-100) REVERT: I 42 ILE cc_start: 0.9410 (tt) cc_final: 0.9184 (tt) REVERT: I 50 SER cc_start: 0.8227 (t) cc_final: 0.7724 (p) REVERT: I 51 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8557 (mtpp) REVERT: J 23 ASP cc_start: 0.8349 (t70) cc_final: 0.8116 (p0) REVERT: J 26 SER cc_start: 0.8472 (p) cc_final: 0.8177 (p) REVERT: J 27 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8600 (tp-100) REVERT: J 51 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8714 (mtpp) REVERT: K 14 MET cc_start: 0.8668 (mmt) cc_final: 0.8079 (mmt) REVERT: K 18 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7798 (ttmm) REVERT: K 47 LYS cc_start: 0.8290 (tttt) cc_final: 0.8067 (ttmm) REVERT: K 51 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8471 (mmmm) REVERT: L 20 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8774 (mm-40) REVERT: L 47 LYS cc_start: 0.8397 (tttt) cc_final: 0.8041 (ttmm) REVERT: L 51 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8419 (mmmm) REVERT: M 14 MET cc_start: 0.8550 (mmm) cc_final: 0.7819 (mmt) REVERT: M 15 ASP cc_start: 0.8443 (m-30) cc_final: 0.8197 (m-30) REVERT: M 27 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8633 (tp-100) REVERT: M 47 LYS cc_start: 0.8423 (tttt) cc_final: 0.8134 (ttmm) REVERT: M 50 SER cc_start: 0.8595 (t) cc_final: 0.8390 (t) REVERT: M 51 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8308 (mmmm) REVERT: N 8 ASN cc_start: 0.7843 (t0) cc_final: 0.6929 (m-40) REVERT: N 47 LYS cc_start: 0.8466 (tttt) cc_final: 0.7988 (ttmm) REVERT: N 50 SER cc_start: 0.8641 (t) cc_final: 0.8227 (p) REVERT: O 14 MET cc_start: 0.8682 (mmm) cc_final: 0.8175 (mmt) REVERT: O 27 GLN cc_start: 0.8912 (tp40) cc_final: 0.8407 (tp40) REVERT: P 15 ASP cc_start: 0.8121 (m-30) cc_final: 0.7814 (m-30) REVERT: P 27 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8333 (tp40) REVERT: P 47 LYS cc_start: 0.8665 (tttt) cc_final: 0.8408 (ttmm) REVERT: Q 8 ASN cc_start: 0.8045 (t0) cc_final: 0.7511 (t0) REVERT: Q 9 TYR cc_start: 0.7200 (m-80) cc_final: 0.6786 (m-80) REVERT: Q 15 ASP cc_start: 0.8328 (m-30) cc_final: 0.7976 (m-30) REVERT: Q 27 GLN cc_start: 0.8889 (tp-100) cc_final: 0.7930 (tp-100) REVERT: Q 42 ILE cc_start: 0.9366 (tt) cc_final: 0.9095 (tp) REVERT: S 15 ASP cc_start: 0.8236 (m-30) cc_final: 0.7957 (m-30) REVERT: T 15 ASP cc_start: 0.8280 (m-30) cc_final: 0.8032 (m-30) REVERT: T 22 ILE cc_start: 0.8335 (mt) cc_final: 0.8130 (mm) REVERT: T 27 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8479 (tp-100) REVERT: T 47 LYS cc_start: 0.8444 (tttt) cc_final: 0.8208 (ttmm) REVERT: U 15 ASP cc_start: 0.8584 (m-30) cc_final: 0.8309 (m-30) REVERT: U 18 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8043 (ttmm) REVERT: U 40 LEU cc_start: 0.9107 (mp) cc_final: 0.8667 (mt) REVERT: V 8 ASN cc_start: 0.7202 (t0) cc_final: 0.6717 (t0) REVERT: V 47 LYS cc_start: 0.8771 (tttm) cc_final: 0.8453 (ttmm) REVERT: V 51 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8276 (mmtm) REVERT: W 9 TYR cc_start: 0.7680 (m-80) cc_final: 0.7281 (m-80) REVERT: W 27 GLN cc_start: 0.8975 (tp40) cc_final: 0.8729 (tp40) REVERT: W 43 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8155 (ttp80) REVERT: X 51 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8297 (mttp) REVERT: Y 8 ASN cc_start: 0.6977 (t0) cc_final: 0.6036 (t0) REVERT: Y 9 TYR cc_start: 0.7468 (m-80) cc_final: 0.7251 (m-80) REVERT: Y 18 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8227 (ttmm) REVERT: Y 43 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7759 (ttp80) REVERT: Y 47 LYS cc_start: 0.8724 (tttm) cc_final: 0.8434 (ttmm) REVERT: Z 18 LYS cc_start: 0.8320 (tttt) cc_final: 0.7953 (mptt) REVERT: Z 23 ASP cc_start: 0.8299 (m-30) cc_final: 0.8050 (t0) REVERT: Z 46 LYS cc_start: 0.8108 (mttt) cc_final: 0.7714 (mtmt) REVERT: Z 49 SER cc_start: 0.8793 (m) cc_final: 0.8450 (t) REVERT: a 9 TYR cc_start: 0.8343 (m-80) cc_final: 0.7474 (p90) REVERT: a 18 LYS cc_start: 0.8456 (tttt) cc_final: 0.7889 (mptt) REVERT: b 15 ASP cc_start: 0.8751 (m-30) cc_final: 0.8449 (m-30) REVERT: b 18 LYS cc_start: 0.8332 (tttt) cc_final: 0.7966 (mptt) REVERT: b 24 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8710 (tp) REVERT: c 14 MET cc_start: 0.8227 (mmm) cc_final: 0.8003 (mmm) REVERT: c 15 ASP cc_start: 0.8559 (m-30) cc_final: 0.8265 (m-30) REVERT: c 18 LYS cc_start: 0.8419 (tttt) cc_final: 0.7991 (mptt) REVERT: c 25 ILE cc_start: 0.8803 (mt) cc_final: 0.8588 (mt) REVERT: c 43 ARG cc_start: 0.8728 (ttt-90) cc_final: 0.8472 (ttp80) REVERT: d 15 ASP cc_start: 0.8526 (m-30) cc_final: 0.8160 (m-30) REVERT: d 18 LYS cc_start: 0.8343 (tttt) cc_final: 0.7731 (mmtt) outliers start: 42 outliers final: 28 residues processed: 829 average time/residue: 0.2225 time to fit residues: 254.3973 Evaluate side-chains 757 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 728 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN D 27 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10980 Z= 0.223 Angle : 0.582 6.112 14940 Z= 0.300 Chirality : 0.042 0.147 1980 Planarity : 0.004 0.030 1740 Dihedral : 4.063 11.473 1440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.90 % Allowed : 22.76 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1350 helix: 0.90 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.64 (0.44), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 29 PHE 0.012 0.001 PHE Q 48 TYR 0.008 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 820 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 772 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8407 (mm-40) REVERT: A 23 ASP cc_start: 0.7956 (p0) cc_final: 0.7752 (p0) REVERT: A 27 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8644 (tp-100) REVERT: A 42 ILE cc_start: 0.8910 (tp) cc_final: 0.8533 (tt) REVERT: A 47 LYS cc_start: 0.9207 (tttt) cc_final: 0.8802 (mmtt) REVERT: A 49 SER cc_start: 0.9058 (t) cc_final: 0.8730 (m) REVERT: A 51 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8681 (mtpt) REVERT: B 20 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8344 (mm-40) REVERT: B 23 ASP cc_start: 0.7807 (p0) cc_final: 0.7591 (p0) REVERT: B 42 ILE cc_start: 0.9374 (tt) cc_final: 0.9035 (tp) REVERT: B 47 LYS cc_start: 0.8944 (tttt) cc_final: 0.8520 (mmtt) REVERT: B 51 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8742 (mttt) REVERT: C 20 GLN cc_start: 0.9029 (tp40) cc_final: 0.8404 (mt0) REVERT: C 23 ASP cc_start: 0.8379 (t0) cc_final: 0.8072 (p0) REVERT: C 47 LYS cc_start: 0.9059 (tttt) cc_final: 0.8464 (tptt) REVERT: D 23 ASP cc_start: 0.8399 (m-30) cc_final: 0.8083 (m-30) REVERT: D 47 LYS cc_start: 0.9066 (tttt) cc_final: 0.8791 (tptt) REVERT: D 51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8650 (mttt) REVERT: E 20 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8532 (mm-40) REVERT: E 42 ILE cc_start: 0.8925 (tp) cc_final: 0.8619 (tt) REVERT: F 8 ASN cc_start: 0.7901 (t0) cc_final: 0.7239 (t0) REVERT: F 9 TYR cc_start: 0.7117 (m-80) cc_final: 0.6842 (m-80) REVERT: F 12 GLU cc_start: 0.7940 (mp0) cc_final: 0.7657 (mp0) REVERT: F 27 GLN cc_start: 0.8666 (tp40) cc_final: 0.8135 (tp40) REVERT: F 51 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8633 (mtpp) REVERT: G 12 GLU cc_start: 0.7858 (mp0) cc_final: 0.7528 (mp0) REVERT: G 51 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8658 (mtpp) REVERT: H 9 TYR cc_start: 0.7606 (m-80) cc_final: 0.7076 (m-80) REVERT: H 43 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8165 (ttm170) REVERT: H 51 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8590 (mtpp) REVERT: I 19 THR cc_start: 0.9248 (t) cc_final: 0.8820 (p) REVERT: I 27 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8404 (tp-100) REVERT: I 42 ILE cc_start: 0.9379 (tt) cc_final: 0.9156 (tt) REVERT: I 50 SER cc_start: 0.8488 (t) cc_final: 0.8014 (p) REVERT: I 51 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8521 (mtpp) REVERT: J 27 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8582 (tp-100) REVERT: J 51 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8746 (mtpp) REVERT: K 14 MET cc_start: 0.8628 (mmt) cc_final: 0.8055 (mmt) REVERT: K 18 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7890 (ttmm) REVERT: K 47 LYS cc_start: 0.8312 (tttt) cc_final: 0.7783 (ttmm) REVERT: K 50 SER cc_start: 0.8278 (t) cc_final: 0.7597 (p) REVERT: K 51 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8590 (mmmm) REVERT: L 14 MET cc_start: 0.8797 (mmt) cc_final: 0.8416 (mmt) REVERT: L 20 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8755 (mm-40) REVERT: L 47 LYS cc_start: 0.8409 (tttt) cc_final: 0.8067 (ttmm) REVERT: L 51 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8511 (mmmm) REVERT: M 14 MET cc_start: 0.8352 (mmm) cc_final: 0.8006 (mmt) REVERT: M 15 ASP cc_start: 0.8391 (m-30) cc_final: 0.8179 (m-30) REVERT: M 27 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8760 (tp40) REVERT: M 47 LYS cc_start: 0.8449 (tttt) cc_final: 0.8151 (ttmm) REVERT: M 51 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8396 (mmmm) REVERT: N 8 ASN cc_start: 0.7800 (t0) cc_final: 0.6842 (m-40) REVERT: N 12 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8040 (mp0) REVERT: N 47 LYS cc_start: 0.8427 (tttt) cc_final: 0.7916 (ttmm) REVERT: N 50 SER cc_start: 0.8652 (t) cc_final: 0.8209 (p) REVERT: O 14 MET cc_start: 0.8719 (mmm) cc_final: 0.8143 (mmt) REVERT: O 27 GLN cc_start: 0.8936 (tp40) cc_final: 0.8439 (tp40) REVERT: P 15 ASP cc_start: 0.8103 (m-30) cc_final: 0.7817 (m-30) REVERT: P 27 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8441 (tp40) REVERT: Q 8 ASN cc_start: 0.8094 (t0) cc_final: 0.7752 (m110) REVERT: Q 15 ASP cc_start: 0.8357 (m-30) cc_final: 0.8041 (m-30) REVERT: Q 27 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8450 (tp40) REVERT: Q 42 ILE cc_start: 0.9334 (tt) cc_final: 0.9036 (tp) REVERT: S 15 ASP cc_start: 0.8160 (m-30) cc_final: 0.7828 (m-30) REVERT: S 40 LEU cc_start: 0.9041 (mp) cc_final: 0.8835 (mt) REVERT: T 22 ILE cc_start: 0.8366 (mt) cc_final: 0.8164 (mm) REVERT: T 27 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8417 (tp-100) REVERT: T 47 LYS cc_start: 0.8574 (tttt) cc_final: 0.8329 (ttmm) REVERT: U 8 ASN cc_start: 0.7270 (t0) cc_final: 0.6566 (t0) REVERT: U 15 ASP cc_start: 0.8565 (m-30) cc_final: 0.8302 (m-30) REVERT: U 18 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8075 (ttmm) REVERT: U 40 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8680 (mt) REVERT: U 51 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7558 (mttm) REVERT: V 8 ASN cc_start: 0.7100 (t0) cc_final: 0.6107 (t0) REVERT: V 47 LYS cc_start: 0.8826 (tttm) cc_final: 0.8616 (ttmm) REVERT: W 43 ARG cc_start: 0.8429 (ttm170) cc_final: 0.8143 (ttp80) REVERT: X 14 MET cc_start: 0.8723 (tpp) cc_final: 0.8519 (mmt) REVERT: X 51 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8393 (mttp) REVERT: Y 43 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7772 (ttp80) REVERT: Y 47 LYS cc_start: 0.8764 (tttm) cc_final: 0.8540 (ttmm) REVERT: Z 18 LYS cc_start: 0.8287 (tttt) cc_final: 0.7936 (mptt) REVERT: Z 23 ASP cc_start: 0.8304 (m-30) cc_final: 0.8053 (t0) REVERT: Z 46 LYS cc_start: 0.7838 (mttt) cc_final: 0.7489 (mtmt) REVERT: Z 49 SER cc_start: 0.8964 (m) cc_final: 0.8578 (t) REVERT: a 18 LYS cc_start: 0.8337 (tttt) cc_final: 0.7830 (mptt) REVERT: b 15 ASP cc_start: 0.8665 (m-30) cc_final: 0.8378 (m-30) REVERT: b 18 LYS cc_start: 0.8338 (tttt) cc_final: 0.7873 (mptt) REVERT: c 15 ASP cc_start: 0.8518 (m-30) cc_final: 0.8248 (m-30) REVERT: c 18 LYS cc_start: 0.8465 (tttt) cc_final: 0.8026 (mptt) REVERT: d 18 LYS cc_start: 0.8312 (tttt) cc_final: 0.7816 (mptt) outliers start: 48 outliers final: 38 residues processed: 777 average time/residue: 0.2160 time to fit residues: 232.8728 Evaluate side-chains 764 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 725 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 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 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 N residue 34 THR Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 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 107 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4796 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= 0.208 Angle : 0.576 7.417 14940 Z= 0.295 Chirality : 0.042 0.143 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.907 11.612 1440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.72 % Allowed : 24.72 % Favored : 70.57 % 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: 1.75 (0.23), residues: 1350 helix: 1.18 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.74 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 29 PHE 0.012 0.001 PHE Q 48 TYR 0.006 0.001 TYR L 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 822 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 764 time to evaluate : 1.372 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 15 ASP cc_start: 0.8654 (m-30) cc_final: 0.8374 (m-30) REVERT: A 20 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8386 (mm-40) REVERT: A 27 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8435 (mt0) REVERT: A 42 ILE cc_start: 0.8882 (tp) cc_final: 0.8467 (tt) REVERT: A 47 LYS cc_start: 0.9181 (tttt) cc_final: 0.8687 (tppt) REVERT: A 49 SER cc_start: 0.9053 (t) cc_final: 0.8716 (m) REVERT: A 51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8679 (mtpt) REVERT: B 47 LYS cc_start: 0.8923 (tttt) cc_final: 0.8503 (mmtt) REVERT: B 51 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8715 (mttt) REVERT: C 9 TYR cc_start: 0.7572 (m-80) cc_final: 0.7262 (m-80) REVERT: C 20 GLN cc_start: 0.9006 (tp40) cc_final: 0.8368 (mt0) REVERT: C 23 ASP cc_start: 0.8554 (t0) cc_final: 0.8115 (p0) REVERT: C 45 PHE cc_start: 0.9286 (t80) cc_final: 0.9034 (t80) REVERT: C 47 LYS cc_start: 0.9057 (tttt) cc_final: 0.8473 (tptt) REVERT: D 23 ASP cc_start: 0.8393 (m-30) cc_final: 0.8090 (m-30) REVERT: D 47 LYS cc_start: 0.9028 (tttt) cc_final: 0.8733 (tptt) REVERT: D 51 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8764 (mttt) REVERT: E 42 ILE cc_start: 0.8862 (tp) cc_final: 0.8579 (tt) REVERT: F 8 ASN cc_start: 0.7965 (t0) cc_final: 0.7396 (t0) REVERT: F 9 TYR cc_start: 0.7137 (m-80) cc_final: 0.6874 (m-80) REVERT: F 12 GLU cc_start: 0.8065 (mp0) cc_final: 0.7777 (mp0) REVERT: F 51 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8607 (mtpp) REVERT: G 12 GLU cc_start: 0.7865 (mp0) cc_final: 0.7488 (mp0) REVERT: G 27 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8478 (mm-40) REVERT: G 49 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8328 (p) REVERT: G 51 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8658 (mtpp) REVERT: H 9 TYR cc_start: 0.7570 (m-80) cc_final: 0.7043 (m-80) REVERT: H 43 ARG cc_start: 0.8527 (mtp180) cc_final: 0.8145 (ttm170) REVERT: H 51 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8590 (mtpp) REVERT: I 27 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8372 (tp-100) REVERT: I 42 ILE cc_start: 0.9395 (tt) cc_final: 0.9155 (tt) REVERT: I 50 SER cc_start: 0.8538 (t) cc_final: 0.8043 (p) REVERT: I 51 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8602 (mtpp) REVERT: J 23 ASP cc_start: 0.7795 (p0) cc_final: 0.7409 (p0) REVERT: J 27 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8521 (tp-100) REVERT: J 51 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8722 (mtpp) REVERT: K 12 GLU cc_start: 0.7761 (mp0) cc_final: 0.7444 (mp0) REVERT: K 14 MET cc_start: 0.8656 (mmt) cc_final: 0.8092 (mmt) REVERT: K 18 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7832 (ttmm) REVERT: K 47 LYS cc_start: 0.8291 (tttt) cc_final: 0.7757 (ttmm) REVERT: K 50 SER cc_start: 0.8521 (t) cc_final: 0.7885 (p) REVERT: K 51 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8606 (mmmm) REVERT: L 14 MET cc_start: 0.8736 (mmt) cc_final: 0.8367 (mmt) REVERT: L 20 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8802 (mm-40) REVERT: L 47 LYS cc_start: 0.8449 (tttt) cc_final: 0.7844 (ttmm) REVERT: L 50 SER cc_start: 0.8641 (t) cc_final: 0.8174 (p) REVERT: L 51 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8518 (mmmm) REVERT: M 14 MET cc_start: 0.8410 (mmm) cc_final: 0.8124 (mmt) REVERT: M 15 ASP cc_start: 0.8460 (m-30) cc_final: 0.8217 (m-30) REVERT: M 20 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8967 (mm-40) REVERT: M 27 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8801 (tp40) REVERT: M 47 LYS cc_start: 0.8449 (tttt) cc_final: 0.8150 (ttmm) REVERT: N 8 ASN cc_start: 0.7878 (t0) cc_final: 0.6837 (m-40) REVERT: N 14 MET cc_start: 0.8793 (mmt) cc_final: 0.8592 (mtp) REVERT: N 18 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7885 (ttmt) REVERT: N 47 LYS cc_start: 0.8394 (tttt) cc_final: 0.7870 (ttmm) REVERT: N 50 SER cc_start: 0.8631 (t) cc_final: 0.8181 (p) REVERT: N 51 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8367 (mtpp) REVERT: O 14 MET cc_start: 0.8700 (mmm) cc_final: 0.8139 (mmt) REVERT: O 27 GLN cc_start: 0.8949 (tp40) cc_final: 0.8459 (tp40) REVERT: P 15 ASP cc_start: 0.8097 (m-30) cc_final: 0.7798 (m-30) REVERT: P 27 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8366 (tp40) REVERT: Q 8 ASN cc_start: 0.8047 (t0) cc_final: 0.7756 (m110) REVERT: Q 15 ASP cc_start: 0.8294 (m-30) cc_final: 0.7928 (m-30) REVERT: Q 27 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8214 (tp40) REVERT: Q 42 ILE cc_start: 0.9366 (tt) cc_final: 0.9148 (tp) REVERT: R 9 TYR cc_start: 0.7631 (m-80) cc_final: 0.7307 (m-80) REVERT: S 15 ASP cc_start: 0.8204 (m-30) cc_final: 0.7849 (m-30) REVERT: T 27 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8444 (tp-100) REVERT: T 47 LYS cc_start: 0.8598 (tttt) cc_final: 0.8377 (ttmm) REVERT: U 8 ASN cc_start: 0.6801 (t0) cc_final: 0.6123 (t0) REVERT: U 15 ASP cc_start: 0.8616 (m-30) cc_final: 0.8281 (m-30) REVERT: U 40 LEU cc_start: 0.9139 (mp) cc_final: 0.8706 (mt) REVERT: U 51 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7669 (mttp) REVERT: V 8 ASN cc_start: 0.6717 (t0) cc_final: 0.5868 (t0) REVERT: V 32 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8323 (p) REVERT: V 47 LYS cc_start: 0.8825 (tttm) cc_final: 0.8590 (ttmm) REVERT: W 15 ASP cc_start: 0.8461 (m-30) cc_final: 0.8258 (m-30) REVERT: W 43 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8149 (ttp80) REVERT: X 32 VAL cc_start: 0.8781 (t) cc_final: 0.8526 (p) REVERT: X 51 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8453 (mttp) REVERT: Y 27 GLN cc_start: 0.9136 (tp40) cc_final: 0.8894 (tp40) REVERT: Y 47 LYS cc_start: 0.8757 (tttm) cc_final: 0.8534 (ttmm) REVERT: Z 18 LYS cc_start: 0.8240 (tttt) cc_final: 0.7869 (mptt) REVERT: Z 46 LYS cc_start: 0.7876 (mttt) cc_final: 0.7559 (mtmt) REVERT: Z 49 SER cc_start: 0.9038 (m) cc_final: 0.8684 (t) REVERT: a 9 TYR cc_start: 0.8360 (m-80) cc_final: 0.7536 (p90) REVERT: a 18 LYS cc_start: 0.8282 (tttt) cc_final: 0.7816 (mptt) REVERT: b 15 ASP cc_start: 0.8649 (m-30) cc_final: 0.8424 (m-30) REVERT: b 18 LYS cc_start: 0.8355 (tttt) cc_final: 0.7853 (mptt) REVERT: c 11 THR cc_start: 0.8939 (p) cc_final: 0.8472 (p) REVERT: c 15 ASP cc_start: 0.8542 (m-30) cc_final: 0.8296 (m-30) REVERT: c 18 LYS cc_start: 0.8549 (tttt) cc_final: 0.8058 (mptt) REVERT: d 15 ASP cc_start: 0.8727 (t0) cc_final: 0.8393 (m-30) REVERT: d 18 LYS cc_start: 0.8310 (tttt) cc_final: 0.7708 (mmtt) outliers start: 58 outliers final: 43 residues processed: 773 average time/residue: 0.2139 time to fit residues: 231.0108 Evaluate side-chains 778 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 733 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 G residue 49 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 51 LYS 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 T residue 51 LYS 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 32 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 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 96 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5076 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= 0.220 Angle : 0.583 8.118 14940 Z= 0.297 Chirality : 0.043 0.162 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.877 11.087 1440 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.15 % Allowed : 27.24 % Favored : 68.62 % 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: 1.95 (0.23), residues: 1350 helix: 1.31 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.69 (0.41), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 29 PHE 0.019 0.001 PHE U 48 TYR 0.007 0.001 TYR L 9 ARG 0.004 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 809 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 758 time to evaluate : 1.253 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 27 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8419 (mt0) REVERT: A 42 ILE cc_start: 0.9018 (tp) cc_final: 0.8592 (tt) REVERT: A 47 LYS cc_start: 0.9175 (tttt) cc_final: 0.8781 (mmtt) REVERT: A 49 SER cc_start: 0.8922 (t) cc_final: 0.8608 (m) REVERT: A 51 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8684 (mtpt) REVERT: B 45 PHE cc_start: 0.9312 (t80) cc_final: 0.9034 (t80) REVERT: B 47 LYS cc_start: 0.8923 (tttt) cc_final: 0.8518 (mmtt) REVERT: B 51 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8684 (mtpt) REVERT: C 9 TYR cc_start: 0.7561 (m-80) cc_final: 0.7178 (m-80) REVERT: C 20 GLN cc_start: 0.9012 (tp40) cc_final: 0.8359 (mt0) REVERT: C 23 ASP cc_start: 0.8548 (t0) cc_final: 0.8162 (p0) REVERT: C 43 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8226 (ttp80) REVERT: C 45 PHE cc_start: 0.9263 (t80) cc_final: 0.9029 (t80) REVERT: C 47 LYS cc_start: 0.9048 (tttt) cc_final: 0.8462 (tptt) REVERT: D 14 MET cc_start: 0.9143 (tpp) cc_final: 0.8927 (mmt) REVERT: D 23 ASP cc_start: 0.8442 (m-30) cc_final: 0.8146 (m-30) REVERT: D 27 GLN cc_start: 0.9084 (tp40) cc_final: 0.8861 (tp-100) REVERT: D 47 LYS cc_start: 0.8971 (tttt) cc_final: 0.8696 (tptt) REVERT: D 51 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8734 (mttt) REVERT: E 8 ASN cc_start: 0.8449 (t0) cc_final: 0.8010 (t0) REVERT: E 19 THR cc_start: 0.8712 (p) cc_final: 0.8035 (p) REVERT: E 42 ILE cc_start: 0.8798 (tp) cc_final: 0.8575 (tt) REVERT: E 51 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8643 (mtpt) REVERT: F 8 ASN cc_start: 0.7978 (t0) cc_final: 0.7437 (t0) REVERT: F 9 TYR cc_start: 0.7230 (m-80) cc_final: 0.6919 (m-80) REVERT: F 12 GLU cc_start: 0.8106 (mp0) cc_final: 0.7795 (mp0) REVERT: F 20 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8201 (mm-40) REVERT: F 42 ILE cc_start: 0.9256 (tt) cc_final: 0.8950 (tp) REVERT: G 12 GLU cc_start: 0.7939 (mp0) cc_final: 0.7700 (mp0) REVERT: G 27 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8473 (mm-40) REVERT: G 49 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8240 (p) REVERT: G 51 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8643 (mtpp) REVERT: H 9 TYR cc_start: 0.7308 (m-80) cc_final: 0.6889 (m-80) REVERT: H 43 ARG cc_start: 0.8534 (mtp180) cc_final: 0.8092 (ttm170) REVERT: H 51 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8572 (mtpp) REVERT: I 20 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8412 (mm-40) REVERT: I 27 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8413 (tp-100) REVERT: I 42 ILE cc_start: 0.9353 (tt) cc_final: 0.9098 (tt) REVERT: I 50 SER cc_start: 0.8617 (t) cc_final: 0.8182 (p) REVERT: I 51 LYS cc_start: 0.9037 (mmtm) cc_final: 0.8651 (mtpp) REVERT: J 12 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8266 (tm-30) REVERT: J 23 ASP cc_start: 0.7806 (p0) cc_final: 0.7395 (p0) REVERT: J 27 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8660 (tp-100) REVERT: K 12 GLU cc_start: 0.7708 (mp0) cc_final: 0.7390 (mp0) REVERT: K 14 MET cc_start: 0.8665 (mmt) cc_final: 0.8094 (mmt) REVERT: K 18 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7836 (ttmm) REVERT: K 47 LYS cc_start: 0.8286 (tttt) cc_final: 0.7764 (ttmm) REVERT: K 50 SER cc_start: 0.8535 (t) cc_final: 0.7898 (p) REVERT: K 51 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8601 (mmmm) REVERT: L 14 MET cc_start: 0.8734 (mmt) cc_final: 0.8399 (mmt) REVERT: L 20 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8832 (mm-40) REVERT: L 47 LYS cc_start: 0.8440 (tttt) cc_final: 0.7842 (ttmm) REVERT: L 50 SER cc_start: 0.8652 (t) cc_final: 0.8180 (p) REVERT: L 51 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8583 (mmmm) REVERT: M 14 MET cc_start: 0.8448 (mmm) cc_final: 0.8128 (mmt) REVERT: M 15 ASP cc_start: 0.8414 (m-30) cc_final: 0.8203 (m-30) REVERT: M 27 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8834 (tp40) REVERT: N 8 ASN cc_start: 0.7290 (t0) cc_final: 0.6870 (m-40) REVERT: N 14 MET cc_start: 0.8704 (mmt) cc_final: 0.8484 (mtp) REVERT: N 47 LYS cc_start: 0.8371 (tttt) cc_final: 0.7860 (ttmm) REVERT: N 50 SER cc_start: 0.8630 (t) cc_final: 0.8183 (p) REVERT: N 51 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8341 (mtpp) REVERT: O 8 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7144 (t0) REVERT: O 9 TYR cc_start: 0.7332 (m-80) cc_final: 0.7112 (m-80) REVERT: O 14 MET cc_start: 0.8681 (mmm) cc_final: 0.8094 (mmt) REVERT: O 27 GLN cc_start: 0.8954 (tp40) cc_final: 0.8438 (tp40) REVERT: P 15 ASP cc_start: 0.8131 (m-30) cc_final: 0.7893 (m-30) REVERT: P 27 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8321 (tp40) REVERT: Q 8 ASN cc_start: 0.7998 (t0) cc_final: 0.7720 (m110) REVERT: Q 15 ASP cc_start: 0.8343 (m-30) cc_final: 0.8047 (m-30) REVERT: Q 27 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8567 (tp40) REVERT: Q 42 ILE cc_start: 0.9342 (tt) cc_final: 0.9106 (tp) REVERT: S 15 ASP cc_start: 0.8203 (m-30) cc_final: 0.7913 (m-30) REVERT: S 51 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: T 27 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8332 (tp-100) REVERT: T 47 LYS cc_start: 0.8688 (tttt) cc_final: 0.8396 (ttmm) REVERT: T 48 PHE cc_start: 0.9168 (m-80) cc_final: 0.8840 (m-80) REVERT: U 8 ASN cc_start: 0.6510 (t0) cc_final: 0.5890 (t0) REVERT: U 15 ASP cc_start: 0.8605 (m-30) cc_final: 0.8287 (m-30) REVERT: U 40 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8778 (mt) REVERT: U 51 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7666 (mttm) REVERT: V 14 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: V 47 LYS cc_start: 0.8775 (tttm) cc_final: 0.8458 (ttmm) REVERT: W 9 TYR cc_start: 0.7368 (m-80) cc_final: 0.7063 (m-80) REVERT: W 43 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8163 (ttp80) REVERT: W 51 LYS cc_start: 0.8641 (mttp) cc_final: 0.8411 (mttp) REVERT: Y 18 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8048 (tttp) REVERT: Y 27 GLN cc_start: 0.9177 (tp40) cc_final: 0.8925 (tp40) REVERT: Z 18 LYS cc_start: 0.8232 (tttt) cc_final: 0.7856 (mptt) REVERT: Z 28 THR cc_start: 0.9088 (m) cc_final: 0.8814 (p) REVERT: Z 46 LYS cc_start: 0.7963 (mttt) cc_final: 0.7731 (mtmt) REVERT: Z 49 SER cc_start: 0.8971 (m) cc_final: 0.8680 (t) REVERT: a 18 LYS cc_start: 0.8243 (tttt) cc_final: 0.7801 (mptt) REVERT: b 15 ASP cc_start: 0.8646 (m-30) cc_final: 0.8439 (m-30) REVERT: b 18 LYS cc_start: 0.8349 (tttt) cc_final: 0.7681 (mptt) REVERT: c 11 THR cc_start: 0.8927 (p) cc_final: 0.8461 (p) REVERT: c 15 ASP cc_start: 0.8490 (m-30) cc_final: 0.8239 (m-30) REVERT: c 18 LYS cc_start: 0.8481 (tttt) cc_final: 0.7908 (mptt) REVERT: c 48 PHE cc_start: 0.8842 (m-80) cc_final: 0.8539 (m-80) REVERT: d 18 LYS cc_start: 0.8268 (tttt) cc_final: 0.7702 (mptt) REVERT: d 49 SER cc_start: 0.9323 (m) cc_final: 0.8699 (t) outliers start: 51 outliers final: 39 residues processed: 767 average time/residue: 0.2055 time to fit residues: 220.7824 Evaluate side-chains 773 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 729 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain 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 G residue 49 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain V residue 14 MET Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5238 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= 0.276 Angle : 0.618 8.028 14940 Z= 0.316 Chirality : 0.044 0.190 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.898 11.529 1440 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.39 % Allowed : 28.46 % 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 : 3.53 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 29 PHE 0.024 0.002 PHE U 48 TYR 0.008 0.001 TYR L 9 ARG 0.004 0.000 ARG c 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 776 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 722 time to evaluate : 1.332 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: 0.9002 (tp-100) cc_final: 0.8437 (mt0) REVERT: A 42 ILE cc_start: 0.9014 (tp) cc_final: 0.8605 (tt) REVERT: A 47 LYS cc_start: 0.9109 (tttt) cc_final: 0.8707 (mmtt) REVERT: A 49 SER cc_start: 0.8898 (t) cc_final: 0.8589 (m) REVERT: A 51 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8713 (mtpt) REVERT: B 42 ILE cc_start: 0.9321 (tt) cc_final: 0.9011 (tp) REVERT: B 45 PHE cc_start: 0.9248 (t80) cc_final: 0.9001 (t80) REVERT: B 47 LYS cc_start: 0.8929 (tttt) cc_final: 0.8507 (mmtt) REVERT: B 51 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8769 (mtpt) REVERT: C 9 TYR cc_start: 0.7593 (m-80) cc_final: 0.7072 (m-80) REVERT: C 20 GLN cc_start: 0.9065 (tp40) cc_final: 0.8391 (mt0) REVERT: C 23 ASP cc_start: 0.8555 (t0) cc_final: 0.8170 (p0) REVERT: C 43 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8245 (ttp80) REVERT: C 47 LYS cc_start: 0.9043 (tttt) cc_final: 0.8442 (tptt) REVERT: D 12 GLU cc_start: 0.7777 (mp0) cc_final: 0.7495 (mp0) REVERT: D 23 ASP cc_start: 0.8433 (m-30) cc_final: 0.8160 (m-30) REVERT: D 27 GLN cc_start: 0.9112 (tp40) cc_final: 0.8872 (tp-100) REVERT: D 37 VAL cc_start: 0.9051 (p) cc_final: 0.8759 (m) REVERT: D 47 LYS cc_start: 0.8970 (tttt) cc_final: 0.8643 (tptt) REVERT: D 51 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8743 (mttt) REVERT: E 8 ASN cc_start: 0.8651 (t0) cc_final: 0.8153 (t0) REVERT: E 51 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8584 (mtpt) REVERT: F 8 ASN cc_start: 0.7896 (t0) cc_final: 0.7385 (t0) REVERT: F 9 TYR cc_start: 0.7198 (m-80) cc_final: 0.6886 (m-80) REVERT: F 12 GLU cc_start: 0.8141 (mp0) cc_final: 0.7799 (mp0) REVERT: F 51 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8622 (mtpp) REVERT: G 12 GLU cc_start: 0.7983 (mp0) cc_final: 0.7713 (mp0) REVERT: G 27 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8458 (mm-40) REVERT: G 49 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8243 (p) REVERT: H 9 TYR cc_start: 0.7395 (m-80) cc_final: 0.7048 (m-80) REVERT: H 43 ARG cc_start: 0.8522 (mtp180) cc_final: 0.8090 (ttm170) REVERT: H 51 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8610 (mtpp) REVERT: I 27 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8430 (tp-100) REVERT: I 42 ILE cc_start: 0.9350 (tt) cc_final: 0.9091 (tt) REVERT: I 50 SER cc_start: 0.8664 (t) cc_final: 0.8229 (p) REVERT: I 51 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8688 (mtpp) REVERT: J 12 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8307 (tm-30) REVERT: J 23 ASP cc_start: 0.7826 (p0) cc_final: 0.7508 (p0) REVERT: J 27 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8633 (tp-100) REVERT: K 12 GLU cc_start: 0.7783 (mp0) cc_final: 0.7399 (mp0) REVERT: K 14 MET cc_start: 0.8650 (mmt) cc_final: 0.8114 (mmt) REVERT: K 18 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7846 (ttmm) REVERT: K 47 LYS cc_start: 0.8288 (tttt) cc_final: 0.7779 (ttmm) REVERT: K 50 SER cc_start: 0.8357 (t) cc_final: 0.7736 (p) REVERT: K 51 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8541 (mmmt) REVERT: L 14 MET cc_start: 0.8768 (mmt) cc_final: 0.8318 (mmt) REVERT: L 47 LYS cc_start: 0.8432 (tttt) cc_final: 0.7833 (ttmm) REVERT: L 50 SER cc_start: 0.8673 (t) cc_final: 0.8204 (p) REVERT: L 51 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8589 (mmmm) REVERT: M 15 ASP cc_start: 0.8557 (m-30) cc_final: 0.8303 (m-30) REVERT: M 27 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8627 (tp-100) REVERT: N 8 ASN cc_start: 0.7353 (t0) cc_final: 0.7032 (m110) REVERT: N 14 MET cc_start: 0.8732 (mmt) cc_final: 0.8261 (mmt) REVERT: N 18 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7624 (ttmm) REVERT: N 47 LYS cc_start: 0.8359 (tttt) cc_final: 0.8033 (ttmm) REVERT: O 8 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.6886 (m-40) REVERT: O 14 MET cc_start: 0.8624 (mmm) cc_final: 0.8354 (mmt) REVERT: P 15 ASP cc_start: 0.8155 (m-30) cc_final: 0.7918 (m-30) REVERT: P 27 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8432 (tp40) REVERT: Q 8 ASN cc_start: 0.7987 (t0) cc_final: 0.7718 (m110) REVERT: Q 15 ASP cc_start: 0.8323 (m-30) cc_final: 0.8012 (m-30) REVERT: Q 27 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8514 (tp40) REVERT: Q 42 ILE cc_start: 0.9347 (tt) cc_final: 0.9103 (tp) REVERT: S 15 ASP cc_start: 0.8209 (m-30) cc_final: 0.7949 (m-30) REVERT: T 27 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8502 (tp-100) REVERT: U 8 ASN cc_start: 0.6326 (t0) cc_final: 0.5519 (t0) REVERT: U 15 ASP cc_start: 0.8544 (m-30) cc_final: 0.8120 (m-30) REVERT: U 40 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8756 (mt) REVERT: V 14 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8250 (ttm) REVERT: W 9 TYR cc_start: 0.7350 (m-80) cc_final: 0.6853 (m-80) REVERT: W 15 ASP cc_start: 0.8640 (m-30) cc_final: 0.8384 (m-30) REVERT: W 43 ARG cc_start: 0.8518 (ttm170) cc_final: 0.8188 (ttp80) REVERT: W 49 SER cc_start: 0.8918 (m) cc_final: 0.8615 (p) REVERT: W 51 LYS cc_start: 0.8646 (mttp) cc_final: 0.8412 (mttp) REVERT: Y 14 MET cc_start: 0.8433 (mtt) cc_final: 0.8038 (mtm) REVERT: Y 27 GLN cc_start: 0.9185 (tp40) cc_final: 0.8965 (tp40) REVERT: Z 18 LYS cc_start: 0.8270 (tttt) cc_final: 0.7896 (mptt) REVERT: Z 33 THR cc_start: 0.8280 (t) cc_final: 0.8074 (p) REVERT: Z 46 LYS cc_start: 0.7953 (mttt) cc_final: 0.7731 (mtmt) REVERT: a 18 LYS cc_start: 0.8277 (tttt) cc_final: 0.7845 (mptt) REVERT: b 18 LYS cc_start: 0.8368 (tttt) cc_final: 0.7672 (mptt) REVERT: c 11 THR cc_start: 0.8817 (p) cc_final: 0.8382 (p) REVERT: c 15 ASP cc_start: 0.8472 (m-30) cc_final: 0.8235 (m-30) REVERT: c 18 LYS cc_start: 0.8611 (tttt) cc_final: 0.7967 (mptt) REVERT: c 48 PHE cc_start: 0.8784 (m-80) cc_final: 0.8547 (m-80) REVERT: d 18 LYS cc_start: 0.8193 (tttt) cc_final: 0.7600 (mptt) outliers start: 54 outliers final: 41 residues processed: 729 average time/residue: 0.2106 time to fit residues: 213.8437 Evaluate side-chains 751 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 706 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 42 ILE 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 40 LEU Chi-restraints excluded: chain V residue 14 MET Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 9 TYR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain c residue 37 VAL Chi-restraints excluded: chain d residue 9 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10980 Z= 0.235 Angle : 0.624 7.401 14940 Z= 0.321 Chirality : 0.044 0.195 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.944 11.688 1440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 4.07 % Allowed : 29.51 % Favored : 66.42 % 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: 1.41 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.35 (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 U 48 TYR 0.008 0.001 TYR L 9 ARG 0.003 0.000 ARG c 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 790 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 740 time to evaluate : 1.354 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 27 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8412 (mt0) REVERT: A 42 ILE cc_start: 0.9084 (tp) cc_final: 0.8738 (tt) REVERT: A 47 LYS cc_start: 0.9104 (tttt) cc_final: 0.8626 (tppt) REVERT: A 49 SER cc_start: 0.8886 (t) cc_final: 0.8576 (m) REVERT: A 51 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8702 (mtpt) REVERT: B 42 ILE cc_start: 0.9303 (tt) cc_final: 0.9000 (tp) REVERT: B 45 PHE cc_start: 0.9242 (t80) cc_final: 0.9001 (t80) REVERT: B 47 LYS cc_start: 0.8910 (tttt) cc_final: 0.8621 (ttpp) REVERT: B 51 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8751 (mtpt) REVERT: C 9 TYR cc_start: 0.7572 (m-80) cc_final: 0.7046 (m-80) REVERT: C 20 GLN cc_start: 0.9046 (tp40) cc_final: 0.8369 (mt0) REVERT: C 23 ASP cc_start: 0.8554 (t0) cc_final: 0.8173 (p0) REVERT: C 43 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8173 (ttp80) REVERT: C 47 LYS cc_start: 0.9031 (tttt) cc_final: 0.8437 (tptt) REVERT: D 12 GLU cc_start: 0.7731 (mp0) cc_final: 0.7513 (mp0) REVERT: D 23 ASP cc_start: 0.8442 (m-30) cc_final: 0.8174 (m-30) REVERT: D 27 GLN cc_start: 0.9113 (tp40) cc_final: 0.8882 (tp-100) REVERT: D 37 VAL cc_start: 0.9027 (p) cc_final: 0.8774 (m) REVERT: D 47 LYS cc_start: 0.8961 (tttt) cc_final: 0.8639 (tptt) REVERT: D 51 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8689 (mttt) REVERT: E 8 ASN cc_start: 0.8647 (t0) cc_final: 0.8144 (t0) REVERT: E 19 THR cc_start: 0.8943 (p) cc_final: 0.8215 (p) REVERT: E 51 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8614 (mtpt) REVERT: F 8 ASN cc_start: 0.7931 (t0) cc_final: 0.7454 (t0) REVERT: F 9 TYR cc_start: 0.7267 (m-80) cc_final: 0.6937 (m-80) REVERT: F 12 GLU cc_start: 0.8091 (mp0) cc_final: 0.7785 (mp0) REVERT: F 51 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8669 (mtpp) REVERT: G 12 GLU cc_start: 0.7952 (mp0) cc_final: 0.7732 (mp0) REVERT: G 27 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8609 (mm-40) REVERT: G 49 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8322 (p) REVERT: H 9 TYR cc_start: 0.7497 (m-80) cc_final: 0.7036 (m-80) REVERT: H 43 ARG cc_start: 0.8510 (mtp180) cc_final: 0.7995 (ttm170) REVERT: H 50 SER cc_start: 0.8911 (m) cc_final: 0.8685 (t) REVERT: H 51 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8593 (mtpp) REVERT: I 27 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8322 (tp40) REVERT: I 42 ILE cc_start: 0.9352 (tt) cc_final: 0.9094 (tt) REVERT: I 50 SER cc_start: 0.8781 (t) cc_final: 0.8340 (p) REVERT: I 51 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8700 (mtpp) REVERT: J 12 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8241 (tm-30) REVERT: J 23 ASP cc_start: 0.7835 (p0) cc_final: 0.7509 (p0) REVERT: J 27 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8607 (tp-100) REVERT: K 12 GLU cc_start: 0.7889 (mp0) cc_final: 0.7583 (mp0) REVERT: K 14 MET cc_start: 0.8646 (mmt) cc_final: 0.8117 (mmt) REVERT: K 18 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7838 (ttmm) REVERT: K 47 LYS cc_start: 0.8280 (tttt) cc_final: 0.7778 (ttmm) REVERT: K 50 SER cc_start: 0.8371 (t) cc_final: 0.7748 (p) REVERT: K 51 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8575 (mmmt) REVERT: L 14 MET cc_start: 0.8745 (mmt) cc_final: 0.8380 (mmt) REVERT: L 20 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8926 (mm-40) REVERT: L 47 LYS cc_start: 0.8410 (tttt) cc_final: 0.7819 (ttmm) REVERT: L 50 SER cc_start: 0.8639 (t) cc_final: 0.8163 (p) REVERT: L 51 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8602 (mmmm) REVERT: M 14 MET cc_start: 0.8317 (mmm) cc_final: 0.8008 (mmt) REVERT: M 15 ASP cc_start: 0.8455 (m-30) cc_final: 0.8205 (m-30) REVERT: M 27 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8672 (tp-100) REVERT: N 8 ASN cc_start: 0.7541 (t0) cc_final: 0.7128 (m-40) REVERT: N 14 MET cc_start: 0.8548 (mmt) cc_final: 0.8068 (mmt) REVERT: N 18 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7691 (ttmm) REVERT: N 47 LYS cc_start: 0.8233 (tttt) cc_final: 0.8014 (ttmm) REVERT: N 51 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8512 (mtpp) REVERT: O 14 MET cc_start: 0.8690 (mmm) cc_final: 0.8030 (mmt) REVERT: P 15 ASP cc_start: 0.8151 (m-30) cc_final: 0.7896 (m-30) REVERT: P 27 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8401 (tp40) REVERT: Q 8 ASN cc_start: 0.7910 (t0) cc_final: 0.7708 (m110) REVERT: Q 15 ASP cc_start: 0.8352 (m-30) cc_final: 0.8038 (m-30) REVERT: Q 27 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8468 (tp40) REVERT: R 9 TYR cc_start: 0.7635 (m-80) cc_final: 0.7280 (m-80) REVERT: S 15 ASP cc_start: 0.8213 (m-30) cc_final: 0.7919 (m-30) REVERT: S 51 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8677 (ttmm) REVERT: T 27 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8415 (tp-100) REVERT: U 8 ASN cc_start: 0.6099 (t0) cc_final: 0.5735 (t0) REVERT: U 15 ASP cc_start: 0.8482 (m-30) cc_final: 0.8153 (m-30) REVERT: V 14 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: W 11 THR cc_start: 0.8600 (p) cc_final: 0.8116 (p) REVERT: W 15 ASP cc_start: 0.8660 (m-30) cc_final: 0.8355 (m-30) REVERT: W 18 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8110 (ttmm) REVERT: W 43 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8209 (ttp80) REVERT: W 51 LYS cc_start: 0.8631 (mttp) cc_final: 0.8387 (mttp) REVERT: X 18 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8243 (tttp) REVERT: X 49 SER cc_start: 0.9353 (t) cc_final: 0.8987 (p) REVERT: Y 27 GLN cc_start: 0.9185 (tp40) cc_final: 0.8928 (tp40) REVERT: Z 18 LYS cc_start: 0.8307 (tttt) cc_final: 0.7953 (mptt) REVERT: Z 33 THR cc_start: 0.8183 (t) cc_final: 0.7976 (p) REVERT: Z 46 LYS cc_start: 0.7961 (mttt) cc_final: 0.7735 (mtmt) REVERT: a 18 LYS cc_start: 0.8276 (tttt) cc_final: 0.7830 (mptt) REVERT: b 18 LYS cc_start: 0.8570 (tttt) cc_final: 0.7791 (mptt) REVERT: b 51 LYS cc_start: 0.8275 (mptt) cc_final: 0.7919 (mttm) REVERT: c 18 LYS cc_start: 0.8602 (tttt) cc_final: 0.7958 (mptt) REVERT: c 23 ASP cc_start: 0.8318 (t0) cc_final: 0.8105 (t0) REVERT: d 18 LYS cc_start: 0.8207 (tttt) cc_final: 0.7486 (mptt) REVERT: d 51 LYS cc_start: 0.8605 (mptt) cc_final: 0.8370 (mptt) outliers start: 50 outliers final: 38 residues processed: 750 average time/residue: 0.2142 time to fit residues: 223.4587 Evaluate side-chains 760 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 720 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain V residue 14 MET Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 41 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 V 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10980 Z= 0.209 Angle : 0.623 6.942 14940 Z= 0.320 Chirality : 0.044 0.199 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.950 11.972 1440 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 3.41 % Allowed : 31.30 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.23), residues: 1350 helix: 1.45 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.47 (0.38), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 29 PHE 0.017 0.001 PHE c 48 TYR 0.008 0.001 TYR L 9 ARG 0.003 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 786 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 744 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8432 (mt0) REVERT: A 42 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8753 (tt) REVERT: A 47 LYS cc_start: 0.9106 (tttt) cc_final: 0.8631 (tppt) REVERT: A 49 SER cc_start: 0.8923 (t) cc_final: 0.8640 (m) REVERT: A 51 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8719 (mtpt) REVERT: B 42 ILE cc_start: 0.9275 (tt) cc_final: 0.8964 (tp) REVERT: B 47 LYS cc_start: 0.8903 (tttt) cc_final: 0.8527 (mmtt) REVERT: B 51 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8773 (mttt) REVERT: C 9 TYR cc_start: 0.7553 (m-80) cc_final: 0.7042 (m-80) REVERT: C 20 GLN cc_start: 0.9022 (tp40) cc_final: 0.8342 (mt0) REVERT: C 23 ASP cc_start: 0.8560 (t0) cc_final: 0.8180 (p0) REVERT: C 43 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8168 (ttp80) REVERT: C 47 LYS cc_start: 0.9019 (tttt) cc_final: 0.8420 (tptt) REVERT: D 12 GLU cc_start: 0.7803 (mp0) cc_final: 0.7545 (mp0) REVERT: D 23 ASP cc_start: 0.8398 (m-30) cc_final: 0.8161 (m-30) REVERT: D 27 GLN cc_start: 0.9070 (tp40) cc_final: 0.8840 (tp-100) REVERT: D 37 VAL cc_start: 0.9013 (p) cc_final: 0.8758 (m) REVERT: D 47 LYS cc_start: 0.8948 (tttt) cc_final: 0.8645 (tptt) REVERT: D 51 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8694 (mttt) REVERT: E 8 ASN cc_start: 0.8574 (t0) cc_final: 0.8079 (t0) REVERT: E 47 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7632 (ttpt) REVERT: E 51 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8627 (mtpt) REVERT: F 8 ASN cc_start: 0.7930 (t0) cc_final: 0.7362 (t0) REVERT: F 9 TYR cc_start: 0.7224 (m-80) cc_final: 0.6945 (m-80) REVERT: F 12 GLU cc_start: 0.8134 (mp0) cc_final: 0.7852 (mp0) REVERT: F 51 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8723 (mtpp) REVERT: G 8 ASN cc_start: 0.8067 (t0) cc_final: 0.7834 (t0) REVERT: G 12 GLU cc_start: 0.7933 (mp0) cc_final: 0.7718 (mp0) REVERT: G 27 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8523 (mm-40) REVERT: G 46 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8241 (mtpt) REVERT: G 49 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8302 (p) REVERT: H 9 TYR cc_start: 0.7477 (m-80) cc_final: 0.7054 (m-80) REVERT: H 43 ARG cc_start: 0.8500 (mtp180) cc_final: 0.8114 (ttm170) REVERT: H 51 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8574 (mtpp) REVERT: I 27 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8193 (tp40) REVERT: I 42 ILE cc_start: 0.9372 (tt) cc_final: 0.9116 (tt) REVERT: I 50 SER cc_start: 0.8781 (t) cc_final: 0.8342 (p) REVERT: I 51 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8700 (mtpp) REVERT: J 23 ASP cc_start: 0.7866 (p0) cc_final: 0.7549 (p0) REVERT: J 27 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8548 (tp-100) REVERT: K 12 GLU cc_start: 0.7863 (mp0) cc_final: 0.7575 (mp0) REVERT: K 14 MET cc_start: 0.8629 (mmt) cc_final: 0.8105 (mmt) REVERT: K 18 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7849 (ttmm) REVERT: K 47 LYS cc_start: 0.8273 (tttt) cc_final: 0.7763 (ttmm) REVERT: K 50 SER cc_start: 0.8499 (t) cc_final: 0.7864 (p) REVERT: K 51 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8583 (mmmt) REVERT: L 14 MET cc_start: 0.8744 (mmt) cc_final: 0.8285 (mmt) REVERT: L 20 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8899 (mm-40) REVERT: L 47 LYS cc_start: 0.8396 (tttt) cc_final: 0.7802 (ttmm) REVERT: L 50 SER cc_start: 0.8619 (t) cc_final: 0.8131 (p) REVERT: L 51 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8568 (mmmm) REVERT: M 14 MET cc_start: 0.8324 (mmm) cc_final: 0.7946 (mmt) REVERT: M 15 ASP cc_start: 0.8472 (m-30) cc_final: 0.8244 (m-30) REVERT: M 27 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8631 (tp-100) REVERT: N 8 ASN cc_start: 0.7560 (t0) cc_final: 0.6992 (t0) REVERT: N 14 MET cc_start: 0.8338 (mmt) cc_final: 0.7953 (mmt) REVERT: N 18 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7707 (ttmm) REVERT: N 47 LYS cc_start: 0.8275 (tttt) cc_final: 0.8050 (ttmm) REVERT: N 51 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8637 (mtpp) REVERT: O 14 MET cc_start: 0.8690 (mmm) cc_final: 0.8277 (mmt) REVERT: P 15 ASP cc_start: 0.8136 (m-30) cc_final: 0.7884 (m-30) REVERT: P 27 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8389 (tp40) REVERT: Q 8 ASN cc_start: 0.7820 (t0) cc_final: 0.7589 (m110) REVERT: Q 15 ASP cc_start: 0.8313 (m-30) cc_final: 0.7977 (m-30) REVERT: Q 27 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8438 (tp40) REVERT: R 9 TYR cc_start: 0.7633 (m-80) cc_final: 0.7199 (m-80) REVERT: S 15 ASP cc_start: 0.8133 (m-30) cc_final: 0.7745 (m-30) REVERT: S 51 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8663 (ttmm) REVERT: T 14 MET cc_start: 0.8930 (tpp) cc_final: 0.8720 (tpp) REVERT: T 27 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8598 (tp-100) REVERT: U 8 ASN cc_start: 0.6214 (t0) cc_final: 0.5888 (t0) REVERT: V 50 SER cc_start: 0.9090 (t) cc_final: 0.8716 (p) REVERT: W 11 THR cc_start: 0.8388 (p) cc_final: 0.7888 (p) REVERT: W 15 ASP cc_start: 0.8669 (m-30) cc_final: 0.8347 (m-30) REVERT: W 18 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8103 (ttmm) REVERT: W 43 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8168 (ttp80) REVERT: W 51 LYS cc_start: 0.8616 (mttp) cc_final: 0.8379 (mttp) REVERT: X 18 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8268 (tttp) REVERT: X 49 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.8940 (p) REVERT: X 51 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8684 (ttmm) REVERT: Y 27 GLN cc_start: 0.9161 (tp40) cc_final: 0.8873 (tp40) REVERT: Z 18 LYS cc_start: 0.8243 (tttt) cc_final: 0.7875 (mptt) REVERT: Z 46 LYS cc_start: 0.7895 (mttt) cc_final: 0.7654 (mtmt) REVERT: Z 47 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8504 (tttm) REVERT: Z 51 LYS cc_start: 0.8315 (mttm) cc_final: 0.7945 (mtmm) REVERT: a 18 LYS cc_start: 0.8252 (tttt) cc_final: 0.7820 (mptt) REVERT: b 18 LYS cc_start: 0.8550 (tttt) cc_final: 0.7773 (mptt) REVERT: b 46 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8245 (ttmt) REVERT: b 51 LYS cc_start: 0.8122 (mptt) cc_final: 0.7835 (mttm) REVERT: c 14 MET cc_start: 0.6231 (mmm) cc_final: 0.5804 (tpp) REVERT: c 18 LYS cc_start: 0.8582 (tttt) cc_final: 0.7943 (mptt) REVERT: d 18 LYS cc_start: 0.8353 (tttt) cc_final: 0.7623 (mptt) outliers start: 42 outliers final: 27 residues processed: 752 average time/residue: 0.2080 time to fit residues: 218.2067 Evaluate side-chains 758 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 727 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain B 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 G residue 49 SER 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 K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 17 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 d residue 42 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10980 Z= 0.240 Angle : 0.642 8.054 14940 Z= 0.330 Chirality : 0.045 0.197 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.927 12.477 1440 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 3.09 % Allowed : 32.52 % Favored : 64.39 % 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: 2.16 (0.23), residues: 1350 helix: 1.45 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.61 (0.37), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 29 PHE 0.022 0.001 PHE c 48 TYR 0.007 0.001 TYR N 9 ARG 0.003 0.000 ARG c 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 760 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 722 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8446 (mt0) REVERT: A 42 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8800 (tt) REVERT: A 47 LYS cc_start: 0.9109 (tttt) cc_final: 0.8627 (tppt) REVERT: A 49 SER cc_start: 0.8853 (t) cc_final: 0.8581 (m) REVERT: A 51 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8733 (mtpt) REVERT: B 42 ILE cc_start: 0.9422 (tt) cc_final: 0.9073 (tp) REVERT: B 47 LYS cc_start: 0.8906 (tttt) cc_final: 0.8479 (mmtt) REVERT: B 51 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8774 (mttt) REVERT: C 9 TYR cc_start: 0.7594 (m-80) cc_final: 0.7059 (m-80) REVERT: C 20 GLN cc_start: 0.9038 (tp40) cc_final: 0.8355 (mt0) REVERT: C 23 ASP cc_start: 0.8566 (t0) cc_final: 0.8186 (p0) REVERT: C 43 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8145 (ttp80) REVERT: C 47 LYS cc_start: 0.9018 (tttt) cc_final: 0.8417 (tptt) REVERT: D 12 GLU cc_start: 0.7766 (mp0) cc_final: 0.7514 (mp0) REVERT: D 23 ASP cc_start: 0.8423 (m-30) cc_final: 0.8176 (m-30) REVERT: D 27 GLN cc_start: 0.9072 (tp40) cc_final: 0.8842 (tp-100) REVERT: D 37 VAL cc_start: 0.9025 (p) cc_final: 0.8773 (m) REVERT: D 47 LYS cc_start: 0.8954 (tttt) cc_final: 0.8649 (tptt) REVERT: D 51 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8686 (mttt) REVERT: E 8 ASN cc_start: 0.8617 (t0) cc_final: 0.8151 (t0) REVERT: E 15 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: E 19 THR cc_start: 0.8891 (p) cc_final: 0.8174 (p) REVERT: E 47 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7669 (ttpt) REVERT: E 51 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8615 (mtpt) REVERT: F 8 ASN cc_start: 0.7903 (t0) cc_final: 0.7354 (t0) REVERT: F 9 TYR cc_start: 0.7231 (m-80) cc_final: 0.6966 (m-80) REVERT: F 12 GLU cc_start: 0.8140 (mp0) cc_final: 0.7821 (mp0) REVERT: F 43 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.8363 (ttp-110) REVERT: F 51 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8732 (mtpp) REVERT: G 12 GLU cc_start: 0.7949 (mp0) cc_final: 0.7701 (mp0) REVERT: G 27 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8520 (mm-40) REVERT: H 9 TYR cc_start: 0.7506 (m-80) cc_final: 0.7090 (m-80) REVERT: H 43 ARG cc_start: 0.8490 (mtp180) cc_final: 0.8056 (ttm170) REVERT: H 50 SER cc_start: 0.8940 (m) cc_final: 0.8701 (t) REVERT: H 51 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8561 (mtpp) REVERT: I 27 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8246 (tp40) REVERT: I 42 ILE cc_start: 0.9362 (tt) cc_final: 0.9105 (tt) REVERT: I 50 SER cc_start: 0.8820 (t) cc_final: 0.8338 (p) REVERT: I 51 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8714 (mtpp) REVERT: J 20 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8616 (mm-40) REVERT: J 23 ASP cc_start: 0.7857 (p0) cc_final: 0.7519 (p0) REVERT: J 27 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8473 (tp-100) REVERT: K 12 GLU cc_start: 0.7873 (mp0) cc_final: 0.7558 (mp0) REVERT: K 14 MET cc_start: 0.8598 (mmt) cc_final: 0.7955 (mmt) REVERT: K 18 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7819 (ttmm) REVERT: K 47 LYS cc_start: 0.8277 (tttt) cc_final: 0.7760 (ttmm) REVERT: K 50 SER cc_start: 0.8501 (t) cc_final: 0.7915 (p) REVERT: K 51 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8584 (mmmt) REVERT: L 20 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8904 (mm-40) REVERT: L 47 LYS cc_start: 0.8396 (tttt) cc_final: 0.8100 (ttmm) REVERT: L 51 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8577 (mmmm) REVERT: M 14 MET cc_start: 0.8279 (mmm) cc_final: 0.7951 (mmt) REVERT: M 15 ASP cc_start: 0.8454 (m-30) cc_final: 0.8225 (m-30) REVERT: M 27 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8627 (tp-100) REVERT: N 8 ASN cc_start: 0.7468 (t0) cc_final: 0.6858 (m-40) REVERT: N 14 MET cc_start: 0.8362 (mmt) cc_final: 0.7946 (mmt) REVERT: N 18 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7662 (ttmm) REVERT: N 47 LYS cc_start: 0.8249 (tttt) cc_final: 0.8024 (ttmm) REVERT: N 51 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8621 (mtpp) REVERT: O 14 MET cc_start: 0.8694 (mmm) cc_final: 0.8345 (mmt) REVERT: P 15 ASP cc_start: 0.8161 (m-30) cc_final: 0.7891 (m-30) REVERT: P 27 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8381 (tp40) REVERT: Q 8 ASN cc_start: 0.7803 (t0) cc_final: 0.7575 (m110) REVERT: Q 15 ASP cc_start: 0.8295 (m-30) cc_final: 0.7960 (m-30) REVERT: Q 27 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8681 (tp40) REVERT: S 15 ASP cc_start: 0.8096 (m-30) cc_final: 0.7682 (m-30) REVERT: S 51 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8671 (ttmm) REVERT: T 14 MET cc_start: 0.8920 (tpp) cc_final: 0.8700 (tpp) REVERT: T 27 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8555 (tp-100) REVERT: V 50 SER cc_start: 0.9047 (t) cc_final: 0.8741 (p) REVERT: V 51 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8783 (ttmm) REVERT: W 11 THR cc_start: 0.8378 (p) cc_final: 0.7866 (p) REVERT: W 15 ASP cc_start: 0.8679 (m-30) cc_final: 0.8333 (m-30) REVERT: W 18 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8105 (ttmm) REVERT: W 43 ARG cc_start: 0.8464 (ttm170) cc_final: 0.8182 (ttp80) REVERT: W 51 LYS cc_start: 0.8610 (mttp) cc_final: 0.8373 (mttp) REVERT: X 49 SER cc_start: 0.9364 (t) cc_final: 0.9000 (p) REVERT: X 51 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8711 (ttmm) REVERT: Y 27 GLN cc_start: 0.9138 (tp40) cc_final: 0.8855 (tp40) REVERT: Z 18 LYS cc_start: 0.8314 (tttt) cc_final: 0.7948 (mptt) REVERT: Z 28 THR cc_start: 0.9227 (m) cc_final: 0.8823 (p) REVERT: Z 46 LYS cc_start: 0.7864 (mttt) cc_final: 0.7660 (mtmt) REVERT: Z 47 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8486 (tttm) REVERT: Z 51 LYS cc_start: 0.8311 (mttm) cc_final: 0.7986 (mtmm) REVERT: a 18 LYS cc_start: 0.8200 (tttt) cc_final: 0.7773 (mptt) REVERT: b 18 LYS cc_start: 0.8548 (tttt) cc_final: 0.7770 (mptt) REVERT: b 46 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8254 (ttmt) REVERT: b 51 LYS cc_start: 0.8144 (mptt) cc_final: 0.7831 (mttm) REVERT: c 14 MET cc_start: 0.6059 (mmm) cc_final: 0.5724 (mmm) REVERT: c 18 LYS cc_start: 0.8580 (tttt) cc_final: 0.7938 (mptt) REVERT: d 18 LYS cc_start: 0.8283 (tttt) cc_final: 0.7542 (mptt) outliers start: 38 outliers final: 29 residues processed: 731 average time/residue: 0.2142 time to fit residues: 217.2842 Evaluate side-chains 740 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 708 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 49 SER 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 K residue 44 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain X residue 24 LEU 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 17 LEU Chi-restraints excluded: chain b residue 41 VAL 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 d residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10980 Z= 0.210 Angle : 0.652 8.277 14940 Z= 0.335 Chirality : 0.044 0.180 1980 Planarity : 0.004 0.029 1740 Dihedral : 3.952 13.730 1440 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.60 % Allowed : 33.98 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.23), residues: 1350 helix: 1.45 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 3.69 (0.49), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 29 PHE 0.021 0.001 PHE c 48 TYR 0.014 0.001 TYR N 9 ARG 0.003 0.000 ARG c 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 774 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 742 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: A 27 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8428 (mt0) REVERT: A 42 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 47 LYS cc_start: 0.9076 (tttt) cc_final: 0.8631 (tppt) REVERT: A 49 SER cc_start: 0.9005 (t) cc_final: 0.8721 (m) REVERT: A 51 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8681 (mtpt) REVERT: B 42 ILE cc_start: 0.9337 (tt) cc_final: 0.9016 (tp) REVERT: B 47 LYS cc_start: 0.8874 (tttt) cc_final: 0.8455 (mmtt) REVERT: B 51 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8793 (mttt) REVERT: C 9 TYR cc_start: 0.7559 (m-80) cc_final: 0.7044 (m-80) REVERT: C 20 GLN cc_start: 0.9011 (tp40) cc_final: 0.8330 (mt0) REVERT: C 23 ASP cc_start: 0.8563 (t0) cc_final: 0.8189 (p0) REVERT: C 43 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8109 (ttp80) REVERT: C 47 LYS cc_start: 0.9004 (tttt) cc_final: 0.8409 (tptt) REVERT: D 12 GLU cc_start: 0.7764 (mp0) cc_final: 0.7502 (mp0) REVERT: D 23 ASP cc_start: 0.8412 (m-30) cc_final: 0.8139 (m-30) REVERT: D 27 GLN cc_start: 0.9086 (tp40) cc_final: 0.8877 (tp-100) REVERT: D 37 VAL cc_start: 0.9008 (p) cc_final: 0.8758 (m) REVERT: D 47 LYS cc_start: 0.8946 (tttt) cc_final: 0.8636 (tptt) REVERT: D 51 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8741 (mttt) REVERT: E 8 ASN cc_start: 0.8594 (t0) cc_final: 0.7172 (t0) REVERT: E 15 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: E 27 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8498 (tt0) REVERT: E 47 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7586 (ttpp) REVERT: E 51 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8627 (mttt) REVERT: F 8 ASN cc_start: 0.7879 (t0) cc_final: 0.7522 (t0) REVERT: F 12 GLU cc_start: 0.8137 (mp0) cc_final: 0.7795 (mp0) REVERT: F 51 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8744 (mtpp) REVERT: G 12 GLU cc_start: 0.7940 (mp0) cc_final: 0.7715 (mp0) REVERT: G 27 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8385 (mm-40) REVERT: H 43 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8029 (ttm170) REVERT: H 50 SER cc_start: 0.8932 (m) cc_final: 0.8693 (t) REVERT: H 51 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8498 (mtpp) REVERT: I 27 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8136 (tp40) REVERT: I 42 ILE cc_start: 0.9343 (tt) cc_final: 0.9067 (tt) REVERT: I 50 SER cc_start: 0.8821 (t) cc_final: 0.8342 (p) REVERT: I 51 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8721 (mtpp) REVERT: J 20 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8600 (mt0) REVERT: J 23 ASP cc_start: 0.7869 (p0) cc_final: 0.7577 (p0) REVERT: J 27 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8436 (tp-100) REVERT: K 12 GLU cc_start: 0.7894 (mp0) cc_final: 0.7569 (mp0) REVERT: K 18 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7929 (ttmm) REVERT: K 43 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8027 (ttm170) REVERT: K 47 LYS cc_start: 0.8261 (tttt) cc_final: 0.7762 (ttmm) REVERT: K 50 SER cc_start: 0.8510 (t) cc_final: 0.7967 (p) REVERT: K 51 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8586 (mmmt) REVERT: L 14 MET cc_start: 0.8723 (mmt) cc_final: 0.8298 (mmm) REVERT: L 20 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8901 (mm-40) REVERT: L 47 LYS cc_start: 0.8385 (tttt) cc_final: 0.8084 (ttmm) REVERT: L 51 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8566 (mmmm) REVERT: M 12 GLU cc_start: 0.7916 (pm20) cc_final: 0.7485 (pm20) REVERT: M 14 MET cc_start: 0.8308 (mmm) cc_final: 0.7962 (mmt) REVERT: M 15 ASP cc_start: 0.8447 (m-30) cc_final: 0.8199 (m-30) REVERT: M 27 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8587 (tp-100) REVERT: N 8 ASN cc_start: 0.7293 (t0) cc_final: 0.6524 (m-40) REVERT: N 18 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7656 (ttmm) REVERT: O 14 MET cc_start: 0.8660 (mmm) cc_final: 0.8069 (mmt) REVERT: P 15 ASP cc_start: 0.8158 (m-30) cc_final: 0.7867 (m-30) REVERT: P 27 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8369 (tp40) REVERT: Q 8 ASN cc_start: 0.7919 (t0) cc_final: 0.7645 (m110) REVERT: Q 15 ASP cc_start: 0.8317 (m-30) cc_final: 0.7975 (m-30) REVERT: Q 27 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8522 (tp40) REVERT: S 15 ASP cc_start: 0.8083 (m-30) cc_final: 0.7700 (m-30) REVERT: T 27 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8502 (tp-100) REVERT: V 50 SER cc_start: 0.9143 (t) cc_final: 0.8807 (p) REVERT: W 11 THR cc_start: 0.8364 (p) cc_final: 0.7856 (p) REVERT: W 15 ASP cc_start: 0.8686 (m-30) cc_final: 0.8334 (m-30) REVERT: W 18 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8105 (ttmm) REVERT: W 43 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8181 (ttp80) REVERT: W 51 LYS cc_start: 0.8586 (mttp) cc_final: 0.8360 (mttp) REVERT: X 49 SER cc_start: 0.9378 (t) cc_final: 0.9014 (p) REVERT: X 51 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8657 (ttmm) REVERT: Z 18 LYS cc_start: 0.8323 (tttt) cc_final: 0.7946 (mptt) REVERT: Z 46 LYS cc_start: 0.7956 (mttt) cc_final: 0.7716 (mtmt) REVERT: Z 47 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8521 (tttm) REVERT: Z 51 LYS cc_start: 0.8341 (mttm) cc_final: 0.8019 (mtmm) REVERT: a 18 LYS cc_start: 0.8190 (tttt) cc_final: 0.7773 (mptt) REVERT: b 18 LYS cc_start: 0.8537 (tttt) cc_final: 0.7690 (mmtt) REVERT: b 46 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8273 (ttmt) REVERT: b 51 LYS cc_start: 0.8119 (mptt) cc_final: 0.7861 (mttm) REVERT: c 8 ASN cc_start: 0.8091 (m-40) cc_final: 0.7103 (m-40) REVERT: c 14 MET cc_start: 0.6278 (mmm) cc_final: 0.5820 (mmm) REVERT: c 18 LYS cc_start: 0.8555 (tttt) cc_final: 0.7958 (mptt) REVERT: d 18 LYS cc_start: 0.8314 (tttt) cc_final: 0.7475 (mptt) outliers start: 32 outliers final: 26 residues processed: 749 average time/residue: 0.2182 time to fit residues: 226.0915 Evaluate side-chains 762 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 733 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 49 SER 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 K residue 44 LEU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain V residue 24 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 9 TYR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain a residue 49 SER Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain d residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086962 restraints weight = 20029.966| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3145 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5939 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= 0.238 Angle : 0.683 7.856 14940 Z= 0.351 Chirality : 0.045 0.191 1980 Planarity : 0.004 0.028 1740 Dihedral : 3.949 13.556 1440 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.85 % Allowed : 33.74 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.23), residues: 1350 helix: 1.42 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : 4.15 (0.40), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 29 PHE 0.019 0.001 PHE U 48 TYR 0.010 0.001 TYR N 9 ARG 0.003 0.000 ARG F 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3680.28 seconds wall clock time: 65 minutes 18.39 seconds (3918.39 seconds total)