Starting phenix.real_space_refine on Thu Mar 5 14:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.map" model { file = "/net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tea_10478/03_2026/6tea_10478.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 48 5.16 5 C 14688 2.51 5 N 3912 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Restraints were copied for chains: B, C, A, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 1.99, per 1000 atoms: 0.09 Number of scatterers: 23328 At special positions: 0 Unit cell: (98.859, 98.859, 170.08, 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 48 16.00 O 4680 8.00 N 3912 7.00 C 14688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 24 sheets defined 10.0% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA L 79 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG M 80 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG O 80 " --> pdb=" O ASP O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA P 79 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 80 " --> pdb=" O ASP P 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA Q 79 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 80 " --> pdb=" O ASP Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA S 79 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG S 80 " --> pdb=" O ASP S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA T 79 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG T 80 " --> pdb=" O ASP T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA V 79 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 80 " --> pdb=" O ASP V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG W 80 " --> pdb=" O ASP W 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA X 79 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG X 80 " --> pdb=" O ASP X 76 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE D 107 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA D 62 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE C 107 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA C 127 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 62 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'F' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE H 107 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA H 127 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA H 62 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE K 107 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA K 127 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA K 62 " --> pdb=" O SER K 128 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE L 107 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA L 127 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA L 62 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE M 107 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA M 127 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA M 62 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'N' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'O' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE O 107 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA O 127 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA O 62 " --> pdb=" O SER O 128 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'P' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE P 107 " --> pdb=" O ALA P 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA P 127 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA P 62 " --> pdb=" O SER P 128 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Q' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE Q 107 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA Q 127 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA Q 62 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'R' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE R 107 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA R 127 " --> pdb=" O ILE R 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA R 62 " --> pdb=" O SER R 128 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'S' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE S 107 " --> pdb=" O ALA S 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA S 127 " --> pdb=" O ILE S 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA S 62 " --> pdb=" O SER S 128 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'T' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE T 107 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA T 127 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA T 62 " --> pdb=" O SER T 128 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'U' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'V' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE V 107 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA V 127 " --> pdb=" O ILE V 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA V 62 " --> pdb=" O SER V 128 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'W' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE W 107 " --> pdb=" O ALA W 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA W 127 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA W 62 " --> pdb=" O SER W 128 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'X' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE X 107 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA X 127 " --> pdb=" O ILE X 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA X 62 " --> pdb=" O SER X 128 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7872 1.34 - 1.45: 3955 1.45 - 1.57: 11765 1.57 - 1.68: 0 1.68 - 1.80: 96 Bond restraints: 23688 Sorted by residual: bond pdb=" C ILE F 95 " pdb=" N PRO F 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE R 95 " pdb=" N PRO R 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.07e+00 bond pdb=" C ILE N 95 " pdb=" N PRO N 96 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.07e+00 bond pdb=" C ILE V 95 " pdb=" N PRO V 96 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.05e+00 ... (remaining 23683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 30738 3.08 - 6.16: 1034 6.16 - 9.25: 124 9.25 - 12.33: 48 12.33 - 15.41: 24 Bond angle restraints: 31968 Sorted by residual: angle pdb=" C ILE H 107 " pdb=" N THR H 108 " pdb=" CA THR H 108 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ILE T 107 " pdb=" N THR T 108 " pdb=" CA THR T 108 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ILE P 107 " pdb=" N THR P 108 " pdb=" CA THR P 108 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ILE A 107 " pdb=" N THR A 108 " pdb=" CA THR A 108 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C ILE L 107 " pdb=" N THR L 108 " pdb=" CA THR L 108 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 ... (remaining 31963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 12648 15.50 - 30.99: 888 30.99 - 46.48: 288 46.48 - 61.98: 0 61.98 - 77.47: 24 Dihedral angle restraints: 13848 sinusoidal: 5208 harmonic: 8640 Sorted by residual: dihedral pdb=" CA GLU X 119 " pdb=" C GLU X 119 " pdb=" N ALA X 120 " pdb=" CA ALA X 120 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLU T 119 " pdb=" C GLU T 119 " pdb=" N ALA T 120 " pdb=" CA ALA T 120 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLU H 119 " pdb=" C GLU H 119 " pdb=" N ALA H 120 " pdb=" CA ALA H 120 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2934 0.092 - 0.184: 546 0.184 - 0.276: 48 0.276 - 0.368: 0 0.368 - 0.460: 48 Chirality restraints: 3576 Sorted by residual: chirality pdb=" CB THR S 42 " pdb=" CA THR S 42 " pdb=" OG1 THR S 42 " pdb=" CG2 THR S 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB THR G 42 " pdb=" CA THR G 42 " pdb=" OG1 THR G 42 " pdb=" CG2 THR G 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB THR K 42 " pdb=" CA THR K 42 " pdb=" OG1 THR K 42 " pdb=" CG2 THR K 42 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 3573 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU M 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU M 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU M 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG M 28 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU D 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU D 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG D 28 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 27 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C LEU E 27 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU E 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG E 28 " -0.013 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6908 2.80 - 3.32: 21788 3.32 - 3.85: 41809 3.85 - 4.37: 48165 4.37 - 4.90: 83098 Nonbonded interactions: 201768 Sorted by model distance: nonbonded pdb=" OD2 ASP A 111 " pdb=" NH2 ARG X 31 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG L 31 " pdb=" OD2 ASP P 111 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG A 31 " pdb=" OD2 ASP H 111 " model vdw 2.274 3.120 nonbonded pdb=" NH2 ARG P 31 " pdb=" OD2 ASP T 111 " model vdw 2.274 3.120 nonbonded pdb=" NH2 ARG H 31 " pdb=" OD2 ASP L 111 " model vdw 2.274 3.120 ... (remaining 201763 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'A' 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.008 0.058 23688 Z= 0.383 Angle : 1.337 15.408 31968 Z= 0.686 Chirality : 0.085 0.460 3576 Planarity : 0.006 0.047 4248 Dihedral : 12.642 77.473 8328 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.12), residues: 3024 helix: -3.41 (0.16), residues: 456 sheet: -2.70 (0.13), residues: 1056 loop : -3.57 (0.12), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG R 60 TYR 0.008 0.002 TYR B 122 PHE 0.022 0.004 PHE J 98 TRP 0.007 0.002 TRP U 50 HIS 0.004 0.002 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00835 (23688) covalent geometry : angle 1.33684 (31968) hydrogen bonds : bond 0.27868 ( 816) hydrogen bonds : angle 9.94326 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1414 time to evaluate : 0.843 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: D 5 ASN cc_start: 0.8345 (t0) cc_final: 0.8124 (t0) REVERT: D 24 ILE cc_start: 0.9006 (pt) cc_final: 0.8752 (tp) REVERT: D 51 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8278 (ttp-170) REVERT: D 77 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9095 (tm-30) REVERT: D 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8918 (tp) REVERT: D 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.8824 (m-30) REVERT: D 124 LEU cc_start: 0.9293 (tt) cc_final: 0.8917 (tt) REVERT: B 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8051 (mp10) REVERT: B 8 ASP cc_start: 0.8894 (m-30) cc_final: 0.8501 (m-30) REVERT: B 24 ILE cc_start: 0.9181 (pt) cc_final: 0.8929 (mp) REVERT: B 70 PHE cc_start: 0.8533 (t80) cc_final: 0.8330 (t80) REVERT: B 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9155 (m-80) REVERT: C 35 ASN cc_start: 0.9193 (m-40) cc_final: 0.8957 (m-40) REVERT: C 76 ASP cc_start: 0.9154 (t0) cc_final: 0.8919 (t0) REVERT: C 82 ILE cc_start: 0.9562 (mt) cc_final: 0.9238 (mt) REVERT: C 111 ASP cc_start: 0.8490 (p0) cc_final: 0.7905 (p0) REVERT: A 60 ARG cc_start: 0.8918 (ptp-110) cc_final: 0.8519 (mtm-85) REVERT: A 91 PHE cc_start: 0.8798 (m-80) cc_final: 0.8416 (m-80) REVERT: A 92 GLN cc_start: 0.9203 (tt0) cc_final: 0.8854 (tt0) REVERT: A 106 MET cc_start: 0.8571 (ptp) cc_final: 0.8305 (ptp) REVERT: A 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9190 (tp) REVERT: A 111 ASP cc_start: 0.8490 (p0) cc_final: 0.8145 (p0) REVERT: A 124 LEU cc_start: 0.9163 (tt) cc_final: 0.8549 (tt) REVERT: E 24 ILE cc_start: 0.9124 (pt) cc_final: 0.8858 (tp) REVERT: E 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7971 (ttp-170) REVERT: E 53 LEU cc_start: 0.8520 (mm) cc_final: 0.8287 (mm) REVERT: E 77 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9183 (tm-30) REVERT: E 82 ILE cc_start: 0.9499 (mt) cc_final: 0.8846 (tp) REVERT: E 85 ASP cc_start: 0.9223 (m-30) cc_final: 0.8848 (m-30) REVERT: E 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8883 (tt) REVERT: F 4 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8212 (mp10) REVERT: F 8 ASP cc_start: 0.8980 (m-30) cc_final: 0.8540 (m-30) REVERT: F 60 ARG cc_start: 0.8871 (ptp-110) cc_final: 0.8551 (mpp80) REVERT: F 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8205 (t80) REVERT: F 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8874 (t0) REVERT: F 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8723 (mm-30) REVERT: G 35 ASN cc_start: 0.9207 (m-40) cc_final: 0.8930 (m-40) REVERT: G 70 PHE cc_start: 0.8726 (t80) cc_final: 0.8494 (t80) REVERT: G 76 ASP cc_start: 0.9190 (t0) cc_final: 0.8972 (t0) REVERT: G 81 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8615 (tm-30) REVERT: G 82 ILE cc_start: 0.9555 (mt) cc_final: 0.9112 (mm) REVERT: G 85 ASP cc_start: 0.8994 (m-30) cc_final: 0.8780 (m-30) REVERT: G 87 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8664 (mt-10) REVERT: G 111 ASP cc_start: 0.8379 (p0) cc_final: 0.8105 (p0) REVERT: H 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8955 (pt) REVERT: H 60 ARG cc_start: 0.8843 (ptp-110) cc_final: 0.8577 (mtm-85) REVERT: H 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8704 (t80) REVERT: H 82 ILE cc_start: 0.9818 (mt) cc_final: 0.9616 (mm) REVERT: H 91 PHE cc_start: 0.8824 (m-80) cc_final: 0.8568 (m-80) REVERT: H 92 GLN cc_start: 0.9130 (tt0) cc_final: 0.8856 (tt0) REVERT: H 124 LEU cc_start: 0.9022 (tt) cc_final: 0.8279 (tt) REVERT: I 22 GLU cc_start: 0.7842 (mp0) cc_final: 0.7600 (mp0) REVERT: I 24 ILE cc_start: 0.8957 (pt) cc_final: 0.8730 (tp) REVERT: I 51 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8061 (ttp-110) REVERT: I 77 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9125 (tm-30) REVERT: I 82 ILE cc_start: 0.9512 (mt) cc_final: 0.8924 (tp) REVERT: I 85 ASP cc_start: 0.9199 (m-30) cc_final: 0.8895 (m-30) REVERT: I 124 LEU cc_start: 0.9209 (tt) cc_final: 0.8842 (tp) REVERT: J 4 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8228 (mp10) REVERT: J 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8546 (m-30) REVERT: J 35 ASN cc_start: 0.9011 (m-40) cc_final: 0.8801 (m-40) REVERT: J 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8671 (mpp80) REVERT: J 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7928 (t80) REVERT: J 76 ASP cc_start: 0.9134 (t0) cc_final: 0.8882 (t0) REVERT: J 112 TYR cc_start: 0.9385 (m-80) cc_final: 0.9154 (m-80) REVERT: K 70 PHE cc_start: 0.8833 (t80) cc_final: 0.8470 (t80) REVERT: K 76 ASP cc_start: 0.9200 (t0) cc_final: 0.8986 (t0) REVERT: K 81 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8487 (pp30) REVERT: K 82 ILE cc_start: 0.9580 (mt) cc_final: 0.9221 (mt) REVERT: K 85 ASP cc_start: 0.8989 (m-30) cc_final: 0.8757 (m-30) REVERT: K 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8780 (mt-10) REVERT: K 111 ASP cc_start: 0.8467 (p0) cc_final: 0.7477 (p0) REVERT: L 60 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8602 (mtm-85) REVERT: L 70 PHE cc_start: 0.9057 (t80) cc_final: 0.8666 (t80) REVERT: L 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8279 (m-80) REVERT: L 92 GLN cc_start: 0.9213 (tt0) cc_final: 0.8978 (tt0) REVERT: L 112 TYR cc_start: 0.9083 (m-80) cc_final: 0.8860 (m-10) REVERT: L 124 LEU cc_start: 0.9048 (tt) cc_final: 0.8284 (tt) REVERT: M 5 ASN cc_start: 0.8351 (t0) cc_final: 0.8131 (t0) REVERT: M 24 ILE cc_start: 0.9003 (pt) cc_final: 0.8748 (tp) REVERT: M 51 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8276 (ttp-170) REVERT: M 77 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9095 (tm-30) REVERT: M 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8913 (tp) REVERT: M 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.8823 (m-30) REVERT: M 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8917 (tt) REVERT: N 4 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8049 (mp10) REVERT: N 8 ASP cc_start: 0.8896 (m-30) cc_final: 0.8503 (m-30) REVERT: N 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8937 (mp) REVERT: N 70 PHE cc_start: 0.8541 (t80) cc_final: 0.7781 (t80) REVERT: N 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9180 (m-80) REVERT: O 35 ASN cc_start: 0.9191 (m-40) cc_final: 0.8953 (m-40) REVERT: O 76 ASP cc_start: 0.9153 (t0) cc_final: 0.8913 (t0) REVERT: O 82 ILE cc_start: 0.9561 (mt) cc_final: 0.9236 (mt) REVERT: P 60 ARG cc_start: 0.8917 (ptp-110) cc_final: 0.8522 (mtm-85) REVERT: P 91 PHE cc_start: 0.8797 (m-80) cc_final: 0.8415 (m-80) REVERT: P 92 GLN cc_start: 0.9197 (tt0) cc_final: 0.8851 (tt0) REVERT: P 106 MET cc_start: 0.8579 (ptp) cc_final: 0.8307 (ptp) REVERT: P 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9192 (tp) REVERT: P 124 LEU cc_start: 0.9164 (tt) cc_final: 0.8555 (tt) REVERT: Q 24 ILE cc_start: 0.9122 (pt) cc_final: 0.8856 (tp) REVERT: Q 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7972 (ttp-170) REVERT: Q 53 LEU cc_start: 0.8519 (mm) cc_final: 0.8284 (mm) REVERT: Q 77 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9181 (tm-30) REVERT: Q 82 ILE cc_start: 0.9501 (mt) cc_final: 0.8848 (tp) REVERT: Q 85 ASP cc_start: 0.9219 (m-30) cc_final: 0.8850 (m-30) REVERT: Q 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8881 (tt) REVERT: R 4 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8214 (mp10) REVERT: R 8 ASP cc_start: 0.8981 (m-30) cc_final: 0.8541 (m-30) REVERT: R 60 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8550 (mpp80) REVERT: R 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8200 (t80) REVERT: R 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8872 (t0) REVERT: R 90 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8724 (mm-30) REVERT: S 35 ASN cc_start: 0.9209 (m-40) cc_final: 0.8935 (m-40) REVERT: S 70 PHE cc_start: 0.8728 (t80) cc_final: 0.8495 (t80) REVERT: S 76 ASP cc_start: 0.9188 (t0) cc_final: 0.8971 (t0) REVERT: S 81 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8615 (tm-30) REVERT: S 82 ILE cc_start: 0.9550 (mt) cc_final: 0.9108 (mm) REVERT: S 85 ASP cc_start: 0.8995 (m-30) cc_final: 0.8778 (m-30) REVERT: S 87 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8662 (mt-10) REVERT: S 111 ASP cc_start: 0.8378 (p0) cc_final: 0.8100 (p0) REVERT: T 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8953 (pt) REVERT: T 60 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8581 (mtm-85) REVERT: T 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8705 (t80) REVERT: T 91 PHE cc_start: 0.8825 (m-80) cc_final: 0.8562 (m-80) REVERT: T 92 GLN cc_start: 0.9125 (tt0) cc_final: 0.8847 (tt0) REVERT: T 124 LEU cc_start: 0.9019 (tt) cc_final: 0.8276 (tt) REVERT: U 22 GLU cc_start: 0.7839 (mp0) cc_final: 0.7599 (mp0) REVERT: U 24 ILE cc_start: 0.8953 (pt) cc_final: 0.8730 (tp) REVERT: U 51 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8056 (ttp-110) REVERT: U 77 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9123 (tm-30) REVERT: U 82 ILE cc_start: 0.9511 (mt) cc_final: 0.8924 (tp) REVERT: U 85 ASP cc_start: 0.9197 (m-30) cc_final: 0.8893 (m-30) REVERT: U 124 LEU cc_start: 0.9206 (tt) cc_final: 0.8844 (tp) REVERT: V 8 ASP cc_start: 0.8922 (m-30) cc_final: 0.8533 (m-30) REVERT: V 35 ASN cc_start: 0.9013 (m-40) cc_final: 0.8800 (m-40) REVERT: V 60 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8676 (mpp80) REVERT: V 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7924 (t80) REVERT: V 76 ASP cc_start: 0.9133 (t0) cc_final: 0.8881 (t0) REVERT: V 112 TYR cc_start: 0.9387 (m-80) cc_final: 0.9148 (m-80) REVERT: W 70 PHE cc_start: 0.8834 (t80) cc_final: 0.8467 (t80) REVERT: W 76 ASP cc_start: 0.9196 (t0) cc_final: 0.8982 (t0) REVERT: W 81 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8487 (pp30) REVERT: W 82 ILE cc_start: 0.9576 (mt) cc_final: 0.9218 (mt) REVERT: W 85 ASP cc_start: 0.8985 (m-30) cc_final: 0.8754 (m-30) REVERT: W 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8777 (mt-10) REVERT: W 111 ASP cc_start: 0.8460 (p0) cc_final: 0.7475 (p0) REVERT: X 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8599 (mtm-85) REVERT: X 70 PHE cc_start: 0.9058 (t80) cc_final: 0.8664 (t80) REVERT: X 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8273 (m-80) REVERT: X 92 GLN cc_start: 0.9210 (tt0) cc_final: 0.8976 (tt0) REVERT: X 112 TYR cc_start: 0.9080 (m-80) cc_final: 0.8854 (m-10) REVERT: X 124 LEU cc_start: 0.9048 (tt) cc_final: 0.8287 (tt) outliers start: 0 outliers final: 0 residues processed: 1414 average time/residue: 0.1730 time to fit residues: 371.4671 Evaluate side-chains 878 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 878 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN D 92 GLN D 102 GLN D 116 HIS B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN A 102 GLN A 116 HIS E 20 GLN E 92 GLN E 102 GLN E 116 HIS F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 116 HIS J 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 HIS M 20 GLN M 92 GLN M 102 GLN M 116 HIS N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN P 102 GLN P 116 HIS Q 20 GLN Q 92 GLN Q 102 GLN Q 116 HIS R 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 HIS U 20 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 102 GLN U 116 HIS V 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 116 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.048701 restraints weight = 106986.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050390 restraints weight = 58392.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051569 restraints weight = 36291.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052345 restraints weight = 24578.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053018 restraints weight = 18116.150| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23688 Z= 0.207 Angle : 0.834 9.220 31968 Z= 0.430 Chirality : 0.053 0.257 3576 Planarity : 0.005 0.038 4248 Dihedral : 6.626 23.967 3264 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 8.63 % Allowed : 21.25 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.13), residues: 3024 helix: -2.52 (0.18), residues: 480 sheet: -1.94 (0.14), residues: 1104 loop : -3.49 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 78 TYR 0.010 0.001 TYR M 112 PHE 0.032 0.002 PHE E 70 TRP 0.014 0.002 TRP P 50 HIS 0.007 0.002 HIS I 116 Details of bonding type rmsd covalent geometry : bond 0.00447 (23688) covalent geometry : angle 0.83395 (31968) hydrogen bonds : bond 0.04278 ( 816) hydrogen bonds : angle 7.00056 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 965 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 ILE cc_start: 0.8982 (pt) cc_final: 0.8732 (tp) REVERT: D 30 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8513 (t) REVERT: D 51 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8261 (ttp-170) REVERT: D 52 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8145 (mp0) REVERT: D 53 LEU cc_start: 0.8855 (mm) cc_final: 0.8534 (mm) REVERT: D 70 PHE cc_start: 0.8901 (t80) cc_final: 0.8470 (t80) REVERT: D 78 ARG cc_start: 0.9315 (tpp80) cc_final: 0.8914 (tpt-90) REVERT: D 82 ILE cc_start: 0.9370 (mt) cc_final: 0.8915 (mm) REVERT: B 20 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6736 (pp30) REVERT: B 74 ASP cc_start: 0.8901 (p0) cc_final: 0.8589 (p0) REVERT: B 92 GLN cc_start: 0.9140 (tt0) cc_final: 0.8785 (tt0) REVERT: B 111 ASP cc_start: 0.8867 (p0) cc_final: 0.8658 (p0) REVERT: B 124 LEU cc_start: 0.9660 (tt) cc_final: 0.8911 (tt) REVERT: C 52 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8491 (mt-10) REVERT: C 53 LEU cc_start: 0.9446 (mm) cc_final: 0.9135 (mt) REVERT: C 81 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8411 (pp30) REVERT: C 82 ILE cc_start: 0.9495 (mt) cc_final: 0.9243 (mt) REVERT: A 60 ARG cc_start: 0.8963 (ptp-110) cc_final: 0.8667 (mpp80) REVERT: A 76 ASP cc_start: 0.8951 (t0) cc_final: 0.8608 (t0) REVERT: A 85 ASP cc_start: 0.8977 (m-30) cc_final: 0.8291 (p0) REVERT: A 87 GLU cc_start: 0.8824 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 92 GLN cc_start: 0.9139 (tt0) cc_final: 0.8709 (tt0) REVERT: E 24 ILE cc_start: 0.9163 (pt) cc_final: 0.8937 (tp) REVERT: E 31 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8387 (tpp80) REVERT: E 52 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7669 (mp0) REVERT: E 70 PHE cc_start: 0.9166 (t80) cc_final: 0.8902 (t80) REVERT: E 78 ARG cc_start: 0.9364 (tpp80) cc_final: 0.9125 (mmm160) REVERT: E 82 ILE cc_start: 0.9401 (mt) cc_final: 0.8956 (mm) REVERT: F 4 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8136 (mp10) REVERT: F 20 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6802 (pp30) REVERT: F 70 PHE cc_start: 0.8525 (t80) cc_final: 0.8245 (t80) REVERT: F 90 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8535 (mm-30) REVERT: G 31 ARG cc_start: 0.8539 (ttt90) cc_final: 0.7489 (ttt90) REVERT: G 51 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8579 (ttp-110) REVERT: G 52 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 78 ARG cc_start: 0.9350 (tpp80) cc_final: 0.8613 (tpp80) REVERT: G 81 GLN cc_start: 0.8990 (tm-30) cc_final: 0.7327 (tm-30) REVERT: G 82 ILE cc_start: 0.9518 (mt) cc_final: 0.8879 (mm) REVERT: G 85 ASP cc_start: 0.8930 (m-30) cc_final: 0.8235 (p0) REVERT: G 87 GLU cc_start: 0.8776 (mt-10) cc_final: 0.7436 (mt-10) REVERT: G 106 MET cc_start: 0.7590 (pmm) cc_final: 0.7063 (pmm) REVERT: H 14 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6995 (t70) REVERT: H 60 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8651 (ptp90) REVERT: H 76 ASP cc_start: 0.8977 (t0) cc_final: 0.8738 (t0) REVERT: H 92 GLN cc_start: 0.8975 (tt0) cc_final: 0.8651 (tt0) REVERT: I 5 ASN cc_start: 0.8476 (t0) cc_final: 0.7125 (t0) REVERT: I 7 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9088 (mtmt) REVERT: I 24 ILE cc_start: 0.8938 (pt) cc_final: 0.8694 (tp) REVERT: I 27 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8518 (tp) REVERT: I 31 ARG cc_start: 0.8805 (mtp-110) cc_final: 0.8563 (mtp-110) REVERT: I 51 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.7873 (ttp-170) REVERT: I 52 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7810 (mt-10) REVERT: I 53 LEU cc_start: 0.8925 (mm) cc_final: 0.8605 (mm) REVERT: I 78 ARG cc_start: 0.9327 (tpp80) cc_final: 0.9028 (tpt-90) REVERT: I 82 ILE cc_start: 0.9435 (mt) cc_final: 0.9080 (mm) REVERT: I 94 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9292 (tp) REVERT: J 4 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8212 (mp10) REVERT: J 20 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6695 (pp30) REVERT: J 31 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8547 (ttt90) REVERT: J 70 PHE cc_start: 0.8398 (t80) cc_final: 0.7878 (t80) REVERT: K 31 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8104 (mmm160) REVERT: K 47 GLN cc_start: 0.8477 (mp10) cc_final: 0.8197 (mp10) REVERT: K 51 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8745 (ttp80) REVERT: K 52 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8391 (mt-10) REVERT: K 81 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 82 ILE cc_start: 0.9469 (mt) cc_final: 0.9062 (mt) REVERT: K 85 ASP cc_start: 0.8925 (m-30) cc_final: 0.8462 (p0) REVERT: K 111 ASP cc_start: 0.7979 (p0) cc_final: 0.7737 (p0) REVERT: K 126 MET cc_start: 0.8424 (mtp) cc_final: 0.8174 (mtm) REVERT: L 20 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6959 (pp30) REVERT: L 60 ARG cc_start: 0.8931 (ptp-110) cc_final: 0.8640 (mpp80) REVERT: L 92 GLN cc_start: 0.9012 (tt0) cc_final: 0.8661 (tt0) REVERT: M 24 ILE cc_start: 0.8974 (pt) cc_final: 0.8726 (tp) REVERT: M 30 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8516 (t) REVERT: M 51 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8258 (ttp-170) REVERT: M 52 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8151 (mp0) REVERT: M 53 LEU cc_start: 0.8860 (mm) cc_final: 0.8538 (mm) REVERT: M 70 PHE cc_start: 0.8907 (t80) cc_final: 0.8480 (t80) REVERT: M 78 ARG cc_start: 0.9319 (tpp80) cc_final: 0.8919 (tpt-90) REVERT: M 82 ILE cc_start: 0.9364 (mt) cc_final: 0.8917 (mm) REVERT: N 20 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6731 (pp30) REVERT: N 70 PHE cc_start: 0.8285 (t80) cc_final: 0.8038 (t80) REVERT: N 74 ASP cc_start: 0.8899 (p0) cc_final: 0.8591 (p0) REVERT: N 92 GLN cc_start: 0.9147 (tt0) cc_final: 0.8786 (tt0) REVERT: N 111 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8652 (p0) REVERT: N 124 LEU cc_start: 0.9665 (tt) cc_final: 0.8892 (tt) REVERT: O 52 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8496 (mt-10) REVERT: O 53 LEU cc_start: 0.9445 (mm) cc_final: 0.9157 (mt) REVERT: O 81 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: O 82 ILE cc_start: 0.9492 (mt) cc_final: 0.9246 (mt) REVERT: P 60 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8671 (mpp80) REVERT: P 76 ASP cc_start: 0.8941 (t0) cc_final: 0.8588 (t0) REVERT: P 85 ASP cc_start: 0.8972 (m-30) cc_final: 0.8290 (p0) REVERT: P 87 GLU cc_start: 0.8829 (mt-10) cc_final: 0.7258 (mt-10) REVERT: P 92 GLN cc_start: 0.9133 (tt0) cc_final: 0.8702 (tt0) REVERT: Q 24 ILE cc_start: 0.9162 (pt) cc_final: 0.8940 (tp) REVERT: Q 31 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8381 (tpp80) REVERT: Q 52 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7675 (mp0) REVERT: Q 70 PHE cc_start: 0.9176 (t80) cc_final: 0.8911 (t80) REVERT: Q 78 ARG cc_start: 0.9366 (tpp80) cc_final: 0.9123 (mmm160) REVERT: Q 82 ILE cc_start: 0.9400 (mt) cc_final: 0.8958 (mm) REVERT: R 4 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8127 (mp10) REVERT: R 20 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: R 70 PHE cc_start: 0.8526 (t80) cc_final: 0.8252 (t80) REVERT: R 90 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8537 (mm-30) REVERT: R 92 GLN cc_start: 0.9090 (tt0) cc_final: 0.8886 (tt0) REVERT: S 31 ARG cc_start: 0.8535 (ttt90) cc_final: 0.7480 (ttt90) REVERT: S 51 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8579 (ttp-110) REVERT: S 52 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8442 (mt-10) REVERT: S 78 ARG cc_start: 0.9351 (tpp80) cc_final: 0.8613 (tpp80) REVERT: S 81 GLN cc_start: 0.8993 (tm-30) cc_final: 0.7311 (tm-30) REVERT: S 82 ILE cc_start: 0.9516 (mt) cc_final: 0.8880 (mm) REVERT: S 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8245 (p0) REVERT: S 87 GLU cc_start: 0.8786 (mt-10) cc_final: 0.7436 (mt-10) REVERT: S 106 MET cc_start: 0.7571 (pmm) cc_final: 0.7081 (pmm) REVERT: T 14 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6999 (t70) REVERT: T 60 ARG cc_start: 0.8873 (ptp-110) cc_final: 0.8649 (ptp90) REVERT: T 76 ASP cc_start: 0.8948 (t0) cc_final: 0.8681 (t0) REVERT: T 92 GLN cc_start: 0.8967 (tt0) cc_final: 0.8643 (tt0) REVERT: U 5 ASN cc_start: 0.8482 (t0) cc_final: 0.7855 (t0) REVERT: U 24 ILE cc_start: 0.8936 (pt) cc_final: 0.8695 (tp) REVERT: U 27 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8501 (tp) REVERT: U 51 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.7877 (ttp-170) REVERT: U 52 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7815 (mt-10) REVERT: U 53 LEU cc_start: 0.8920 (mm) cc_final: 0.8546 (mm) REVERT: U 78 ARG cc_start: 0.9329 (tpp80) cc_final: 0.9033 (tpt-90) REVERT: U 82 ILE cc_start: 0.9433 (mt) cc_final: 0.9081 (mm) REVERT: U 94 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9292 (tp) REVERT: V 20 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6706 (pp30) REVERT: V 70 PHE cc_start: 0.8408 (t80) cc_final: 0.7873 (t80) REVERT: W 47 GLN cc_start: 0.8485 (mp10) cc_final: 0.8205 (mp10) REVERT: W 51 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8760 (ttp80) REVERT: W 52 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8391 (mt-10) REVERT: W 81 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8060 (tm-30) REVERT: W 82 ILE cc_start: 0.9469 (mt) cc_final: 0.9065 (mt) REVERT: W 85 ASP cc_start: 0.8927 (m-30) cc_final: 0.8468 (p0) REVERT: W 111 ASP cc_start: 0.7956 (p0) cc_final: 0.7721 (p0) REVERT: W 126 MET cc_start: 0.8436 (mtp) cc_final: 0.8184 (mtm) REVERT: X 20 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6957 (pp30) REVERT: X 60 ARG cc_start: 0.8956 (ptp-110) cc_final: 0.8649 (mpp80) REVERT: X 92 GLN cc_start: 0.9017 (tt0) cc_final: 0.8658 (tt0) outliers start: 205 outliers final: 112 residues processed: 1035 average time/residue: 0.1522 time to fit residues: 248.3975 Evaluate side-chains 971 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 840 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 20 GLN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 20 GLN Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 35 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 228 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS C 20 GLN C 102 GLN A 20 GLN F 92 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 116 HIS K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 HIS O 20 GLN O 102 GLN P 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 GLN V 116 HIS W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045855 restraints weight = 111219.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.047480 restraints weight = 58605.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048599 restraints weight = 35766.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049395 restraints weight = 23961.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049980 restraints weight = 17140.763| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23688 Z= 0.227 Angle : 0.847 9.583 31968 Z= 0.421 Chirality : 0.052 0.271 3576 Planarity : 0.004 0.031 4248 Dihedral : 6.153 23.062 3264 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 10.44 % Allowed : 22.01 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.13), residues: 3024 helix: -1.92 (0.20), residues: 480 sheet: -1.70 (0.14), residues: 1104 loop : -3.43 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 31 TYR 0.015 0.001 TYR X 122 PHE 0.021 0.002 PHE K 70 TRP 0.011 0.002 TRP K 50 HIS 0.004 0.002 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00491 (23688) covalent geometry : angle 0.84663 (31968) hydrogen bonds : bond 0.03729 ( 816) hydrogen bonds : angle 6.25808 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 882 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8272 (ttp-170) REVERT: D 52 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8143 (mp0) REVERT: D 70 PHE cc_start: 0.8948 (t80) cc_final: 0.8355 (t80) REVERT: D 78 ARG cc_start: 0.9317 (tpp80) cc_final: 0.9054 (tpp80) REVERT: D 82 ILE cc_start: 0.9471 (mt) cc_final: 0.9216 (mm) REVERT: D 87 GLU cc_start: 0.8782 (pm20) cc_final: 0.8557 (pm20) REVERT: B 4 GLN cc_start: 0.8722 (mm-40) cc_final: 0.7963 (mp10) REVERT: B 74 ASP cc_start: 0.8931 (p0) cc_final: 0.8637 (p0) REVERT: B 76 ASP cc_start: 0.8577 (t0) cc_final: 0.7386 (t0) REVERT: B 98 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 111 ASP cc_start: 0.8829 (p0) cc_final: 0.8624 (p0) REVERT: C 81 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8587 (pp30) REVERT: C 82 ILE cc_start: 0.9489 (mt) cc_final: 0.9253 (mt) REVERT: A 35 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.9037 (p0) REVERT: A 70 PHE cc_start: 0.8709 (t80) cc_final: 0.7524 (t80) REVERT: A 76 ASP cc_start: 0.8961 (t0) cc_final: 0.8200 (t0) REVERT: A 85 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 87 GLU cc_start: 0.8731 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 92 GLN cc_start: 0.9017 (tt0) cc_final: 0.8735 (tt0) REVERT: A 98 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: A 119 GLU cc_start: 0.8698 (pm20) cc_final: 0.8480 (pm20) REVERT: A 126 MET cc_start: 0.8272 (mmm) cc_final: 0.7639 (mmt) REVERT: E 24 ILE cc_start: 0.9110 (pt) cc_final: 0.8767 (tp) REVERT: E 51 ARG cc_start: 0.8960 (ttp-110) cc_final: 0.8459 (ttp-170) REVERT: E 52 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7813 (mp0) REVERT: E 70 PHE cc_start: 0.9185 (t80) cc_final: 0.8834 (t80) REVERT: F 70 PHE cc_start: 0.8427 (t80) cc_final: 0.5865 (t80) REVERT: F 74 ASP cc_start: 0.9019 (p0) cc_final: 0.8795 (p0) REVERT: F 76 ASP cc_start: 0.8784 (t0) cc_final: 0.7973 (t0) REVERT: F 98 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: G 31 ARG cc_start: 0.8199 (ttt90) cc_final: 0.7604 (ttt90) REVERT: G 51 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8641 (ttp-170) REVERT: G 78 ARG cc_start: 0.9306 (tpp80) cc_final: 0.8589 (tpp80) REVERT: G 81 GLN cc_start: 0.9001 (tm-30) cc_final: 0.7766 (tm-30) REVERT: G 82 ILE cc_start: 0.9510 (mt) cc_final: 0.8929 (mm) REVERT: G 85 ASP cc_start: 0.8849 (m-30) cc_final: 0.8457 (p0) REVERT: H 31 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8379 (ptm-80) REVERT: H 76 ASP cc_start: 0.8943 (t0) cc_final: 0.8596 (t0) REVERT: H 85 ASP cc_start: 0.8978 (m-30) cc_final: 0.8567 (p0) REVERT: H 87 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7860 (mt-10) REVERT: I 5 ASN cc_start: 0.8682 (t0) cc_final: 0.7394 (t0) REVERT: I 7 LYS cc_start: 0.9310 (mtpt) cc_final: 0.8982 (mtmm) REVERT: I 24 ILE cc_start: 0.8973 (pt) cc_final: 0.8568 (tp) REVERT: I 27 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8615 (tp) REVERT: I 51 ARG cc_start: 0.9004 (ttp-110) cc_final: 0.8204 (ttp-170) REVERT: I 52 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7679 (mt-10) REVERT: I 82 ILE cc_start: 0.9505 (mt) cc_final: 0.9112 (mm) REVERT: I 87 GLU cc_start: 0.8858 (pm20) cc_final: 0.8391 (pm20) REVERT: I 98 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: I 124 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.8786 (tt) REVERT: J 4 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8246 (mm-40) REVERT: J 70 PHE cc_start: 0.8296 (t80) cc_final: 0.5666 (t80) REVERT: J 76 ASP cc_start: 0.8523 (t0) cc_final: 0.7156 (t0) REVERT: J 98 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: K 7 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9084 (mtmm) REVERT: K 31 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8199 (mmm160) REVERT: K 51 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8669 (ttp-170) REVERT: K 52 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8265 (mt-10) REVERT: K 81 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8411 (tm-30) REVERT: K 82 ILE cc_start: 0.9497 (mt) cc_final: 0.8890 (mt) REVERT: K 85 ASP cc_start: 0.8882 (m-30) cc_final: 0.8478 (p0) REVERT: K 98 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: K 106 MET cc_start: 0.8464 (ttm) cc_final: 0.8258 (ttt) REVERT: K 111 ASP cc_start: 0.8591 (p0) cc_final: 0.8155 (p0) REVERT: K 123 GLU cc_start: 0.8294 (mp0) cc_final: 0.8080 (mp0) REVERT: L 60 ARG cc_start: 0.8919 (ptp-110) cc_final: 0.8638 (mpp80) REVERT: L 92 GLN cc_start: 0.9035 (tt0) cc_final: 0.8675 (tt0) REVERT: L 98 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: L 111 ASP cc_start: 0.8488 (p0) cc_final: 0.8017 (p0) REVERT: M 51 ARG cc_start: 0.8976 (ttp-110) cc_final: 0.8268 (ttp-170) REVERT: M 52 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8150 (mp0) REVERT: M 70 PHE cc_start: 0.8956 (t80) cc_final: 0.8369 (t80) REVERT: M 78 ARG cc_start: 0.9319 (tpp80) cc_final: 0.9057 (tpp80) REVERT: N 4 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7944 (mp10) REVERT: N 70 PHE cc_start: 0.8422 (t80) cc_final: 0.6766 (t80) REVERT: N 74 ASP cc_start: 0.8928 (p0) cc_final: 0.8622 (p0) REVERT: N 76 ASP cc_start: 0.8680 (t0) cc_final: 0.8099 (t0) REVERT: N 98 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.6577 (m-10) REVERT: O 70 PHE cc_start: 0.8329 (t80) cc_final: 0.5852 (t80) REVERT: O 76 ASP cc_start: 0.9159 (t0) cc_final: 0.8531 (t0) REVERT: O 81 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8574 (pp30) REVERT: O 82 ILE cc_start: 0.9491 (mt) cc_final: 0.9251 (mt) REVERT: P 35 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.9029 (p0) REVERT: P 70 PHE cc_start: 0.8710 (t80) cc_final: 0.8239 (t80) REVERT: P 76 ASP cc_start: 0.8963 (t0) cc_final: 0.8663 (t0) REVERT: P 85 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8315 (p0) REVERT: P 87 GLU cc_start: 0.8727 (mt-10) cc_final: 0.7392 (mt-10) REVERT: P 92 GLN cc_start: 0.9013 (tt0) cc_final: 0.8735 (tt0) REVERT: P 98 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: P 119 GLU cc_start: 0.8693 (pm20) cc_final: 0.8475 (pm20) REVERT: P 126 MET cc_start: 0.8277 (mmm) cc_final: 0.7646 (mmt) REVERT: Q 24 ILE cc_start: 0.9116 (pt) cc_final: 0.8773 (tp) REVERT: Q 51 ARG cc_start: 0.8956 (ttp-110) cc_final: 0.8156 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7806 (mp0) REVERT: Q 70 PHE cc_start: 0.9189 (t80) cc_final: 0.8838 (t80) REVERT: R 70 PHE cc_start: 0.8426 (t80) cc_final: 0.5897 (t80) REVERT: R 74 ASP cc_start: 0.9015 (p0) cc_final: 0.8774 (p0) REVERT: R 76 ASP cc_start: 0.8784 (t0) cc_final: 0.7995 (t0) REVERT: R 98 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: S 31 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7607 (ttt90) REVERT: S 51 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8633 (ttp-170) REVERT: S 78 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8587 (tpp80) REVERT: S 81 GLN cc_start: 0.8997 (tm-30) cc_final: 0.7764 (tm-30) REVERT: S 82 ILE cc_start: 0.9510 (mt) cc_final: 0.8927 (mm) REVERT: S 85 ASP cc_start: 0.8861 (m-30) cc_final: 0.8464 (p0) REVERT: T 31 ARG cc_start: 0.9089 (ptm-80) cc_final: 0.8377 (ptm-80) REVERT: T 76 ASP cc_start: 0.8987 (t0) cc_final: 0.8689 (t0) REVERT: T 85 ASP cc_start: 0.8940 (m-30) cc_final: 0.8698 (p0) REVERT: U 5 ASN cc_start: 0.9054 (t0) cc_final: 0.8800 (t0) REVERT: U 24 ILE cc_start: 0.8983 (pt) cc_final: 0.8573 (tp) REVERT: U 27 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8614 (tp) REVERT: U 31 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8756 (mmm-85) REVERT: U 51 ARG cc_start: 0.9011 (ttp-110) cc_final: 0.8201 (ttp-170) REVERT: U 52 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7711 (mt-10) REVERT: U 82 ILE cc_start: 0.9513 (mt) cc_final: 0.9119 (mm) REVERT: U 87 GLU cc_start: 0.8872 (pm20) cc_final: 0.8426 (pm20) REVERT: U 98 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: U 124 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.8796 (tt) REVERT: V 70 PHE cc_start: 0.8308 (t80) cc_final: 0.5751 (t80) REVERT: V 76 ASP cc_start: 0.8541 (t0) cc_final: 0.7284 (t0) REVERT: V 98 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: W 7 LYS cc_start: 0.9433 (mtmt) cc_final: 0.9087 (mtmm) REVERT: W 51 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8692 (ttp-170) REVERT: W 52 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8282 (mt-10) REVERT: W 81 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8411 (tm-30) REVERT: W 82 ILE cc_start: 0.9492 (mt) cc_final: 0.8889 (mt) REVERT: W 85 ASP cc_start: 0.8892 (m-30) cc_final: 0.8478 (p0) REVERT: W 111 ASP cc_start: 0.8585 (p0) cc_final: 0.8160 (p0) REVERT: W 123 GLU cc_start: 0.8297 (mp0) cc_final: 0.8080 (mp0) REVERT: X 60 ARG cc_start: 0.8922 (ptp-110) cc_final: 0.8634 (mpp80) REVERT: X 92 GLN cc_start: 0.9045 (tt0) cc_final: 0.8690 (tt0) REVERT: X 98 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.6883 (m-10) REVERT: X 111 ASP cc_start: 0.8484 (p0) cc_final: 0.8012 (p0) outliers start: 248 outliers final: 154 residues processed: 996 average time/residue: 0.1531 time to fit residues: 239.7854 Evaluate side-chains 975 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 798 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 46 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 102 GLN C 20 GLN A 20 GLN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 102 GLN I 92 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN N 102 GLN O 20 GLN P 20 GLN R 92 GLN R 102 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN T 102 GLN U 92 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045696 restraints weight = 109110.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047259 restraints weight = 59094.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048360 restraints weight = 36935.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049160 restraints weight = 24965.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049742 restraints weight = 17956.006| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23688 Z= 0.200 Angle : 0.826 11.298 31968 Z= 0.408 Chirality : 0.051 0.261 3576 Planarity : 0.004 0.040 4248 Dihedral : 5.861 24.007 3264 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 11.03 % Allowed : 23.15 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.13), residues: 3024 helix: -1.49 (0.21), residues: 480 sheet: -1.60 (0.13), residues: 1224 loop : -3.59 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 51 TYR 0.014 0.001 TYR H 122 PHE 0.024 0.002 PHE F 91 TRP 0.011 0.002 TRP L 50 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00434 (23688) covalent geometry : angle 0.82579 (31968) hydrogen bonds : bond 0.03352 ( 816) hydrogen bonds : angle 5.90104 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 847 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8680 (tp) REVERT: D 51 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8466 (ttp-170) REVERT: D 52 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8069 (mp0) REVERT: D 70 PHE cc_start: 0.9008 (t80) cc_final: 0.8388 (t80) REVERT: D 76 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: B 4 GLN cc_start: 0.8704 (mm-40) cc_final: 0.7951 (mp10) REVERT: B 8 ASP cc_start: 0.8873 (m-30) cc_final: 0.8588 (m-30) REVERT: B 74 ASP cc_start: 0.8925 (p0) cc_final: 0.8639 (p0) REVERT: B 76 ASP cc_start: 0.8590 (t0) cc_final: 0.7404 (t0) REVERT: B 98 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: B 123 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8584 (mt-10) REVERT: C 20 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: C 31 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.7661 (ttt90) REVERT: C 81 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8551 (pp30) REVERT: C 82 ILE cc_start: 0.9441 (mt) cc_final: 0.9234 (mt) REVERT: C 133 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9207 (p) REVERT: A 35 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9084 (p0) REVERT: A 70 PHE cc_start: 0.8732 (t80) cc_final: 0.7459 (t80) REVERT: A 76 ASP cc_start: 0.8988 (t0) cc_final: 0.8382 (t0) REVERT: A 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8388 (p0) REVERT: A 87 GLU cc_start: 0.8763 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 92 GLN cc_start: 0.8991 (tt0) cc_final: 0.8665 (tt0) REVERT: A 98 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: E 13 LEU cc_start: 0.9418 (pp) cc_final: 0.9202 (pp) REVERT: E 51 ARG cc_start: 0.8956 (ttp-170) cc_final: 0.8215 (ttp-170) REVERT: E 52 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7700 (mp0) REVERT: E 70 PHE cc_start: 0.9139 (t80) cc_final: 0.8818 (t80) REVERT: F 4 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7862 (mp10) REVERT: F 70 PHE cc_start: 0.8387 (t80) cc_final: 0.5866 (t80) REVERT: F 74 ASP cc_start: 0.9001 (p0) cc_final: 0.8768 (p0) REVERT: F 76 ASP cc_start: 0.8788 (t0) cc_final: 0.7868 (t0) REVERT: F 98 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: G 31 ARG cc_start: 0.8212 (ttt90) cc_final: 0.7662 (ttt90) REVERT: G 51 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8649 (ttp-170) REVERT: G 81 GLN cc_start: 0.9038 (tm-30) cc_final: 0.7722 (tm-30) REVERT: G 82 ILE cc_start: 0.9503 (mt) cc_final: 0.9131 (mt) REVERT: G 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8361 (p0) REVERT: G 87 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7535 (mt-10) REVERT: G 111 ASP cc_start: 0.8244 (p0) cc_final: 0.7693 (p0) REVERT: H 31 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8281 (ptm-80) REVERT: H 76 ASP cc_start: 0.9020 (t0) cc_final: 0.8794 (t0) REVERT: H 85 ASP cc_start: 0.8983 (m-30) cc_final: 0.8446 (p0) REVERT: H 87 GLU cc_start: 0.8796 (mt-10) cc_final: 0.7905 (mt-10) REVERT: I 5 ASN cc_start: 0.8742 (t0) cc_final: 0.8438 (t0) REVERT: I 51 ARG cc_start: 0.9018 (ttp-170) cc_final: 0.8447 (ttp-170) REVERT: I 52 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7722 (mt-10) REVERT: I 85 ASP cc_start: 0.8892 (m-30) cc_final: 0.8575 (m-30) REVERT: J 4 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8422 (mm-40) REVERT: J 70 PHE cc_start: 0.8286 (t80) cc_final: 0.5799 (t80) REVERT: J 76 ASP cc_start: 0.8580 (t0) cc_final: 0.7271 (t0) REVERT: J 98 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: K 7 LYS cc_start: 0.9401 (mtmt) cc_final: 0.9071 (mtmm) REVERT: K 31 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8303 (mtp85) REVERT: K 81 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8050 (tm-30) REVERT: K 82 ILE cc_start: 0.9464 (mt) cc_final: 0.8170 (mt) REVERT: K 85 ASP cc_start: 0.8873 (m-30) cc_final: 0.7913 (p0) REVERT: K 87 GLU cc_start: 0.8850 (mt-10) cc_final: 0.7921 (mp0) REVERT: K 98 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: K 111 ASP cc_start: 0.8653 (p0) cc_final: 0.8145 (p0) REVERT: K 123 GLU cc_start: 0.8357 (mp0) cc_final: 0.8139 (mp0) REVERT: L 35 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.9079 (p0) REVERT: L 92 GLN cc_start: 0.8989 (tt0) cc_final: 0.8694 (tt0) REVERT: L 98 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: L 111 ASP cc_start: 0.8462 (p0) cc_final: 0.7714 (p0) REVERT: M 27 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8684 (tp) REVERT: M 51 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8463 (ttp-170) REVERT: M 52 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8071 (mp0) REVERT: M 70 PHE cc_start: 0.9002 (t80) cc_final: 0.8537 (t80) REVERT: M 76 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8966 (m-30) REVERT: N 4 GLN cc_start: 0.8695 (mm-40) cc_final: 0.7930 (mp10) REVERT: N 8 ASP cc_start: 0.8876 (m-30) cc_final: 0.8599 (m-30) REVERT: N 74 ASP cc_start: 0.8924 (p0) cc_final: 0.8584 (p0) REVERT: N 76 ASP cc_start: 0.8725 (t0) cc_final: 0.7813 (t0) REVERT: N 98 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: O 20 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: O 31 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.7673 (ttt90) REVERT: O 70 PHE cc_start: 0.8244 (t80) cc_final: 0.5907 (t80) REVERT: O 76 ASP cc_start: 0.9218 (t0) cc_final: 0.8827 (t0) REVERT: O 81 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8576 (pp30) REVERT: O 133 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.9207 (p) REVERT: P 35 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9053 (p0) REVERT: P 70 PHE cc_start: 0.8733 (t80) cc_final: 0.8408 (t80) REVERT: P 85 ASP cc_start: 0.8951 (m-30) cc_final: 0.8394 (p0) REVERT: P 87 GLU cc_start: 0.8777 (mt-10) cc_final: 0.7549 (mt-10) REVERT: P 92 GLN cc_start: 0.9000 (tt0) cc_final: 0.8671 (tt0) REVERT: P 98 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: Q 13 LEU cc_start: 0.9418 (pp) cc_final: 0.9203 (pp) REVERT: Q 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8234 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7685 (mp0) REVERT: Q 70 PHE cc_start: 0.9140 (t80) cc_final: 0.8824 (t80) REVERT: R 4 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7867 (mp10) REVERT: R 70 PHE cc_start: 0.8393 (t80) cc_final: 0.5909 (t80) REVERT: R 74 ASP cc_start: 0.8998 (p0) cc_final: 0.8744 (p0) REVERT: R 76 ASP cc_start: 0.8786 (t0) cc_final: 0.7885 (t0) REVERT: R 98 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: S 31 ARG cc_start: 0.8204 (ttt90) cc_final: 0.7665 (ttt90) REVERT: S 51 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8640 (ttp-170) REVERT: S 81 GLN cc_start: 0.9031 (tm-30) cc_final: 0.7725 (tm-30) REVERT: S 82 ILE cc_start: 0.9506 (mt) cc_final: 0.9141 (mt) REVERT: S 85 ASP cc_start: 0.8885 (m-30) cc_final: 0.8366 (p0) REVERT: S 87 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7538 (mt-10) REVERT: S 111 ASP cc_start: 0.8248 (p0) cc_final: 0.7706 (p0) REVERT: T 31 ARG cc_start: 0.9187 (ptm-80) cc_final: 0.8307 (ptm-80) REVERT: T 76 ASP cc_start: 0.9044 (t0) cc_final: 0.8777 (t0) REVERT: U 5 ASN cc_start: 0.9094 (t0) cc_final: 0.8018 (t0) REVERT: U 7 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9097 (mtmm) REVERT: U 51 ARG cc_start: 0.9014 (ttp-170) cc_final: 0.8444 (ttp-170) REVERT: U 52 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7743 (mt-10) REVERT: U 85 ASP cc_start: 0.8880 (m-30) cc_final: 0.8564 (m-30) REVERT: U 98 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: V 70 PHE cc_start: 0.8299 (t80) cc_final: 0.5784 (t80) REVERT: V 76 ASP cc_start: 0.8587 (t0) cc_final: 0.7324 (t0) REVERT: V 98 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6654 (m-10) REVERT: W 7 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9072 (mtmm) REVERT: W 81 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8057 (tm-30) REVERT: W 82 ILE cc_start: 0.9455 (mt) cc_final: 0.8166 (mt) REVERT: W 85 ASP cc_start: 0.8896 (m-30) cc_final: 0.7916 (p0) REVERT: W 87 GLU cc_start: 0.8832 (mt-10) cc_final: 0.7921 (mp0) REVERT: W 111 ASP cc_start: 0.8661 (p0) cc_final: 0.8166 (p0) REVERT: X 31 ARG cc_start: 0.9179 (ptm-80) cc_final: 0.8695 (ptm-80) REVERT: X 35 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9085 (p0) REVERT: X 71 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8294 (mtmm) REVERT: X 92 GLN cc_start: 0.8993 (tt0) cc_final: 0.8718 (tt0) REVERT: X 98 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.6658 (m-10) REVERT: X 111 ASP cc_start: 0.8461 (p0) cc_final: 0.7639 (p0) outliers start: 262 outliers final: 152 residues processed: 984 average time/residue: 0.1552 time to fit residues: 241.1490 Evaluate side-chains 931 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 752 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 235 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN C 102 GLN A 20 GLN F 102 GLN G 20 GLN H 20 GLN I 92 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN O 20 GLN O 102 GLN P 20 GLN S 20 GLN T 20 GLN U 92 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 92 GLN X 102 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047527 restraints weight = 107076.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049214 restraints weight = 56923.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050373 restraints weight = 35089.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051198 restraints weight = 23539.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051794 restraints weight = 16810.534| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23688 Z= 0.149 Angle : 0.838 10.385 31968 Z= 0.410 Chirality : 0.052 0.229 3576 Planarity : 0.004 0.041 4248 Dihedral : 5.630 24.320 3264 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 9.85 % Allowed : 25.13 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.13), residues: 3024 helix: -1.02 (0.23), residues: 456 sheet: -1.44 (0.13), residues: 1224 loop : -3.50 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 78 TYR 0.015 0.001 TYR L 122 PHE 0.029 0.002 PHE R 91 TRP 0.004 0.001 TRP V 50 HIS 0.002 0.001 HIS G 116 Details of bonding type rmsd covalent geometry : bond 0.00333 (23688) covalent geometry : angle 0.83824 (31968) hydrogen bonds : bond 0.03125 ( 816) hydrogen bonds : angle 5.59970 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 857 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8697 (tp) REVERT: D 31 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8811 (mmm-85) REVERT: D 51 ARG cc_start: 0.9035 (ttp-110) cc_final: 0.8461 (ttp-170) REVERT: D 52 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8132 (mp0) REVERT: D 60 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8646 (ptp90) REVERT: D 70 PHE cc_start: 0.8957 (t80) cc_final: 0.8526 (t80) REVERT: D 87 GLU cc_start: 0.8839 (pm20) cc_final: 0.8187 (pp20) REVERT: B 4 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8168 (mp10) REVERT: B 74 ASP cc_start: 0.8825 (p0) cc_final: 0.8529 (p0) REVERT: B 76 ASP cc_start: 0.8480 (t0) cc_final: 0.7288 (t0) REVERT: B 98 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.5658 (m-10) REVERT: B 111 ASP cc_start: 0.8792 (p0) cc_final: 0.8589 (p0) REVERT: B 123 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 31 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.6358 (ttt90) REVERT: C 51 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8550 (ttp-110) REVERT: C 82 ILE cc_start: 0.9422 (mt) cc_final: 0.9120 (mt) REVERT: A 20 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: A 35 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.9065 (p0) REVERT: A 70 PHE cc_start: 0.8705 (t80) cc_final: 0.7291 (t80) REVERT: A 76 ASP cc_start: 0.8867 (t0) cc_final: 0.8228 (t0) REVERT: A 85 ASP cc_start: 0.8895 (m-30) cc_final: 0.8359 (p0) REVERT: A 92 GLN cc_start: 0.8951 (tt0) cc_final: 0.8719 (tt0) REVERT: A 98 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: A 111 ASP cc_start: 0.8387 (p0) cc_final: 0.5715 (p0) REVERT: A 122 TYR cc_start: 0.8222 (p90) cc_final: 0.7591 (p90) REVERT: E 51 ARG cc_start: 0.8912 (ttp-170) cc_final: 0.8458 (ttp-170) REVERT: E 52 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7804 (mp0) REVERT: E 60 ARG cc_start: 0.9092 (ptp-110) cc_final: 0.8702 (ptp90) REVERT: E 70 PHE cc_start: 0.8987 (t80) cc_final: 0.8782 (t80) REVERT: F 4 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7900 (mp10) REVERT: F 52 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8201 (mt-10) REVERT: F 70 PHE cc_start: 0.8298 (t80) cc_final: 0.5763 (t80) REVERT: F 76 ASP cc_start: 0.8685 (t0) cc_final: 0.7952 (t0) REVERT: F 98 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: F 117 ASN cc_start: 0.9448 (p0) cc_final: 0.9171 (p0) REVERT: G 31 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7558 (ttt90) REVERT: G 51 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8524 (ttp-110) REVERT: G 81 GLN cc_start: 0.9007 (tm-30) cc_final: 0.7603 (tm-30) REVERT: G 82 ILE cc_start: 0.9503 (mt) cc_final: 0.9008 (mt) REVERT: G 85 ASP cc_start: 0.8790 (m-30) cc_final: 0.8269 (p0) REVERT: G 87 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7569 (mt-10) REVERT: G 111 ASP cc_start: 0.8191 (p0) cc_final: 0.7083 (p0) REVERT: H 20 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7184 (pp30) REVERT: H 31 ARG cc_start: 0.9169 (ptm-80) cc_final: 0.8464 (ptm-80) REVERT: H 71 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8082 (mtmm) REVERT: H 76 ASP cc_start: 0.8981 (t0) cc_final: 0.8738 (t0) REVERT: H 85 ASP cc_start: 0.8914 (m-30) cc_final: 0.8457 (p0) REVERT: I 5 ASN cc_start: 0.8779 (t0) cc_final: 0.8395 (t0) REVERT: I 31 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8730 (mtp85) REVERT: I 51 ARG cc_start: 0.9027 (ttp-170) cc_final: 0.8578 (ttp-170) REVERT: I 52 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7836 (mt-10) REVERT: I 60 ARG cc_start: 0.9019 (ptp-110) cc_final: 0.8661 (ptp90) REVERT: J 4 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8134 (mp10) REVERT: J 70 PHE cc_start: 0.8170 (t80) cc_final: 0.5629 (t80) REVERT: J 76 ASP cc_start: 0.8589 (t0) cc_final: 0.7334 (t0) REVERT: J 98 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.6497 (m-10) REVERT: J 111 ASP cc_start: 0.8799 (p0) cc_final: 0.8551 (p0) REVERT: K 7 LYS cc_start: 0.9379 (mtmt) cc_final: 0.9111 (mtmm) REVERT: K 81 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8235 (tm-30) REVERT: K 82 ILE cc_start: 0.9473 (mt) cc_final: 0.8178 (mt) REVERT: K 85 ASP cc_start: 0.8778 (m-30) cc_final: 0.7884 (p0) REVERT: K 87 GLU cc_start: 0.8824 (mt-10) cc_final: 0.7972 (mp0) REVERT: K 92 GLN cc_start: 0.9002 (tt0) cc_final: 0.8704 (tt0) REVERT: K 106 MET cc_start: 0.8455 (ttm) cc_final: 0.8245 (ttm) REVERT: K 111 ASP cc_start: 0.8656 (p0) cc_final: 0.7926 (p0) REVERT: K 123 GLU cc_start: 0.8353 (mp0) cc_final: 0.7848 (mp0) REVERT: L 35 ASN cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (p0) REVERT: L 71 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8280 (mtmm) REVERT: L 98 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: L 111 ASP cc_start: 0.8408 (p0) cc_final: 0.7716 (p0) REVERT: M 27 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8694 (tp) REVERT: M 31 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8809 (mmm-85) REVERT: M 51 ARG cc_start: 0.9032 (ttp-110) cc_final: 0.8450 (ttp-170) REVERT: M 52 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8134 (mp0) REVERT: M 60 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8644 (ptp90) REVERT: M 70 PHE cc_start: 0.8913 (t80) cc_final: 0.8680 (t80) REVERT: M 77 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9202 (tp30) REVERT: N 4 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8159 (mp10) REVERT: N 76 ASP cc_start: 0.8603 (t0) cc_final: 0.7597 (t0) REVERT: N 98 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.5648 (m-10) REVERT: O 31 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.6353 (ttt90) REVERT: O 51 ARG cc_start: 0.8926 (ttp-110) cc_final: 0.8564 (ttp-110) REVERT: O 111 ASP cc_start: 0.8708 (p0) cc_final: 0.8424 (p0) REVERT: O 123 GLU cc_start: 0.8264 (mp0) cc_final: 0.8037 (mp0) REVERT: P 20 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7193 (pp30) REVERT: P 35 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.9064 (p0) REVERT: P 70 PHE cc_start: 0.8706 (t80) cc_final: 0.8504 (t80) REVERT: P 85 ASP cc_start: 0.8894 (m-30) cc_final: 0.8363 (p0) REVERT: P 92 GLN cc_start: 0.8951 (tt0) cc_final: 0.8719 (tt0) REVERT: P 98 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: Q 31 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8718 (tpp80) REVERT: Q 51 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8464 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7792 (mp0) REVERT: Q 60 ARG cc_start: 0.9093 (ptp-110) cc_final: 0.8698 (ptp90) REVERT: Q 70 PHE cc_start: 0.8985 (t80) cc_final: 0.8781 (t80) REVERT: R 4 GLN cc_start: 0.8595 (mm-40) cc_final: 0.7906 (mp10) REVERT: R 52 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8218 (mt-10) REVERT: R 70 PHE cc_start: 0.8300 (t80) cc_final: 0.5773 (t80) REVERT: R 76 ASP cc_start: 0.8678 (t0) cc_final: 0.7939 (t0) REVERT: R 98 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: R 117 ASN cc_start: 0.9448 (p0) cc_final: 0.9171 (p0) REVERT: S 31 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7581 (ttt90) REVERT: S 81 GLN cc_start: 0.9004 (tm-30) cc_final: 0.7606 (tm-30) REVERT: S 82 ILE cc_start: 0.9501 (mt) cc_final: 0.9013 (mt) REVERT: S 85 ASP cc_start: 0.8796 (m-30) cc_final: 0.8275 (p0) REVERT: S 87 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7568 (mt-10) REVERT: S 111 ASP cc_start: 0.8197 (p0) cc_final: 0.7072 (p0) REVERT: T 20 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7191 (pp30) REVERT: T 31 ARG cc_start: 0.9189 (ptm-80) cc_final: 0.8590 (ptm-80) REVERT: T 71 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8071 (mtmm) REVERT: T 76 ASP cc_start: 0.8936 (t0) cc_final: 0.8686 (t0) REVERT: U 5 ASN cc_start: 0.9119 (t0) cc_final: 0.8763 (t0) REVERT: U 51 ARG cc_start: 0.9026 (ttp-170) cc_final: 0.8319 (ttp-170) REVERT: U 52 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7803 (mt-10) REVERT: U 60 ARG cc_start: 0.9038 (ptp-110) cc_final: 0.8640 (ptp90) REVERT: V 70 PHE cc_start: 0.8207 (t80) cc_final: 0.5776 (t80) REVERT: V 76 ASP cc_start: 0.8566 (t0) cc_final: 0.7250 (t0) REVERT: V 98 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.6501 (m-10) REVERT: V 111 ASP cc_start: 0.8785 (p0) cc_final: 0.8533 (p0) REVERT: W 7 LYS cc_start: 0.9371 (mtmt) cc_final: 0.9094 (mtmm) REVERT: W 81 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8243 (tm-30) REVERT: W 82 ILE cc_start: 0.9466 (mt) cc_final: 0.8191 (mt) REVERT: W 85 ASP cc_start: 0.8801 (m-30) cc_final: 0.7891 (p0) REVERT: W 87 GLU cc_start: 0.8822 (mt-10) cc_final: 0.7969 (mp0) REVERT: W 111 ASP cc_start: 0.8681 (p0) cc_final: 0.8016 (p0) REVERT: W 123 GLU cc_start: 0.8343 (mp0) cc_final: 0.7908 (mp0) REVERT: X 31 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8724 (ptm-80) REVERT: X 35 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9065 (p0) REVERT: X 71 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8227 (mtmm) REVERT: X 98 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6671 (m-10) outliers start: 234 outliers final: 155 residues processed: 977 average time/residue: 0.1548 time to fit residues: 236.6580 Evaluate side-chains 943 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 768 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 156 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 chunk 3 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN A 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN M 20 GLN O 20 GLN P 20 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.046050 restraints weight = 109962.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047664 restraints weight = 58657.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048820 restraints weight = 36397.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049630 restraints weight = 24359.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050206 restraints weight = 17467.089| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23688 Z= 0.198 Angle : 0.850 12.522 31968 Z= 0.417 Chirality : 0.051 0.243 3576 Planarity : 0.004 0.041 4248 Dihedral : 5.615 26.287 3264 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 11.24 % Allowed : 26.85 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.14), residues: 3024 helix: -0.95 (0.22), residues: 480 sheet: -1.34 (0.13), residues: 1224 loop : -3.39 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 78 TYR 0.014 0.001 TYR T 122 PHE 0.023 0.002 PHE R 91 TRP 0.010 0.001 TRP F 50 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00436 (23688) covalent geometry : angle 0.84988 (31968) hydrogen bonds : bond 0.03167 ( 816) hydrogen bonds : angle 5.49575 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 781 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8722 (tp) REVERT: D 51 ARG cc_start: 0.9003 (ttp-170) cc_final: 0.8489 (ttp-170) REVERT: D 52 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8066 (mp0) REVERT: D 60 ARG cc_start: 0.9113 (ptp-110) cc_final: 0.8812 (ptp90) REVERT: D 70 PHE cc_start: 0.8951 (t80) cc_final: 0.8653 (t80) REVERT: D 77 GLU cc_start: 0.9460 (tm-30) cc_final: 0.9185 (tp30) REVERT: D 87 GLU cc_start: 0.8799 (pm20) cc_final: 0.8296 (pp20) REVERT: B 8 ASP cc_start: 0.8840 (m-30) cc_final: 0.8579 (m-30) REVERT: B 74 ASP cc_start: 0.8920 (p0) cc_final: 0.8645 (p0) REVERT: B 76 ASP cc_start: 0.8579 (t0) cc_final: 0.7435 (t0) REVERT: B 98 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.5919 (m-10) REVERT: C 31 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7760 (ttm-80) REVERT: A 14 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6844 (t70) REVERT: A 20 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7191 (pp30) REVERT: A 35 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9105 (p0) REVERT: A 76 ASP cc_start: 0.8935 (t0) cc_final: 0.8078 (t0) REVERT: A 85 ASP cc_start: 0.8941 (m-30) cc_final: 0.8461 (p0) REVERT: A 92 GLN cc_start: 0.9035 (tt0) cc_final: 0.8716 (tt0) REVERT: A 98 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: E 51 ARG cc_start: 0.8956 (ttp-170) cc_final: 0.8346 (ttp-170) REVERT: E 52 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7630 (mp0) REVERT: E 60 ARG cc_start: 0.9118 (ptp-110) cc_final: 0.8847 (ptp90) REVERT: E 70 PHE cc_start: 0.9049 (t80) cc_final: 0.8838 (t80) REVERT: E 71 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7959 (mtmm) REVERT: E 92 GLN cc_start: 0.9020 (tt0) cc_final: 0.8789 (tt0) REVERT: F 4 GLN cc_start: 0.8627 (mm-40) cc_final: 0.7911 (mp10) REVERT: F 70 PHE cc_start: 0.8434 (t80) cc_final: 0.5813 (t80) REVERT: F 74 ASP cc_start: 0.8957 (p0) cc_final: 0.8703 (p0) REVERT: F 76 ASP cc_start: 0.8713 (t0) cc_final: 0.7967 (t0) REVERT: F 92 GLN cc_start: 0.8969 (tt0) cc_final: 0.8588 (tt0) REVERT: F 98 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.6262 (m-10) REVERT: G 31 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7419 (ttt90) REVERT: G 51 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8532 (ttp-110) REVERT: G 81 GLN cc_start: 0.8985 (tm-30) cc_final: 0.7970 (tm-30) REVERT: G 82 ILE cc_start: 0.9490 (mt) cc_final: 0.8970 (mt) REVERT: G 85 ASP cc_start: 0.8798 (m-30) cc_final: 0.8326 (p0) REVERT: G 87 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7365 (mt-10) REVERT: G 123 GLU cc_start: 0.8252 (mp0) cc_final: 0.7891 (mp0) REVERT: H 20 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7395 (pp30) REVERT: H 31 ARG cc_start: 0.9194 (ptm-80) cc_final: 0.8486 (ptm-80) REVERT: H 71 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8074 (mtmm) REVERT: H 76 ASP cc_start: 0.8979 (t0) cc_final: 0.8766 (t0) REVERT: H 85 ASP cc_start: 0.8967 (m-30) cc_final: 0.8491 (p0) REVERT: H 119 GLU cc_start: 0.9014 (pm20) cc_final: 0.8752 (pm20) REVERT: I 5 ASN cc_start: 0.8823 (t0) cc_final: 0.8537 (t0) REVERT: I 51 ARG cc_start: 0.9025 (ttp-170) cc_final: 0.8381 (ttp-170) REVERT: I 52 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7199 (mp0) REVERT: I 60 ARG cc_start: 0.9042 (ptp-110) cc_final: 0.8771 (ptp90) REVERT: J 70 PHE cc_start: 0.8337 (t80) cc_final: 0.5748 (t80) REVERT: J 74 ASP cc_start: 0.8956 (p0) cc_final: 0.8678 (p0) REVERT: J 76 ASP cc_start: 0.8625 (t0) cc_final: 0.7291 (t0) REVERT: J 98 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: K 7 LYS cc_start: 0.9433 (mtmt) cc_final: 0.9167 (mtmm) REVERT: K 81 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8284 (tm-30) REVERT: K 82 ILE cc_start: 0.9466 (mt) cc_final: 0.8113 (mt) REVERT: K 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.7902 (p0) REVERT: K 87 GLU cc_start: 0.8845 (mt-10) cc_final: 0.7955 (mp0) REVERT: K 111 ASP cc_start: 0.8674 (p0) cc_final: 0.8034 (p0) REVERT: K 123 GLU cc_start: 0.8345 (mp0) cc_final: 0.8111 (mp0) REVERT: L 35 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9166 (p0) REVERT: L 71 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8344 (mtmm) REVERT: M 27 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8688 (tp) REVERT: M 51 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8491 (ttp-170) REVERT: M 52 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8089 (mp0) REVERT: M 70 PHE cc_start: 0.9020 (t80) cc_final: 0.8721 (t80) REVERT: N 8 ASP cc_start: 0.8855 (m-30) cc_final: 0.8591 (m-30) REVERT: N 70 PHE cc_start: 0.8595 (t80) cc_final: 0.8295 (t80) REVERT: N 74 ASP cc_start: 0.8851 (p0) cc_final: 0.8582 (p0) REVERT: N 98 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: O 31 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: O 76 ASP cc_start: 0.8905 (t0) cc_final: 0.8610 (t0) REVERT: O 81 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8440 (pp30) REVERT: P 14 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6851 (t70) REVERT: P 20 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7191 (pp30) REVERT: P 35 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9106 (p0) REVERT: P 85 ASP cc_start: 0.8939 (m-30) cc_final: 0.8455 (p0) REVERT: P 92 GLN cc_start: 0.9006 (tt0) cc_final: 0.8700 (tt0) REVERT: P 98 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: Q 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8338 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7628 (mp0) REVERT: Q 60 ARG cc_start: 0.9116 (ptp-110) cc_final: 0.8833 (ptp90) REVERT: Q 70 PHE cc_start: 0.9047 (t80) cc_final: 0.8836 (t80) REVERT: Q 71 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7948 (mtmm) REVERT: Q 92 GLN cc_start: 0.9024 (tt0) cc_final: 0.8786 (tt0) REVERT: R 4 GLN cc_start: 0.8649 (mm-40) cc_final: 0.7920 (mp10) REVERT: R 70 PHE cc_start: 0.8454 (t80) cc_final: 0.5741 (t80) REVERT: R 74 ASP cc_start: 0.8957 (p0) cc_final: 0.8696 (p0) REVERT: R 76 ASP cc_start: 0.8722 (t0) cc_final: 0.7962 (t0) REVERT: R 98 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.6295 (m-10) REVERT: S 31 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7574 (ttt90) REVERT: S 81 GLN cc_start: 0.8980 (tm-30) cc_final: 0.7963 (tm-30) REVERT: S 82 ILE cc_start: 0.9487 (mt) cc_final: 0.8965 (mt) REVERT: S 85 ASP cc_start: 0.8799 (m-30) cc_final: 0.8323 (p0) REVERT: S 87 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7357 (mt-10) REVERT: S 123 GLU cc_start: 0.8258 (mp0) cc_final: 0.7895 (mp0) REVERT: T 20 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: T 31 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.8598 (ptm-80) REVERT: T 71 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8075 (mtmm) REVERT: T 98 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: T 119 GLU cc_start: 0.9032 (pm20) cc_final: 0.8750 (pm20) REVERT: U 5 ASN cc_start: 0.9115 (t0) cc_final: 0.8094 (t0) REVERT: U 7 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9152 (mtmm) REVERT: U 51 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8425 (ttp-170) REVERT: U 52 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7215 (mp0) REVERT: U 60 ARG cc_start: 0.9044 (ptp-110) cc_final: 0.8748 (ptp90) REVERT: V 70 PHE cc_start: 0.8380 (t80) cc_final: 0.5641 (t80) REVERT: V 74 ASP cc_start: 0.8959 (p0) cc_final: 0.8676 (p0) REVERT: V 76 ASP cc_start: 0.8632 (t0) cc_final: 0.7358 (t0) REVERT: V 98 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.6609 (m-10) REVERT: W 7 LYS cc_start: 0.9432 (mtmt) cc_final: 0.9161 (mtmm) REVERT: W 31 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8387 (mtp85) REVERT: W 81 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8283 (tm-30) REVERT: W 82 ILE cc_start: 0.9463 (mt) cc_final: 0.8120 (mt) REVERT: W 85 ASP cc_start: 0.8826 (m-30) cc_final: 0.7890 (p0) REVERT: W 87 GLU cc_start: 0.8823 (mt-10) cc_final: 0.7931 (mp0) REVERT: W 111 ASP cc_start: 0.8695 (p0) cc_final: 0.7899 (p0) REVERT: W 123 GLU cc_start: 0.8341 (mp0) cc_final: 0.7898 (mp0) REVERT: X 31 ARG cc_start: 0.9195 (ptm-80) cc_final: 0.8767 (ptm-80) REVERT: X 71 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8244 (mtmm) REVERT: X 76 ASP cc_start: 0.8642 (t0) cc_final: 0.7523 (t0) REVERT: X 98 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6420 (m-10) outliers start: 267 outliers final: 181 residues processed: 929 average time/residue: 0.1515 time to fit residues: 223.1969 Evaluate side-chains 951 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 747 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN A 20 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN P 20 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.046225 restraints weight = 110408.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047854 restraints weight = 58422.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048988 restraints weight = 35995.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049734 restraints weight = 24164.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050357 restraints weight = 17763.388| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23688 Z= 0.183 Angle : 0.862 12.288 31968 Z= 0.422 Chirality : 0.051 0.247 3576 Planarity : 0.004 0.038 4248 Dihedral : 5.596 27.230 3264 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 11.11 % Allowed : 27.06 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.14), residues: 3024 helix: -0.79 (0.22), residues: 480 sheet: -1.27 (0.14), residues: 1224 loop : -3.24 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 78 TYR 0.015 0.001 TYR A 122 PHE 0.027 0.002 PHE J 91 TRP 0.007 0.001 TRP F 50 HIS 0.002 0.001 HIS O 116 Details of bonding type rmsd covalent geometry : bond 0.00411 (23688) covalent geometry : angle 0.86250 (31968) hydrogen bonds : bond 0.03089 ( 816) hydrogen bonds : angle 5.47784 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 794 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8692 (tp) REVERT: D 31 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8597 (mmm-85) REVERT: D 51 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8477 (ttp-170) REVERT: D 52 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8067 (mp0) REVERT: D 70 PHE cc_start: 0.8933 (t80) cc_final: 0.8625 (t80) REVERT: D 77 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9187 (tm-30) REVERT: D 87 GLU cc_start: 0.8726 (pm20) cc_final: 0.8199 (pp20) REVERT: B 8 ASP cc_start: 0.8832 (m-30) cc_final: 0.8585 (m-30) REVERT: B 74 ASP cc_start: 0.8939 (p0) cc_final: 0.8666 (p0) REVERT: B 76 ASP cc_start: 0.8551 (t0) cc_final: 0.7351 (t0) REVERT: B 98 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: C 51 ARG cc_start: 0.8929 (ttp-110) cc_final: 0.8687 (ttp-110) REVERT: A 14 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6877 (t70) REVERT: A 20 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7264 (pp30) REVERT: A 35 ASN cc_start: 0.9396 (OUTLIER) cc_final: 0.9163 (p0) REVERT: A 76 ASP cc_start: 0.8907 (t0) cc_final: 0.8078 (t0) REVERT: A 85 ASP cc_start: 0.8927 (m-30) cc_final: 0.8471 (p0) REVERT: A 92 GLN cc_start: 0.8976 (tt0) cc_final: 0.8708 (tt0) REVERT: A 98 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: A 119 GLU cc_start: 0.9102 (pm20) cc_final: 0.8860 (pm20) REVERT: E 51 ARG cc_start: 0.8929 (ttp-170) cc_final: 0.8327 (ttp-170) REVERT: E 52 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7616 (mp0) REVERT: E 60 ARG cc_start: 0.9112 (ptp-110) cc_final: 0.8824 (ptp90) REVERT: E 71 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7973 (mtmm) REVERT: E 92 GLN cc_start: 0.8933 (tt0) cc_final: 0.8710 (tt0) REVERT: F 74 ASP cc_start: 0.8967 (p0) cc_final: 0.8679 (p0) REVERT: F 76 ASP cc_start: 0.8744 (t0) cc_final: 0.8190 (t0) REVERT: F 92 GLN cc_start: 0.9015 (tt0) cc_final: 0.8540 (tt0) REVERT: F 98 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6184 (m-10) REVERT: G 51 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8552 (ttp-110) REVERT: G 81 GLN cc_start: 0.9007 (tm-30) cc_final: 0.7957 (tm-30) REVERT: G 82 ILE cc_start: 0.9476 (mt) cc_final: 0.8670 (mt) REVERT: G 85 ASP cc_start: 0.8818 (m-30) cc_final: 0.8356 (p0) REVERT: G 87 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7483 (mt-10) REVERT: H 20 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: H 31 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8570 (ptm-80) REVERT: H 71 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8129 (mtmm) REVERT: H 85 ASP cc_start: 0.8965 (m-30) cc_final: 0.8554 (p0) REVERT: H 119 GLU cc_start: 0.9021 (pm20) cc_final: 0.8795 (pm20) REVERT: I 5 ASN cc_start: 0.8820 (t0) cc_final: 0.8536 (t0) REVERT: I 51 ARG cc_start: 0.8989 (ttp-170) cc_final: 0.8541 (ttp-170) REVERT: I 52 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7741 (mt-10) REVERT: J 4 GLN cc_start: 0.8590 (mm-40) cc_final: 0.7872 (mp10) REVERT: J 60 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7944 (mtp85) REVERT: J 70 PHE cc_start: 0.8397 (t80) cc_final: 0.5712 (t80) REVERT: J 74 ASP cc_start: 0.8954 (p0) cc_final: 0.8554 (p0) REVERT: J 76 ASP cc_start: 0.8653 (t0) cc_final: 0.7454 (t0) REVERT: J 92 GLN cc_start: 0.8955 (tt0) cc_final: 0.8610 (tt0) REVERT: J 98 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: K 7 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9167 (mtmm) REVERT: K 81 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8353 (tm-30) REVERT: K 82 ILE cc_start: 0.9457 (mt) cc_final: 0.8135 (mt) REVERT: K 85 ASP cc_start: 0.8795 (m-30) cc_final: 0.7826 (p0) REVERT: K 87 GLU cc_start: 0.8853 (mt-10) cc_final: 0.7964 (mp0) REVERT: L 35 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.9153 (p0) REVERT: L 71 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8196 (mtmm) REVERT: M 27 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8632 (tp) REVERT: M 31 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8586 (mmm-85) REVERT: M 51 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8478 (ttp-170) REVERT: M 52 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8066 (mp0) REVERT: M 70 PHE cc_start: 0.8965 (t80) cc_final: 0.8718 (t80) REVERT: M 77 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9173 (tp30) REVERT: N 8 ASP cc_start: 0.8843 (m-30) cc_final: 0.8589 (m-30) REVERT: N 74 ASP cc_start: 0.8839 (p0) cc_final: 0.8583 (p0) REVERT: N 76 ASP cc_start: 0.8660 (t0) cc_final: 0.7513 (t0) REVERT: N 98 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: O 51 ARG cc_start: 0.8953 (ttp-110) cc_final: 0.8719 (ttp-110) REVERT: O 81 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8339 (pp30) REVERT: O 111 ASP cc_start: 0.8743 (p0) cc_final: 0.8529 (p0) REVERT: O 123 GLU cc_start: 0.8355 (mp0) cc_final: 0.8136 (mp0) REVERT: P 14 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6899 (t70) REVERT: P 20 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7219 (pp30) REVERT: P 35 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9144 (p0) REVERT: P 85 ASP cc_start: 0.8949 (m-30) cc_final: 0.8482 (p0) REVERT: P 92 GLN cc_start: 0.8918 (tt0) cc_final: 0.8671 (tt0) REVERT: P 119 GLU cc_start: 0.9033 (pm20) cc_final: 0.8777 (pm20) REVERT: Q 51 ARG cc_start: 0.8934 (ttp-170) cc_final: 0.8328 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7614 (mp0) REVERT: Q 60 ARG cc_start: 0.9116 (ptp-110) cc_final: 0.8826 (ptp90) REVERT: Q 71 LYS cc_start: 0.8335 (mtmm) cc_final: 0.7971 (mtmm) REVERT: Q 92 GLN cc_start: 0.8926 (tt0) cc_final: 0.8697 (tt0) REVERT: R 74 ASP cc_start: 0.8967 (p0) cc_final: 0.8700 (p0) REVERT: R 76 ASP cc_start: 0.8786 (t0) cc_final: 0.8207 (t0) REVERT: R 92 GLN cc_start: 0.9012 (tt0) cc_final: 0.8750 (tt0) REVERT: R 98 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: S 31 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7432 (ttt90) REVERT: S 81 GLN cc_start: 0.9005 (tm-30) cc_final: 0.7960 (tm-30) REVERT: S 82 ILE cc_start: 0.9476 (mt) cc_final: 0.8669 (mt) REVERT: S 85 ASP cc_start: 0.8801 (m-30) cc_final: 0.8361 (p0) REVERT: S 87 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7473 (mt-10) REVERT: T 20 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: T 31 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.8582 (ptm-80) REVERT: T 71 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8086 (mtmm) REVERT: T 98 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: T 119 GLU cc_start: 0.9006 (pm20) cc_final: 0.8787 (pm20) REVERT: U 5 ASN cc_start: 0.9095 (t0) cc_final: 0.8884 (t0) REVERT: U 51 ARG cc_start: 0.8987 (ttp-170) cc_final: 0.8523 (ttp-170) REVERT: U 52 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7207 (mp0) REVERT: U 60 ARG cc_start: 0.9031 (ptp-110) cc_final: 0.8732 (ptp90) REVERT: V 60 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7890 (mtp85) REVERT: V 70 PHE cc_start: 0.8446 (t80) cc_final: 0.5714 (t80) REVERT: V 74 ASP cc_start: 0.8955 (p0) cc_final: 0.8571 (p0) REVERT: V 76 ASP cc_start: 0.8671 (t0) cc_final: 0.7552 (t0) REVERT: V 98 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.6374 (m-10) REVERT: W 31 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8302 (mtp85) REVERT: W 81 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8266 (tm-30) REVERT: W 82 ILE cc_start: 0.9453 (mt) cc_final: 0.8148 (mt) REVERT: W 85 ASP cc_start: 0.8817 (m-30) cc_final: 0.7837 (p0) REVERT: W 87 GLU cc_start: 0.8831 (mt-10) cc_final: 0.7950 (mp0) REVERT: W 111 ASP cc_start: 0.8712 (p0) cc_final: 0.7854 (p0) REVERT: W 123 GLU cc_start: 0.8346 (mp0) cc_final: 0.7911 (mp0) REVERT: X 31 ARG cc_start: 0.9244 (ptm-80) cc_final: 0.8848 (ptm-80) REVERT: X 71 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8142 (mtmm) REVERT: X 76 ASP cc_start: 0.8642 (t0) cc_final: 0.7470 (t0) REVERT: X 85 ASP cc_start: 0.8911 (m-30) cc_final: 0.8623 (p0) REVERT: X 98 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6372 (m-10) outliers start: 264 outliers final: 195 residues processed: 941 average time/residue: 0.1561 time to fit residues: 232.3904 Evaluate side-chains 976 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 758 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 225 optimal weight: 4.9990 chunk 289 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 chunk 287 optimal weight: 0.5980 chunk 283 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.048308 restraints weight = 106370.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049965 restraints weight = 56182.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051129 restraints weight = 34552.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051907 restraints weight = 23083.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052558 restraints weight = 16831.426| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23688 Z= 0.148 Angle : 0.899 14.151 31968 Z= 0.432 Chirality : 0.052 0.239 3576 Planarity : 0.004 0.039 4248 Dihedral : 5.408 27.994 3264 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 9.34 % Allowed : 29.42 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.14), residues: 3024 helix: -0.57 (0.23), residues: 480 sheet: -1.26 (0.14), residues: 1224 loop : -3.22 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 31 TYR 0.018 0.001 TYR X 122 PHE 0.025 0.002 PHE R 91 TRP 0.003 0.001 TRP R 50 HIS 0.001 0.000 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00342 (23688) covalent geometry : angle 0.89888 (31968) hydrogen bonds : bond 0.03001 ( 816) hydrogen bonds : angle 5.38316 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 835 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 31 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8578 (mmm-85) REVERT: D 51 ARG cc_start: 0.9008 (ttp-170) cc_final: 0.8457 (ttp-170) REVERT: D 52 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8026 (mp0) REVERT: D 70 PHE cc_start: 0.8812 (t80) cc_final: 0.8484 (t80) REVERT: D 77 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9221 (tm-30) REVERT: B 4 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8109 (mp10) REVERT: B 8 ASP cc_start: 0.8786 (m-30) cc_final: 0.8563 (m-30) REVERT: B 74 ASP cc_start: 0.8841 (p0) cc_final: 0.8553 (p0) REVERT: B 76 ASP cc_start: 0.8490 (t0) cc_final: 0.7327 (t0) REVERT: B 98 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6263 (m-10) REVERT: C 85 ASP cc_start: 0.8512 (m-30) cc_final: 0.7986 (m-30) REVERT: A 76 ASP cc_start: 0.8839 (t0) cc_final: 0.7973 (t0) REVERT: A 85 ASP cc_start: 0.8928 (m-30) cc_final: 0.8652 (p0) REVERT: A 119 GLU cc_start: 0.9058 (pm20) cc_final: 0.8791 (pm20) REVERT: E 51 ARG cc_start: 0.8927 (ttp-170) cc_final: 0.8542 (ttp-170) REVERT: E 52 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7751 (mp0) REVERT: E 60 ARG cc_start: 0.9093 (ptp-110) cc_final: 0.8773 (ptp90) REVERT: E 71 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7793 (mtmm) REVERT: F 4 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7924 (mp10) REVERT: F 76 ASP cc_start: 0.8716 (t0) cc_final: 0.8171 (t0) REVERT: F 92 GLN cc_start: 0.8953 (tt0) cc_final: 0.8528 (tt0) REVERT: F 98 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.5833 (m-10) REVERT: F 117 ASN cc_start: 0.9312 (p0) cc_final: 0.9071 (p0) REVERT: G 31 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8007 (ttt90) REVERT: G 51 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8627 (ttp-110) REVERT: G 81 GLN cc_start: 0.9013 (tm-30) cc_final: 0.7804 (tm-30) REVERT: G 82 ILE cc_start: 0.9499 (mt) cc_final: 0.9060 (mt) REVERT: G 85 ASP cc_start: 0.8710 (m-30) cc_final: 0.8314 (p0) REVERT: G 87 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7596 (mt-10) REVERT: H 31 ARG cc_start: 0.9193 (ptm-80) cc_final: 0.8663 (ptm-80) REVERT: H 71 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8103 (mtmm) REVERT: H 85 ASP cc_start: 0.8939 (m-30) cc_final: 0.8385 (p0) REVERT: H 87 GLU cc_start: 0.8626 (mt-10) cc_final: 0.7810 (mt-10) REVERT: H 107 ILE cc_start: 0.9315 (tp) cc_final: 0.8920 (tt) REVERT: H 119 GLU cc_start: 0.9032 (pm20) cc_final: 0.8829 (pm20) REVERT: H 122 TYR cc_start: 0.8092 (p90) cc_final: 0.7428 (p90) REVERT: I 5 ASN cc_start: 0.8812 (t0) cc_final: 0.8514 (t0) REVERT: I 51 ARG cc_start: 0.9016 (ttp-170) cc_final: 0.8494 (ttp-170) REVERT: I 52 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7797 (mt-10) REVERT: J 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7883 (mp10) REVERT: J 60 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7983 (mtp85) REVERT: J 70 PHE cc_start: 0.8357 (t80) cc_final: 0.6002 (t80) REVERT: J 74 ASP cc_start: 0.8818 (p0) cc_final: 0.8495 (p0) REVERT: J 76 ASP cc_start: 0.8667 (t0) cc_final: 0.7436 (t0) REVERT: J 92 GLN cc_start: 0.8822 (tt0) cc_final: 0.8158 (tp-100) REVERT: J 98 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: K 81 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8324 (tm-30) REVERT: K 82 ILE cc_start: 0.9438 (mt) cc_final: 0.7875 (mt) REVERT: K 85 ASP cc_start: 0.8768 (m-30) cc_final: 0.7817 (p0) REVERT: K 87 GLU cc_start: 0.8790 (mt-10) cc_final: 0.7900 (mp0) REVERT: L 70 PHE cc_start: 0.8777 (t80) cc_final: 0.8376 (t80) REVERT: L 71 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8142 (mtmm) REVERT: L 122 TYR cc_start: 0.8167 (p90) cc_final: 0.7446 (p90) REVERT: M 27 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8533 (tp) REVERT: M 51 ARG cc_start: 0.9001 (ttp-170) cc_final: 0.8465 (ttp-170) REVERT: M 52 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8023 (mp0) REVERT: M 70 PHE cc_start: 0.8849 (t80) cc_final: 0.8557 (t80) REVERT: M 77 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9187 (tp30) REVERT: M 78 ARG cc_start: 0.9171 (tpt-90) cc_final: 0.8903 (tpt-90) REVERT: M 122 TYR cc_start: 0.8639 (p90) cc_final: 0.8320 (p90) REVERT: N 4 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8069 (mp10) REVERT: N 74 ASP cc_start: 0.8737 (p0) cc_final: 0.8440 (p0) REVERT: N 76 ASP cc_start: 0.8585 (t0) cc_final: 0.7609 (t0) REVERT: N 98 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.6192 (m-10) REVERT: N 123 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8367 (mp0) REVERT: P 85 ASP cc_start: 0.8914 (m-30) cc_final: 0.8495 (p0) REVERT: P 119 GLU cc_start: 0.9034 (pm20) cc_final: 0.8775 (pm20) REVERT: Q 51 ARG cc_start: 0.8904 (ttp-170) cc_final: 0.8486 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7739 (mp0) REVERT: Q 60 ARG cc_start: 0.9094 (ptp-110) cc_final: 0.8797 (ptp90) REVERT: Q 71 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7719 (mtmm) REVERT: R 4 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7944 (mp10) REVERT: R 76 ASP cc_start: 0.8717 (t0) cc_final: 0.8173 (t0) REVERT: R 98 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: R 117 ASN cc_start: 0.9276 (p0) cc_final: 0.9025 (p0) REVERT: S 31 ARG cc_start: 0.8242 (ttt90) cc_final: 0.7592 (ttt90) REVERT: S 52 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8150 (mm-30) REVERT: S 81 GLN cc_start: 0.9006 (tm-30) cc_final: 0.7791 (tm-30) REVERT: S 82 ILE cc_start: 0.9494 (mt) cc_final: 0.9050 (mt) REVERT: S 85 ASP cc_start: 0.8710 (m-30) cc_final: 0.8315 (p0) REVERT: S 87 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7575 (mt-10) REVERT: T 31 ARG cc_start: 0.9275 (ptm-80) cc_final: 0.8778 (ptm-80) REVERT: T 71 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8082 (mtmm) REVERT: T 98 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: T 111 ASP cc_start: 0.8227 (p0) cc_final: 0.6908 (p0) REVERT: T 122 TYR cc_start: 0.8053 (p90) cc_final: 0.7478 (p90) REVERT: U 5 ASN cc_start: 0.9043 (t0) cc_final: 0.7959 (t0) REVERT: U 7 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9114 (mtmm) REVERT: U 51 ARG cc_start: 0.8998 (ttp-170) cc_final: 0.8465 (ttp-170) REVERT: U 52 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7282 (mp0) REVERT: U 60 ARG cc_start: 0.9017 (ptp-110) cc_final: 0.8738 (ptp90) REVERT: V 60 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: V 70 PHE cc_start: 0.8412 (t80) cc_final: 0.6079 (t80) REVERT: V 74 ASP cc_start: 0.8789 (p0) cc_final: 0.8475 (p0) REVERT: V 76 ASP cc_start: 0.8646 (t0) cc_final: 0.7489 (t0) REVERT: V 92 GLN cc_start: 0.8912 (tt0) cc_final: 0.8644 (tt0) REVERT: V 98 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: W 81 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8322 (tm-30) REVERT: W 82 ILE cc_start: 0.9454 (mt) cc_final: 0.8224 (mt) REVERT: W 85 ASP cc_start: 0.8791 (m-30) cc_final: 0.7820 (p0) REVERT: W 87 GLU cc_start: 0.8762 (mt-10) cc_final: 0.7898 (mp0) REVERT: W 111 ASP cc_start: 0.8693 (p0) cc_final: 0.7868 (p0) REVERT: W 123 GLU cc_start: 0.8332 (mp0) cc_final: 0.7895 (mp0) REVERT: X 31 ARG cc_start: 0.9215 (ptm-80) cc_final: 0.8907 (ptm-80) REVERT: X 71 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8110 (mtmm) REVERT: X 76 ASP cc_start: 0.8602 (t0) cc_final: 0.7536 (t0) REVERT: X 85 ASP cc_start: 0.8894 (m-30) cc_final: 0.8594 (p0) REVERT: X 98 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.6320 (m-10) REVERT: X 122 TYR cc_start: 0.8133 (p90) cc_final: 0.7420 (p90) REVERT: X 126 MET cc_start: 0.8805 (mpp) cc_final: 0.8540 (mpp) outliers start: 222 outliers final: 161 residues processed: 955 average time/residue: 0.1531 time to fit residues: 231.0381 Evaluate side-chains 946 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 773 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN O 102 GLN P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.046424 restraints weight = 110569.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048068 restraints weight = 58512.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049209 restraints weight = 36219.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.049971 restraints weight = 24438.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050566 restraints weight = 17921.926| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23688 Z= 0.199 Angle : 0.931 12.416 31968 Z= 0.454 Chirality : 0.052 0.317 3576 Planarity : 0.004 0.064 4248 Dihedral : 5.582 28.499 3264 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 8.80 % Allowed : 31.36 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.14), residues: 3024 helix: -0.36 (0.24), residues: 456 sheet: -1.25 (0.14), residues: 1224 loop : -3.08 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 78 TYR 0.015 0.001 TYR X 122 PHE 0.024 0.002 PHE R 91 TRP 0.009 0.001 TRP R 50 HIS 0.001 0.001 HIS S 116 Details of bonding type rmsd covalent geometry : bond 0.00456 (23688) covalent geometry : angle 0.93073 (31968) hydrogen bonds : bond 0.03231 ( 816) hydrogen bonds : angle 5.52771 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 778 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 51 ARG cc_start: 0.8943 (ttp-170) cc_final: 0.8450 (ttp-170) REVERT: D 52 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7981 (mp0) REVERT: D 70 PHE cc_start: 0.8856 (t80) cc_final: 0.8562 (t80) REVERT: D 77 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9132 (tm-30) REVERT: D 87 GLU cc_start: 0.8675 (pm20) cc_final: 0.8215 (pp20) REVERT: B 8 ASP cc_start: 0.8853 (m-30) cc_final: 0.8602 (m-30) REVERT: B 74 ASP cc_start: 0.8906 (p0) cc_final: 0.8614 (p0) REVERT: B 76 ASP cc_start: 0.8569 (t0) cc_final: 0.7392 (t0) REVERT: B 98 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.6223 (m-10) REVERT: B 123 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8268 (mp0) REVERT: A 35 ASN cc_start: 0.9387 (OUTLIER) cc_final: 0.9143 (p0) REVERT: A 76 ASP cc_start: 0.8914 (t0) cc_final: 0.8246 (t0) REVERT: A 85 ASP cc_start: 0.8868 (m-30) cc_final: 0.8379 (p0) REVERT: A 119 GLU cc_start: 0.9094 (pm20) cc_final: 0.8801 (pm20) REVERT: E 51 ARG cc_start: 0.8938 (ttp-170) cc_final: 0.8514 (ttp-170) REVERT: E 52 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7961 (mt-10) REVERT: E 71 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7779 (mtmm) REVERT: E 77 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9080 (tp30) REVERT: E 92 GLN cc_start: 0.8891 (tt0) cc_final: 0.8594 (tt0) REVERT: F 74 ASP cc_start: 0.8974 (p0) cc_final: 0.8691 (p0) REVERT: F 76 ASP cc_start: 0.8753 (t0) cc_final: 0.8161 (t0) REVERT: F 92 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: F 98 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: F 123 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8241 (mp0) REVERT: G 51 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8588 (ttp-110) REVERT: G 81 GLN cc_start: 0.9045 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 82 ILE cc_start: 0.9482 (mt) cc_final: 0.9004 (mt) REVERT: G 85 ASP cc_start: 0.8771 (m-30) cc_final: 0.8302 (p0) REVERT: G 87 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7598 (mt-10) REVERT: H 20 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6895 (pp30) REVERT: H 31 ARG cc_start: 0.9200 (ptm-80) cc_final: 0.8583 (ptm-80) REVERT: H 71 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8162 (mtmm) REVERT: H 85 ASP cc_start: 0.8967 (m-30) cc_final: 0.8345 (p0) REVERT: H 87 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7812 (mt-10) REVERT: I 5 ASN cc_start: 0.8861 (t0) cc_final: 0.8548 (t0) REVERT: I 51 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8484 (ttp-170) REVERT: I 52 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7245 (mp0) REVERT: J 60 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8038 (mtp85) REVERT: J 70 PHE cc_start: 0.8370 (t80) cc_final: 0.5371 (t80) REVERT: J 74 ASP cc_start: 0.8876 (p0) cc_final: 0.8534 (p0) REVERT: J 76 ASP cc_start: 0.8721 (t0) cc_final: 0.7489 (t0) REVERT: J 92 GLN cc_start: 0.8949 (tt0) cc_final: 0.8575 (tt0) REVERT: J 98 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: K 31 ARG cc_start: 0.8566 (mmm160) cc_final: 0.7780 (tpt90) REVERT: K 81 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8246 (tm-30) REVERT: K 82 ILE cc_start: 0.9400 (mt) cc_final: 0.7835 (mt) REVERT: K 85 ASP cc_start: 0.8832 (m-30) cc_final: 0.7848 (p0) REVERT: K 87 GLU cc_start: 0.8788 (mt-10) cc_final: 0.7876 (mp0) REVERT: L 71 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8270 (mtmm) REVERT: M 27 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8629 (tp) REVERT: M 51 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8477 (ttp-170) REVERT: M 52 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7967 (mp0) REVERT: M 70 PHE cc_start: 0.8913 (t80) cc_final: 0.8644 (t80) REVERT: M 77 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9169 (tp30) REVERT: N 8 ASP cc_start: 0.8845 (m-30) cc_final: 0.8592 (m-30) REVERT: N 74 ASP cc_start: 0.8875 (p0) cc_final: 0.8610 (p0) REVERT: N 76 ASP cc_start: 0.8652 (t0) cc_final: 0.7319 (t0) REVERT: N 98 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.6567 (m-10) REVERT: N 123 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8514 (mp0) REVERT: O 76 ASP cc_start: 0.9054 (t0) cc_final: 0.8731 (t0) REVERT: P 85 ASP cc_start: 0.8974 (m-30) cc_final: 0.8197 (p0) REVERT: P 87 GLU cc_start: 0.8901 (pt0) cc_final: 0.7877 (pm20) REVERT: P 119 GLU cc_start: 0.9087 (pm20) cc_final: 0.8808 (pm20) REVERT: P 123 GLU cc_start: 0.8639 (tt0) cc_final: 0.8378 (tp30) REVERT: Q 51 ARG cc_start: 0.8933 (ttp-170) cc_final: 0.8504 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7943 (mt-10) REVERT: Q 71 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7830 (mtmm) REVERT: Q 77 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9073 (tp30) REVERT: Q 92 GLN cc_start: 0.8893 (tt0) cc_final: 0.8590 (tt0) REVERT: R 74 ASP cc_start: 0.8979 (p0) cc_final: 0.8702 (p0) REVERT: R 76 ASP cc_start: 0.8784 (t0) cc_final: 0.8207 (t0) REVERT: R 98 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: S 52 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8183 (mm-30) REVERT: S 81 GLN cc_start: 0.9030 (tm-30) cc_final: 0.7748 (tm-30) REVERT: S 82 ILE cc_start: 0.9484 (mt) cc_final: 0.8873 (mt) REVERT: S 85 ASP cc_start: 0.8769 (m-30) cc_final: 0.8301 (p0) REVERT: S 87 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7569 (mt-10) REVERT: T 20 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6990 (pp30) REVERT: T 31 ARG cc_start: 0.9225 (ptm-80) cc_final: 0.8757 (ptm-80) REVERT: T 71 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8168 (mtmm) REVERT: T 98 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: U 5 ASN cc_start: 0.9031 (t0) cc_final: 0.8172 (t0) REVERT: U 7 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9031 (mtmm) REVERT: U 51 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8537 (ttp-170) REVERT: U 52 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7269 (mp0) REVERT: V 60 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8013 (mtp85) REVERT: V 70 PHE cc_start: 0.8421 (t80) cc_final: 0.5540 (t80) REVERT: V 74 ASP cc_start: 0.8874 (p0) cc_final: 0.8527 (p0) REVERT: V 76 ASP cc_start: 0.8682 (t0) cc_final: 0.7456 (t0) REVERT: V 92 GLN cc_start: 0.9027 (tt0) cc_final: 0.8327 (tp-100) REVERT: V 98 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: W 31 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8033 (mmm160) REVERT: W 81 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8259 (tm-30) REVERT: W 82 ILE cc_start: 0.9420 (mt) cc_final: 0.8142 (mt) REVERT: W 85 ASP cc_start: 0.8835 (m-30) cc_final: 0.7853 (p0) REVERT: W 87 GLU cc_start: 0.8729 (mt-10) cc_final: 0.7863 (mp0) REVERT: W 92 GLN cc_start: 0.9112 (tt0) cc_final: 0.8753 (tt0) REVERT: W 123 GLU cc_start: 0.8357 (mp0) cc_final: 0.8044 (mp0) REVERT: X 31 ARG cc_start: 0.9229 (ptm-80) cc_final: 0.8826 (ptm-80) REVERT: X 71 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8155 (mtmm) REVERT: X 76 ASP cc_start: 0.8651 (t0) cc_final: 0.7599 (t0) REVERT: X 85 ASP cc_start: 0.8912 (m-30) cc_final: 0.8556 (p0) REVERT: X 98 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: X 126 MET cc_start: 0.8877 (mpp) cc_final: 0.8624 (mpp) outliers start: 209 outliers final: 178 residues processed: 898 average time/residue: 0.1512 time to fit residues: 215.5695 Evaluate side-chains 952 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 757 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 132 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 20 GLN Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN U 92 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.044833 restraints weight = 111888.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046440 restraints weight = 59242.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047569 restraints weight = 36389.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048278 restraints weight = 24306.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048847 restraints weight = 17989.156| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23688 Z= 0.245 Angle : 0.955 13.976 31968 Z= 0.470 Chirality : 0.053 0.254 3576 Planarity : 0.004 0.047 4248 Dihedral : 5.767 28.457 3264 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 8.71 % Allowed : 31.14 % Favored : 60.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.14), residues: 3024 helix: -0.50 (0.23), residues: 456 sheet: -1.11 (0.14), residues: 1200 loop : -3.04 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 78 TYR 0.015 0.001 TYR A 122 PHE 0.027 0.002 PHE S 91 TRP 0.011 0.001 TRP R 50 HIS 0.002 0.001 HIS K 116 Details of bonding type rmsd covalent geometry : bond 0.00550 (23688) covalent geometry : angle 0.95512 (31968) hydrogen bonds : bond 0.03281 ( 816) hydrogen bonds : angle 5.69161 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 755 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8709 (tp) REVERT: D 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8397 (ttp-170) REVERT: D 52 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7972 (mp0) REVERT: D 70 PHE cc_start: 0.8922 (t80) cc_final: 0.8691 (t80) REVERT: D 87 GLU cc_start: 0.8677 (pm20) cc_final: 0.8241 (pp20) REVERT: D 126 MET cc_start: 0.8809 (ptm) cc_final: 0.8581 (ptm) REVERT: B 8 ASP cc_start: 0.8863 (m-30) cc_final: 0.8608 (m-30) REVERT: B 74 ASP cc_start: 0.8993 (p0) cc_final: 0.8722 (p0) REVERT: B 76 ASP cc_start: 0.8545 (t0) cc_final: 0.7106 (t0) REVERT: B 98 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: B 123 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8299 (mp0) REVERT: A 35 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9210 (p0) REVERT: A 76 ASP cc_start: 0.8931 (t0) cc_final: 0.8126 (t0) REVERT: A 85 ASP cc_start: 0.9004 (m-30) cc_final: 0.8219 (p0) REVERT: A 87 GLU cc_start: 0.8778 (pt0) cc_final: 0.7389 (pm20) REVERT: A 119 GLU cc_start: 0.9110 (pm20) cc_final: 0.8835 (pm20) REVERT: E 7 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8807 (mtmm) REVERT: E 51 ARG cc_start: 0.8918 (ttp-170) cc_final: 0.8383 (ttp-170) REVERT: E 52 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7881 (mt-10) REVERT: E 71 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7921 (mtmm) REVERT: F 31 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8471 (ttm-80) REVERT: F 70 PHE cc_start: 0.8626 (t80) cc_final: 0.5988 (t80) REVERT: F 74 ASP cc_start: 0.8994 (p0) cc_final: 0.8710 (p0) REVERT: F 76 ASP cc_start: 0.8717 (t0) cc_final: 0.7869 (t0) REVERT: F 92 GLN cc_start: 0.8979 (tt0) cc_final: 0.8523 (tt0) REVERT: F 98 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: F 123 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8260 (mp0) REVERT: G 51 ARG cc_start: 0.8887 (ttp80) cc_final: 0.8583 (ttp-110) REVERT: G 81 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 82 ILE cc_start: 0.9471 (mt) cc_final: 0.9216 (mt) REVERT: G 85 ASP cc_start: 0.8838 (m-30) cc_final: 0.8586 (p0) REVERT: G 123 GLU cc_start: 0.8322 (mp0) cc_final: 0.8088 (mp0) REVERT: H 20 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: H 31 ARG cc_start: 0.9279 (ptm-80) cc_final: 0.8613 (ptm-80) REVERT: H 71 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8196 (mtmm) REVERT: H 85 ASP cc_start: 0.9039 (m-30) cc_final: 0.8468 (p0) REVERT: H 87 GLU cc_start: 0.8773 (mt-10) cc_final: 0.7926 (mt-10) REVERT: H 122 TYR cc_start: 0.8348 (p90) cc_final: 0.7984 (p90) REVERT: I 5 ASN cc_start: 0.8872 (t0) cc_final: 0.8515 (t0) REVERT: I 51 ARG cc_start: 0.8942 (ttp-170) cc_final: 0.8504 (ttp-170) REVERT: I 52 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7123 (mp0) REVERT: J 4 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7868 (mp10) REVERT: J 8 ASP cc_start: 0.8843 (m-30) cc_final: 0.8625 (m-30) REVERT: J 60 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8030 (mtp85) REVERT: J 70 PHE cc_start: 0.8517 (t80) cc_final: 0.5903 (t80) REVERT: J 74 ASP cc_start: 0.8895 (p0) cc_final: 0.8522 (p0) REVERT: J 76 ASP cc_start: 0.8775 (t0) cc_final: 0.7486 (t0) REVERT: J 98 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: J 122 TYR cc_start: 0.8696 (p90) cc_final: 0.8420 (p90) REVERT: K 7 LYS cc_start: 0.9417 (mtmt) cc_final: 0.9122 (mtmm) REVERT: K 31 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8260 (mmm160) REVERT: K 81 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8322 (tm-30) REVERT: K 82 ILE cc_start: 0.9393 (mt) cc_final: 0.8043 (mt) REVERT: K 85 ASP cc_start: 0.8865 (m-30) cc_final: 0.7819 (p0) REVERT: K 87 GLU cc_start: 0.8800 (mt-10) cc_final: 0.7653 (mp0) REVERT: L 71 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8257 (mtmm) REVERT: M 27 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8663 (tp) REVERT: M 31 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8540 (tpp80) REVERT: M 51 ARG cc_start: 0.8972 (ttp-170) cc_final: 0.8409 (ttp-170) REVERT: M 52 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7966 (mp0) REVERT: M 70 PHE cc_start: 0.8979 (t80) cc_final: 0.8771 (t80) REVERT: M 77 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9132 (tp30) REVERT: N 8 ASP cc_start: 0.8854 (m-30) cc_final: 0.8611 (m-30) REVERT: N 74 ASP cc_start: 0.8922 (p0) cc_final: 0.8658 (p0) REVERT: N 76 ASP cc_start: 0.8736 (t0) cc_final: 0.7401 (t0) REVERT: N 98 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: N 123 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8518 (mp0) REVERT: O 76 ASP cc_start: 0.9038 (t0) cc_final: 0.8724 (t0) REVERT: O 85 ASP cc_start: 0.8812 (m-30) cc_final: 0.8256 (m-30) REVERT: O 111 ASP cc_start: 0.8664 (p0) cc_final: 0.8371 (p0) REVERT: P 85 ASP cc_start: 0.9017 (m-30) cc_final: 0.8442 (p0) REVERT: P 119 GLU cc_start: 0.9108 (pm20) cc_final: 0.8835 (pm20) REVERT: P 123 GLU cc_start: 0.8618 (tt0) cc_final: 0.8375 (tp30) REVERT: Q 7 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8813 (mtmm) REVERT: Q 51 ARG cc_start: 0.8931 (ttp-170) cc_final: 0.8365 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7893 (mt-10) REVERT: Q 71 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7919 (mtmm) REVERT: R 74 ASP cc_start: 0.9011 (p0) cc_final: 0.8726 (p0) REVERT: R 76 ASP cc_start: 0.8755 (t0) cc_final: 0.8035 (t0) REVERT: R 98 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.6279 (m-10) REVERT: R 123 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8211 (mp0) REVERT: S 31 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.7431 (ttt90) REVERT: S 52 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8228 (mm-30) REVERT: S 81 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8096 (tm-30) REVERT: S 82 ILE cc_start: 0.9493 (mt) cc_final: 0.9146 (mt) REVERT: S 85 ASP cc_start: 0.8827 (m-30) cc_final: 0.8588 (p0) REVERT: S 123 GLU cc_start: 0.8314 (mp0) cc_final: 0.7899 (mp0) REVERT: T 20 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7323 (pp30) REVERT: T 31 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.8661 (ptm-80) REVERT: T 71 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8240 (mtmm) REVERT: T 98 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: U 5 ASN cc_start: 0.9073 (t0) cc_final: 0.8606 (t0) REVERT: U 51 ARG cc_start: 0.8949 (ttp-170) cc_final: 0.8480 (ttp-170) REVERT: U 52 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7153 (mp0) REVERT: V 8 ASP cc_start: 0.8914 (m-30) cc_final: 0.8676 (m-30) REVERT: V 60 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8024 (mtp85) REVERT: V 70 PHE cc_start: 0.8533 (t80) cc_final: 0.5901 (t80) REVERT: V 74 ASP cc_start: 0.8902 (p0) cc_final: 0.8521 (p0) REVERT: V 76 ASP cc_start: 0.8731 (t0) cc_final: 0.7466 (t0) REVERT: V 98 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6397 (m-10) REVERT: V 122 TYR cc_start: 0.8698 (p90) cc_final: 0.8415 (p90) REVERT: W 7 LYS cc_start: 0.9417 (mtmt) cc_final: 0.9118 (mtmm) REVERT: W 81 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8338 (tm-30) REVERT: W 82 ILE cc_start: 0.9414 (mt) cc_final: 0.8107 (mt) REVERT: W 85 ASP cc_start: 0.8856 (m-30) cc_final: 0.7814 (p0) REVERT: W 87 GLU cc_start: 0.8748 (mt-10) cc_final: 0.7691 (mp0) REVERT: W 111 ASP cc_start: 0.8728 (p0) cc_final: 0.8137 (p0) REVERT: W 123 GLU cc_start: 0.8469 (mp0) cc_final: 0.7977 (mp0) REVERT: X 71 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8174 (mtmm) REVERT: X 76 ASP cc_start: 0.8675 (t0) cc_final: 0.7640 (t0) REVERT: X 85 ASP cc_start: 0.9035 (m-30) cc_final: 0.8556 (p0) REVERT: X 98 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: X 126 MET cc_start: 0.8810 (mpp) cc_final: 0.8579 (mpp) outliers start: 207 outliers final: 165 residues processed: 885 average time/residue: 0.1481 time to fit residues: 207.9554 Evaluate side-chains 916 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 734 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 20 GLN Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 189 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.046038 restraints weight = 109565.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047650 restraints weight = 58000.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048818 restraints weight = 35881.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049546 restraints weight = 24007.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050131 restraints weight = 17693.284| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23688 Z= 0.193 Angle : 0.966 15.808 31968 Z= 0.469 Chirality : 0.053 0.310 3576 Planarity : 0.004 0.047 4248 Dihedral : 5.731 26.838 3264 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 8.29 % Allowed : 31.65 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.14), residues: 3024 helix: -0.53 (0.23), residues: 456 sheet: -1.27 (0.14), residues: 1224 loop : -2.93 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 78 TYR 0.017 0.001 TYR X 122 PHE 0.024 0.002 PHE R 91 TRP 0.006 0.001 TRP R 50 HIS 0.002 0.001 HIS S 116 Details of bonding type rmsd covalent geometry : bond 0.00451 (23688) covalent geometry : angle 0.96649 (31968) hydrogen bonds : bond 0.03258 ( 816) hydrogen bonds : angle 5.70242 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.06 seconds wall clock time: 78 minutes 48.02 seconds (4728.02 seconds total)