Starting phenix.real_space_refine on Thu Jun 19 22:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tea_10478/06_2025/6tea_10478.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tea_10478/06_2025/6tea_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_10478/06_2025/6tea_10478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tea_10478/06_2025/6tea_10478.map" model { file = "/net/cci-nas-00/data/ceres_data/6tea_10478/06_2025/6tea_10478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tea_10478/06_2025/6tea_10478.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 5.36, per 1000 atoms: 0.23 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: 5.27 Conformation dependent library (CDL) restraints added in 3.0 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: 2.75 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: 7.33 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain '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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 41.660 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.002 TRP U 50 HIS 0.004 0.002 HIS L 116 PHE 0.022 0.004 PHE J 98 TYR 0.008 0.002 TYR B 122 ARG 0.008 0.002 ARG R 60 Details of bonding type rmsd hydrogen bonds : bond 0.27868 ( 816) hydrogen bonds : angle 9.94326 ( 2232) covalent geometry : bond 0.00835 (23688) covalent geometry : angle 1.33684 (31968) *********************** 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 : 2.407 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: D 5 ASN cc_start: 0.8345 (t0) cc_final: 0.8124 (t0) REVERT: D 24 ILE cc_start: 0.9006 (pt) cc_final: 0.8751 (tp) 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: 0.8919 (tp) REVERT: D 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.8825 (m-30) REVERT: D 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8916 (tt) REVERT: B 4 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8052 (mp10) REVERT: B 8 ASP cc_start: 0.8894 (m-30) cc_final: 0.8502 (m-30) REVERT: B 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8934 (mp) REVERT: B 70 PHE cc_start: 0.8534 (t80) cc_final: 0.8330 (t80) REVERT: B 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9156 (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: 0.7907 (p0) REVERT: A 60 ARG cc_start: 0.8918 (ptp-110) cc_final: 0.8520 (mtm-85) REVERT: A 91 PHE cc_start: 0.8798 (m-80) cc_final: 0.8415 (m-80) REVERT: A 92 GLN cc_start: 0.9203 (tt0) cc_final: 0.8853 (tt0) REVERT: A 106 MET cc_start: 0.8571 (ptp) cc_final: 0.8303 (ptp) REVERT: A 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9190 (tp) REVERT: A 124 LEU cc_start: 0.9162 (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: 0.7954 (ttp-170) REVERT: E 53 LEU cc_start: 0.8520 (mm) cc_final: 0.8288 (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: 0.8850 (m-30) REVERT: E 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8884 (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: 0.8202 (t80) REVERT: F 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8877 (t0) REVERT: F 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8724 (mm-30) REVERT: G 35 ASN cc_start: 0.9207 (m-40) cc_final: 0.8929 (m-40) REVERT: G 70 PHE cc_start: 0.8726 (t80) cc_final: 0.8496 (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: 0.8614 (tm-30) REVERT: G 82 ILE cc_start: 0.9555 (mt) cc_final: 0.9113 (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: 0.8665 (mt-10) REVERT: G 111 ASP cc_start: 0.8379 (p0) cc_final: 0.8106 (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: 0.8983 (t80) cc_final: 0.8704 (t80) REVERT: H 82 ILE cc_start: 0.9817 (mt) cc_final: 0.9616 (mm) REVERT: H 91 PHE cc_start: 0.8823 (m-80) cc_final: 0.8568 (m-80) REVERT: H 92 GLN cc_start: 0.9130 (tt0) cc_final: 0.8855 (tt0) REVERT: H 124 LEU cc_start: 0.9022 (tt) cc_final: 0.8281 (tt) REVERT: I 22 GLU cc_start: 0.7843 (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: 0.8043 (ttp-110) REVERT: I 77 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9124 (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: 0.8896 (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: 0.8227 (mp10) REVERT: J 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8544 (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: 0.7925 (t80) REVERT: J 76 ASP cc_start: 0.9134 (t0) cc_final: 0.8887 (t0) REVERT: J 112 TYR cc_start: 0.9385 (m-80) cc_final: 0.9157 (m-80) REVERT: K 70 PHE cc_start: 0.8833 (t80) cc_final: 0.8467 (t80) REVERT: K 76 ASP cc_start: 0.9200 (t0) cc_final: 0.8986 (t0) REVERT: K 81 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8487 (pp30) REVERT: K 82 ILE cc_start: 0.9580 (mt) cc_final: 0.9222 (mt) REVERT: K 85 ASP cc_start: 0.8989 (m-30) cc_final: 0.8755 (m-30) REVERT: K 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8781 (mt-10) REVERT: L 60 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8604 (mtm-85) REVERT: L 70 PHE cc_start: 0.9057 (t80) cc_final: 0.8665 (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: 0.8979 (tt0) REVERT: L 112 TYR cc_start: 0.9084 (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: 0.8130 (t0) REVERT: M 24 ILE cc_start: 0.9003 (pt) cc_final: 0.8747 (tp) REVERT: M 77 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9096 (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: 0.8825 (m-30) REVERT: M 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8916 (tt) REVERT: N 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8049 (mp10) REVERT: N 8 ASP cc_start: 0.8896 (m-30) cc_final: 0.8504 (m-30) REVERT: N 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8942 (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: 0.9181 (m-80) REVERT: O 35 ASN cc_start: 0.9191 (m-40) cc_final: 0.8954 (m-40) REVERT: O 76 ASP cc_start: 0.9153 (t0) cc_final: 0.8911 (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: 0.8523 (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: 0.8578 (ptp) cc_final: 0.8305 (ptp) REVERT: P 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9191 (tp) REVERT: P 124 LEU cc_start: 0.9164 (tt) cc_final: 0.8555 (tt) REVERT: Q 24 ILE cc_start: 0.9123 (pt) cc_final: 0.8856 (tp) REVERT: Q 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7953 (ttp-170) REVERT: Q 53 LEU cc_start: 0.8519 (mm) cc_final: 0.8285 (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: 0.8852 (m-30) REVERT: Q 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8882 (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: 0.8549 (mpp80) REVERT: R 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8197 (t80) REVERT: R 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8876 (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: 0.8933 (m-40) REVERT: S 70 PHE cc_start: 0.8728 (t80) cc_final: 0.8497 (t80) REVERT: S 76 ASP cc_start: 0.9188 (t0) cc_final: 0.8970 (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: 0.8954 (pt) REVERT: T 60 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8582 (mtm-85) REVERT: T 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8706 (t80) REVERT: T 91 PHE cc_start: 0.8826 (m-80) cc_final: 0.8563 (m-80) REVERT: T 92 GLN cc_start: 0.9125 (tt0) cc_final: 0.8846 (tt0) REVERT: T 124 LEU cc_start: 0.9019 (tt) cc_final: 0.8279 (tt) REVERT: U 22 GLU cc_start: 0.7839 (mp0) cc_final: 0.7598 (mp0) REVERT: U 24 ILE cc_start: 0.8953 (pt) cc_final: 0.8730 (tp) REVERT: U 51 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: U 77 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9122 (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: 0.8894 (m-30) REVERT: U 124 LEU cc_start: 0.9206 (tt) cc_final: 0.8844 (tp) REVERT: V 4 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8353 (mm-40) REVERT: V 8 ASP cc_start: 0.8922 (m-30) cc_final: 0.8531 (m-30) REVERT: V 35 ASN cc_start: 0.9013 (m-40) cc_final: 0.8801 (m-40) REVERT: V 60 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8675 (mpp80) REVERT: V 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7922 (t80) REVERT: V 76 ASP cc_start: 0.9133 (t0) cc_final: 0.8885 (t0) REVERT: V 112 TYR cc_start: 0.9387 (m-80) cc_final: 0.9151 (m-80) REVERT: W 70 PHE cc_start: 0.8834 (t80) cc_final: 0.8465 (t80) REVERT: W 76 ASP cc_start: 0.9196 (t0) cc_final: 0.8983 (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: 0.9219 (mt) REVERT: W 85 ASP cc_start: 0.8985 (m-30) cc_final: 0.8753 (m-30) REVERT: W 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8778 (mt-10) REVERT: X 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8603 (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: 0.8272 (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: 0.8282 (tt) outliers start: 0 outliers final: 0 residues processed: 1414 average time/residue: 0.3744 time to fit residues: 796.7732 Evaluate side-chains 877 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 877 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051213 restraints weight = 104420.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052930 restraints weight = 56543.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054141 restraints weight = 35091.742| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4067 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= 0.167 Angle : 0.840 9.503 31968 Z= 0.428 Chirality : 0.054 0.258 3576 Planarity : 0.005 0.038 4248 Dihedral : 6.545 23.730 3264 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 8.00 % Allowed : 21.30 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.12), residues: 3024 helix: -2.49 (0.19), residues: 480 sheet: -2.14 (0.14), residues: 1104 loop : -3.53 (0.12), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 50 HIS 0.008 0.002 HIS I 116 PHE 0.031 0.002 PHE E 70 TYR 0.009 0.001 TYR A 122 ARG 0.007 0.001 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 816) hydrogen bonds : angle 7.10864 ( 2232) covalent geometry : bond 0.00367 (23688) covalent geometry : angle 0.84014 (31968) *********************** 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 1193 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1003 time to evaluate : 2.377 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: D 24 ILE cc_start: 0.8856 (pt) cc_final: 0.8648 (tp) REVERT: D 30 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8303 (t) REVERT: D 51 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.7470 (ttp-170) REVERT: D 52 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8219 (mp0) REVERT: D 70 PHE cc_start: 0.8780 (t80) cc_final: 0.8298 (t80) REVERT: D 78 ARG cc_start: 0.9282 (tpp80) cc_final: 0.8984 (tpt-90) REVERT: D 82 ILE cc_start: 0.9413 (mt) cc_final: 0.8966 (mm) REVERT: B 8 ASP cc_start: 0.8756 (m-30) cc_final: 0.8551 (m-30) REVERT: B 31 ARG cc_start: 0.8110 (ttt90) cc_final: 0.7780 (ttm-80) REVERT: B 74 ASP cc_start: 0.8850 (p0) cc_final: 0.8556 (p0) REVERT: B 111 ASP cc_start: 0.8848 (p0) cc_final: 0.8632 (p0) REVERT: B 117 ASN cc_start: 0.9381 (p0) cc_final: 0.9122 (p0) REVERT: B 124 LEU cc_start: 0.9633 (tt) cc_final: 0.8826 (tt) REVERT: C 52 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 53 LEU cc_start: 0.9426 (mm) cc_final: 0.9191 (mt) REVERT: A 60 ARG cc_start: 0.8865 (ptp-110) cc_final: 0.8623 (mpp80) REVERT: A 76 ASP cc_start: 0.8994 (t0) cc_final: 0.8615 (t0) REVERT: A 87 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8555 (mp0) REVERT: A 92 GLN cc_start: 0.9073 (tt0) cc_final: 0.8747 (tt0) REVERT: E 5 ASN cc_start: 0.8541 (t0) cc_final: 0.7916 (t0) REVERT: E 24 ILE cc_start: 0.9039 (pt) cc_final: 0.8767 (tp) REVERT: E 31 ARG cc_start: 0.8645 (mtp-110) cc_final: 0.8341 (tpp80) REVERT: E 51 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.7877 (ttp-170) REVERT: E 52 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7764 (mp0) REVERT: E 78 ARG cc_start: 0.9329 (tpp80) cc_final: 0.9093 (mmm160) REVERT: E 82 ILE cc_start: 0.9411 (mt) cc_final: 0.8891 (mm) REVERT: F 20 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6719 (pp30) REVERT: F 70 PHE cc_start: 0.8430 (t80) cc_final: 0.7434 (t80) REVERT: F 76 ASP cc_start: 0.8956 (t0) cc_final: 0.8346 (t0) REVERT: F 90 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8515 (mm-30) REVERT: F 111 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8471 (p0) REVERT: F 117 ASN cc_start: 0.9381 (p0) cc_final: 0.9093 (p0) REVERT: G 31 ARG cc_start: 0.8486 (ttt90) cc_final: 0.7516 (ttt90) REVERT: G 78 ARG cc_start: 0.9331 (tpp80) cc_final: 0.8730 (tpp80) REVERT: G 81 GLN cc_start: 0.8935 (tm-30) cc_final: 0.7240 (tm-30) REVERT: G 82 ILE cc_start: 0.9538 (mt) cc_final: 0.8923 (mm) REVERT: G 85 ASP cc_start: 0.8775 (m-30) cc_final: 0.8235 (p0) REVERT: G 87 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7672 (mt-10) REVERT: G 106 MET cc_start: 0.7471 (pmm) cc_final: 0.7025 (pmm) REVERT: H 14 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6675 (t70) REVERT: H 20 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7359 (pp30) REVERT: H 76 ASP cc_start: 0.8932 (t0) cc_final: 0.8689 (t0) REVERT: I 27 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8456 (tp) REVERT: I 51 ARG cc_start: 0.8771 (ttp-110) cc_final: 0.7988 (ttp-110) REVERT: I 52 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7736 (mt-10) REVERT: I 70 PHE cc_start: 0.8938 (t80) cc_final: 0.8488 (t80) REVERT: I 82 ILE cc_start: 0.9464 (mt) cc_final: 0.8798 (mm) REVERT: I 85 ASP cc_start: 0.9252 (m-30) cc_final: 0.9043 (m-30) REVERT: I 94 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9312 (tp) REVERT: J 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8282 (mp10) REVERT: J 20 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6729 (pp30) REVERT: J 52 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8328 (mt-10) REVERT: J 70 PHE cc_start: 0.8289 (t80) cc_final: 0.8036 (t80) REVERT: J 92 GLN cc_start: 0.8922 (tt0) cc_final: 0.8715 (tt0) REVERT: J 111 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (p0) REVERT: J 117 ASN cc_start: 0.9419 (p0) cc_final: 0.9178 (p0) REVERT: K 47 GLN cc_start: 0.8343 (mp10) cc_final: 0.8054 (mp10) REVERT: K 51 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8434 (ttp-110) REVERT: K 82 ILE cc_start: 0.9462 (mt) cc_final: 0.9004 (mm) REVERT: K 85 ASP cc_start: 0.8897 (m-30) cc_final: 0.8282 (p0) REVERT: K 87 GLU cc_start: 0.8807 (mt-10) cc_final: 0.7650 (mt-10) REVERT: K 126 MET cc_start: 0.8128 (mtp) cc_final: 0.7914 (mtm) REVERT: L 20 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (pp30) REVERT: M 24 ILE cc_start: 0.8850 (pt) cc_final: 0.8644 (tp) REVERT: M 30 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8312 (t) REVERT: M 51 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.7473 (ttp-170) REVERT: M 52 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8226 (mp0) REVERT: M 70 PHE cc_start: 0.8781 (t80) cc_final: 0.8306 (t80) REVERT: M 78 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8982 (tpt-90) REVERT: M 82 ILE cc_start: 0.9416 (mt) cc_final: 0.8963 (mm) REVERT: N 8 ASP cc_start: 0.8753 (m-30) cc_final: 0.8548 (m-30) REVERT: N 31 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7788 (ttm-80) REVERT: N 74 ASP cc_start: 0.8873 (p0) cc_final: 0.8584 (p0) REVERT: N 111 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8587 (p0) REVERT: N 117 ASN cc_start: 0.9374 (p0) cc_final: 0.9113 (p0) REVERT: N 124 LEU cc_start: 0.9634 (tt) cc_final: 0.8853 (tt) REVERT: O 52 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8481 (mt-10) REVERT: O 53 LEU cc_start: 0.9430 (mm) cc_final: 0.9190 (mt) REVERT: P 60 ARG cc_start: 0.8868 (ptp-110) cc_final: 0.8655 (mpp80) REVERT: P 76 ASP cc_start: 0.8991 (t0) cc_final: 0.8614 (t0) REVERT: P 92 GLN cc_start: 0.9080 (tt0) cc_final: 0.8832 (tt0) REVERT: P 124 LEU cc_start: 0.8957 (tt) cc_final: 0.8714 (tt) REVERT: Q 5 ASN cc_start: 0.8539 (t0) cc_final: 0.7917 (t0) REVERT: Q 24 ILE cc_start: 0.9039 (pt) cc_final: 0.8766 (tp) REVERT: Q 31 ARG cc_start: 0.8651 (mtp-110) cc_final: 0.8340 (tpp80) REVERT: Q 51 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.7879 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7770 (mp0) REVERT: Q 78 ARG cc_start: 0.9333 (tpp80) cc_final: 0.9092 (mmm160) REVERT: Q 82 ILE cc_start: 0.9410 (mt) cc_final: 0.8892 (mm) REVERT: R 20 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6702 (pp30) REVERT: R 70 PHE cc_start: 0.8424 (t80) cc_final: 0.7430 (t80) REVERT: R 76 ASP cc_start: 0.8959 (t0) cc_final: 0.8352 (t0) REVERT: R 90 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8516 (mm-30) REVERT: R 111 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8468 (p0) REVERT: R 117 ASN cc_start: 0.9393 (p0) cc_final: 0.9106 (p0) REVERT: S 31 ARG cc_start: 0.8486 (ttt90) cc_final: 0.7523 (ttt90) REVERT: S 78 ARG cc_start: 0.9333 (tpp80) cc_final: 0.8735 (tpp80) REVERT: S 81 GLN cc_start: 0.8934 (tm-30) cc_final: 0.7235 (tm-30) REVERT: S 82 ILE cc_start: 0.9538 (mt) cc_final: 0.8928 (mm) REVERT: S 85 ASP cc_start: 0.8808 (m-30) cc_final: 0.8272 (p0) REVERT: S 87 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7670 (mt-10) REVERT: S 106 MET cc_start: 0.7450 (pmm) cc_final: 0.7014 (pmm) REVERT: T 14 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6673 (t70) REVERT: T 20 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7347 (pp30) REVERT: T 76 ASP cc_start: 0.8888 (t0) cc_final: 0.8627 (t0) REVERT: U 27 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8434 (tp) REVERT: U 31 ARG cc_start: 0.8995 (ttp80) cc_final: 0.8764 (tpp80) REVERT: U 51 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.7991 (ttp-110) REVERT: U 52 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7722 (mt-10) REVERT: U 70 PHE cc_start: 0.8949 (t80) cc_final: 0.8498 (t80) REVERT: U 82 ILE cc_start: 0.9462 (mt) cc_final: 0.8800 (mm) REVERT: U 85 ASP cc_start: 0.9254 (m-30) cc_final: 0.9042 (m-30) REVERT: U 94 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9309 (tp) REVERT: V 20 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6729 (pp30) REVERT: V 31 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8403 (ttt90) REVERT: V 52 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8332 (mt-10) REVERT: V 70 PHE cc_start: 0.8266 (t80) cc_final: 0.8008 (t80) REVERT: V 92 GLN cc_start: 0.8918 (tt0) cc_final: 0.8714 (tt0) REVERT: V 111 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8491 (p0) REVERT: V 117 ASN cc_start: 0.9423 (p0) cc_final: 0.9186 (p0) REVERT: W 47 GLN cc_start: 0.8323 (mp10) cc_final: 0.8031 (mp10) REVERT: W 51 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8449 (ttp-110) REVERT: W 82 ILE cc_start: 0.9460 (mt) cc_final: 0.9001 (mm) REVERT: W 85 ASP cc_start: 0.8895 (m-30) cc_final: 0.8278 (p0) REVERT: W 87 GLU cc_start: 0.8826 (mt-10) cc_final: 0.7651 (mt-10) REVERT: W 126 MET cc_start: 0.8109 (mtp) cc_final: 0.7900 (mtm) REVERT: X 20 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6715 (pp30) outliers start: 190 outliers final: 89 residues processed: 1071 average time/residue: 0.3705 time to fit residues: 613.1815 Evaluate side-chains 933 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 823 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain B residue 9 LEU 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 24 ILE Chi-restraints excluded: chain C residue 41 VAL 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 121 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 88 VAL 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 111 ASP 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 20 GLN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 27 LEU 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 J residue 111 ASP 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 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 9 LEU 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 24 ILE Chi-restraints excluded: chain O residue 41 VAL 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 121 SER Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 88 VAL 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 111 ASP 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 20 GLN Chi-restraints excluded: chain T residue 35 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain U residue 27 LEU 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 V residue 111 ASP Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE 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 95 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 308 optimal weight: 0.3980 chunk 155 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN B 20 GLN ** 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 E 20 GLN F 81 GLN F 92 GLN 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 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** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN N 20 GLN ** 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 Q 20 GLN R 92 GLN 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 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** ** X 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.047599 restraints weight = 109155.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.049271 restraints weight = 58350.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050406 restraints weight = 35482.627| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23688 Z= 0.216 Angle : 0.841 10.173 31968 Z= 0.416 Chirality : 0.053 0.289 3576 Planarity : 0.004 0.033 4248 Dihedral : 6.090 21.740 3264 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 10.14 % Allowed : 22.90 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.13), residues: 3024 helix: -1.96 (0.20), residues: 480 sheet: -1.80 (0.14), residues: 1104 loop : -3.42 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 50 HIS 0.003 0.001 HIS T 116 PHE 0.024 0.002 PHE N 91 TYR 0.014 0.002 TYR L 122 ARG 0.007 0.001 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 816) hydrogen bonds : angle 6.35674 ( 2232) covalent geometry : bond 0.00470 (23688) covalent geometry : angle 0.84124 (31968) *********************** 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 1129 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 888 time to evaluate : 2.410 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: D 5 ASN cc_start: 0.8795 (t0) cc_final: 0.8340 (t0) REVERT: D 7 LYS cc_start: 0.9289 (mtpt) cc_final: 0.9032 (mtmt) REVERT: D 51 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.7641 (ttp-170) REVERT: D 52 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8121 (mp0) REVERT: D 70 PHE cc_start: 0.8914 (t80) cc_final: 0.8471 (t80) REVERT: D 111 ASP cc_start: 0.8289 (p0) cc_final: 0.7987 (p0) REVERT: B 74 ASP cc_start: 0.8872 (p0) cc_final: 0.8564 (p0) REVERT: B 76 ASP cc_start: 0.8655 (t0) cc_final: 0.7684 (t0) REVERT: B 98 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: B 111 ASP cc_start: 0.8858 (p0) cc_final: 0.8641 (p0) REVERT: C 31 ARG cc_start: 0.8477 (ttt90) cc_final: 0.7763 (ttm-80) REVERT: C 81 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8356 (pp30) REVERT: C 126 MET cc_start: 0.8338 (mtm) cc_final: 0.8128 (mtm) REVERT: A 70 PHE cc_start: 0.8718 (t80) cc_final: 0.7403 (t80) REVERT: A 76 ASP cc_start: 0.9035 (t0) cc_final: 0.8199 (t0) REVERT: A 85 ASP cc_start: 0.8934 (m-30) cc_final: 0.8325 (p0) REVERT: A 92 GLN cc_start: 0.9119 (tt0) cc_final: 0.8801 (tt0) REVERT: A 98 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: A 107 ILE cc_start: 0.9631 (tp) cc_final: 0.9316 (tt) REVERT: E 5 ASN cc_start: 0.8837 (t0) cc_final: 0.7973 (t0) REVERT: E 7 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8957 (mtmm) REVERT: E 24 ILE cc_start: 0.9031 (pt) cc_final: 0.8658 (tp) REVERT: E 51 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8146 (ttp-170) REVERT: E 70 PHE cc_start: 0.9141 (t80) cc_final: 0.8732 (t80) REVERT: E 78 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9066 (mmm160) REVERT: F 76 ASP cc_start: 0.8983 (t0) cc_final: 0.8430 (t0) REVERT: F 98 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: F 111 ASP cc_start: 0.8800 (p0) cc_final: 0.8569 (p0) REVERT: G 31 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7851 (ttt90) REVERT: G 78 ARG cc_start: 0.9297 (tpp80) cc_final: 0.8585 (tpp80) REVERT: G 81 GLN cc_start: 0.9017 (tm-30) cc_final: 0.7165 (tm-30) REVERT: G 82 ILE cc_start: 0.9510 (mt) cc_final: 0.8858 (mm) REVERT: G 85 ASP cc_start: 0.8920 (m-30) cc_final: 0.8344 (p0) REVERT: G 87 GLU cc_start: 0.8702 (mt-10) cc_final: 0.7547 (mt-10) REVERT: H 76 ASP cc_start: 0.8979 (t0) cc_final: 0.7792 (t0) REVERT: H 85 ASP cc_start: 0.8935 (m-30) cc_final: 0.8583 (p0) REVERT: H 87 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7809 (mt-10) REVERT: H 92 GLN cc_start: 0.8919 (tt0) cc_final: 0.8380 (tt0) REVERT: H 100 ILE cc_start: 0.9391 (pt) cc_final: 0.9076 (pt) REVERT: I 27 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8620 (tp) REVERT: I 51 ARG cc_start: 0.8912 (ttp-170) cc_final: 0.8051 (ttp-170) REVERT: I 52 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7634 (mt-10) REVERT: I 70 PHE cc_start: 0.9105 (t80) cc_final: 0.8671 (t80) REVERT: I 124 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.8758 (tt) REVERT: J 4 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8447 (mm-40) REVERT: J 31 ARG cc_start: 0.8564 (ttt90) cc_final: 0.8315 (ttm-80) REVERT: J 52 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8397 (mt-10) REVERT: J 76 ASP cc_start: 0.8694 (t0) cc_final: 0.7708 (t0) REVERT: J 98 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.6917 (m-10) REVERT: J 106 MET cc_start: 0.7871 (ptm) cc_final: 0.7447 (ttp) REVERT: J 107 ILE cc_start: 0.9671 (tp) cc_final: 0.9038 (tp) REVERT: J 117 ASN cc_start: 0.9488 (p0) cc_final: 0.9274 (p0) REVERT: J 126 MET cc_start: 0.8089 (mtp) cc_final: 0.7813 (mmm) REVERT: K 7 LYS cc_start: 0.9457 (mtmt) cc_final: 0.9157 (mtmm) REVERT: K 51 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8643 (ttp-170) REVERT: K 81 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8585 (pp30) REVERT: K 85 ASP cc_start: 0.8824 (m-30) cc_final: 0.7915 (p0) REVERT: K 87 GLU cc_start: 0.8842 (mt-10) cc_final: 0.7988 (mp0) REVERT: K 123 GLU cc_start: 0.8311 (mp0) cc_final: 0.7785 (mp0) REVERT: L 92 GLN cc_start: 0.8961 (tt0) cc_final: 0.8531 (tt0) REVERT: L 98 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: L 100 ILE cc_start: 0.9376 (pt) cc_final: 0.9090 (pt) REVERT: L 126 MET cc_start: 0.8727 (mpp) cc_final: 0.8504 (mpp) REVERT: M 5 ASN cc_start: 0.8787 (t0) cc_final: 0.8335 (t0) REVERT: M 7 LYS cc_start: 0.9281 (mtpt) cc_final: 0.9029 (mtmt) REVERT: M 51 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.7649 (ttp-170) REVERT: M 52 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8123 (mp0) REVERT: M 70 PHE cc_start: 0.8917 (t80) cc_final: 0.8471 (t80) REVERT: N 74 ASP cc_start: 0.8858 (p0) cc_final: 0.8551 (p0) REVERT: N 76 ASP cc_start: 0.8656 (t0) cc_final: 0.7690 (t0) REVERT: N 98 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.6517 (m-10) REVERT: N 111 ASP cc_start: 0.8856 (p0) cc_final: 0.8651 (p0) REVERT: O 31 ARG cc_start: 0.8489 (ttt90) cc_final: 0.7775 (ttm-80) REVERT: O 81 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8372 (pp30) REVERT: P 70 PHE cc_start: 0.8717 (t80) cc_final: 0.8281 (t80) REVERT: P 76 ASP cc_start: 0.9054 (t0) cc_final: 0.8746 (t0) REVERT: P 92 GLN cc_start: 0.9114 (tt0) cc_final: 0.8843 (tt0) REVERT: P 98 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: P 124 LEU cc_start: 0.9298 (tt) cc_final: 0.8659 (tt) REVERT: Q 5 ASN cc_start: 0.8817 (t0) cc_final: 0.7963 (t0) REVERT: Q 7 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8947 (mtmm) REVERT: Q 24 ILE cc_start: 0.9033 (pt) cc_final: 0.8669 (tp) REVERT: Q 51 ARG cc_start: 0.8854 (ttp-170) cc_final: 0.8150 (ttp-170) REVERT: Q 70 PHE cc_start: 0.9143 (t80) cc_final: 0.8742 (t80) REVERT: Q 78 ARG cc_start: 0.9440 (tpp80) cc_final: 0.9066 (mmm160) REVERT: R 76 ASP cc_start: 0.8980 (t0) cc_final: 0.8427 (t0) REVERT: R 98 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: R 111 ASP cc_start: 0.8795 (p0) cc_final: 0.8562 (p0) REVERT: S 31 ARG cc_start: 0.8153 (ttt90) cc_final: 0.7848 (ttt90) REVERT: S 78 ARG cc_start: 0.9297 (tpp80) cc_final: 0.8585 (tpp80) REVERT: S 81 GLN cc_start: 0.9016 (tm-30) cc_final: 0.7157 (tm-30) REVERT: S 82 ILE cc_start: 0.9513 (mt) cc_final: 0.8863 (mm) REVERT: S 85 ASP cc_start: 0.8908 (m-30) cc_final: 0.8335 (p0) REVERT: S 87 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7545 (mt-10) REVERT: T 76 ASP cc_start: 0.8987 (t0) cc_final: 0.7794 (t0) REVERT: T 85 ASP cc_start: 0.8903 (m-30) cc_final: 0.8413 (p0) REVERT: T 92 GLN cc_start: 0.8934 (tt0) cc_final: 0.8388 (tt0) REVERT: T 100 ILE cc_start: 0.9391 (pt) cc_final: 0.9075 (pt) REVERT: U 27 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (tp) REVERT: U 31 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8669 (ttp80) REVERT: U 51 ARG cc_start: 0.8924 (ttp-170) cc_final: 0.8083 (ttp-170) REVERT: U 52 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7633 (mt-10) REVERT: U 70 PHE cc_start: 0.9105 (t80) cc_final: 0.8665 (t80) REVERT: U 124 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.8762 (tt) REVERT: V 52 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8382 (mt-10) REVERT: V 76 ASP cc_start: 0.8695 (t0) cc_final: 0.7718 (t0) REVERT: V 98 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: V 117 ASN cc_start: 0.9489 (p0) cc_final: 0.9274 (p0) REVERT: W 7 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9152 (mtmm) REVERT: W 51 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8623 (ttp-170) REVERT: W 81 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8582 (pp30) REVERT: W 85 ASP cc_start: 0.8814 (m-30) cc_final: 0.7913 (p0) REVERT: W 87 GLU cc_start: 0.8827 (mt-10) cc_final: 0.7978 (mp0) REVERT: W 123 GLU cc_start: 0.8312 (mp0) cc_final: 0.7789 (mp0) REVERT: X 92 GLN cc_start: 0.8981 (tt0) cc_final: 0.8543 (tt0) REVERT: X 98 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: X 100 ILE cc_start: 0.9385 (pt) cc_final: 0.9111 (pt) REVERT: X 126 MET cc_start: 0.8756 (mpp) cc_final: 0.8525 (mpp) outliers start: 241 outliers final: 144 residues processed: 991 average time/residue: 0.3948 time to fit residues: 612.3792 Evaluate side-chains 963 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 799 time to evaluate : 3.025 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 30 THR 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 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER 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 20 GLN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 39 VAL 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 E residue 7 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL 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 39 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 27 LEU 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 20 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 42 THR 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 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 41 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE 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 81 GLN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE 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 44 LEU 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 88 VAL Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 20 GLN Chi-restraints excluded: chain N residue 30 THR 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 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 126 MET 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 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 39 VAL 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 Q residue 7 LYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL 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 39 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE 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 20 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 42 THR 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 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 41 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE 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 81 GLN 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 44 LEU 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 128 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 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 E 20 GLN E 92 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 HIS ** 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN J 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN N 20 GLN ** 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 Q 20 GLN Q 92 GLN R 20 GLN R 81 GLN ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 HIS ** 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN V 20 GLN V 81 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 GLN W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043999 restraints weight = 114509.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.045554 restraints weight = 60338.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.046649 restraints weight = 37159.831| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 23688 Z= 0.325 Angle : 0.889 9.957 31968 Z= 0.452 Chirality : 0.054 0.272 3576 Planarity : 0.005 0.038 4248 Dihedral : 6.224 25.215 3264 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 13.26 % Allowed : 22.69 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.13), residues: 3024 helix: -1.52 (0.21), residues: 456 sheet: -1.62 (0.13), residues: 1224 loop : -3.67 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 50 HIS 0.004 0.001 HIS G 116 PHE 0.034 0.002 PHE N 91 TYR 0.020 0.001 TYR E 122 ARG 0.008 0.001 ARG O 31 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 816) hydrogen bonds : angle 6.16731 ( 2232) covalent geometry : bond 0.00686 (23688) covalent geometry : angle 0.88922 (31968) *********************** 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 1124 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 315 poor density : 809 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8797 (t0) cc_final: 0.7953 (t0) REVERT: D 7 LYS cc_start: 0.9327 (mtpt) cc_final: 0.8953 (mtmm) REVERT: D 27 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8650 (tp) REVERT: D 51 ARG cc_start: 0.8889 (ttp-170) cc_final: 0.8005 (ttp-170) REVERT: D 52 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7944 (mp0) REVERT: D 70 PHE cc_start: 0.9138 (t80) cc_final: 0.8522 (t80) REVERT: D 76 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: D 78 ARG cc_start: 0.9343 (tpp80) cc_final: 0.9118 (tpt-90) REVERT: D 87 GLU cc_start: 0.8924 (pm20) cc_final: 0.8409 (pp20) REVERT: B 8 ASP cc_start: 0.9009 (m-30) cc_final: 0.8777 (m-30) REVERT: B 74 ASP cc_start: 0.9122 (p0) cc_final: 0.8867 (p0) REVERT: B 76 ASP cc_start: 0.8659 (t0) cc_final: 0.7422 (t0) REVERT: B 98 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: B 123 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8612 (mt-10) REVERT: C 20 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: C 98 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: A 20 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7631 (pp30) REVERT: A 70 PHE cc_start: 0.8696 (t80) cc_final: 0.7623 (t80) REVERT: A 71 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8327 (mtmm) REVERT: A 76 ASP cc_start: 0.9081 (t0) cc_final: 0.8332 (t0) REVERT: A 85 ASP cc_start: 0.9052 (m-30) cc_final: 0.8432 (p0) REVERT: A 92 GLN cc_start: 0.9125 (tt0) cc_final: 0.8723 (tt0) REVERT: A 98 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: A 107 ILE cc_start: 0.9609 (tp) cc_final: 0.9371 (tp) REVERT: E 5 ASN cc_start: 0.8835 (t0) cc_final: 0.8029 (t0) REVERT: E 7 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9025 (mtmm) REVERT: E 52 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: E 70 PHE cc_start: 0.9126 (t80) cc_final: 0.8869 (t80) REVERT: E 78 ARG cc_start: 0.9466 (tpp80) cc_final: 0.9145 (tpt-90) REVERT: E 87 GLU cc_start: 0.8981 (pm20) cc_final: 0.8680 (pp20) REVERT: E 98 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: F 74 ASP cc_start: 0.9195 (p0) cc_final: 0.8950 (p0) REVERT: F 76 ASP cc_start: 0.9052 (t0) cc_final: 0.8521 (t0) REVERT: F 98 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: G 70 PHE cc_start: 0.8698 (t80) cc_final: 0.6768 (t80) REVERT: G 71 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8479 (mtmm) REVERT: G 76 ASP cc_start: 0.9183 (t0) cc_final: 0.8907 (t0) REVERT: G 81 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8082 (tm-30) REVERT: G 82 ILE cc_start: 0.9470 (mt) cc_final: 0.9037 (mt) REVERT: G 85 ASP cc_start: 0.9010 (m-30) cc_final: 0.8429 (p0) REVERT: G 87 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7125 (mt-10) REVERT: H 31 ARG cc_start: 0.9204 (ptm-80) cc_final: 0.8593 (ptm-80) REVERT: H 71 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8086 (mtmm) REVERT: H 76 ASP cc_start: 0.9123 (t0) cc_final: 0.8746 (t0) REVERT: H 85 ASP cc_start: 0.9085 (m-30) cc_final: 0.8675 (p0) REVERT: H 92 GLN cc_start: 0.9029 (tt0) cc_final: 0.8809 (tt0) REVERT: H 98 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: I 27 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8795 (tp) REVERT: I 51 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8115 (ttp-170) REVERT: I 52 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7493 (mt-10) REVERT: I 92 GLN cc_start: 0.8584 (tt0) cc_final: 0.8365 (tt0) REVERT: I 98 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8555 (m-80) REVERT: J 4 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8520 (mm-40) REVERT: J 8 ASP cc_start: 0.8943 (m-30) cc_final: 0.8658 (m-30) REVERT: J 20 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7221 (pp30) REVERT: J 52 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8444 (mt-10) REVERT: J 70 PHE cc_start: 0.8575 (t80) cc_final: 0.7734 (t80) REVERT: J 74 ASP cc_start: 0.9108 (p0) cc_final: 0.8887 (p0) REVERT: J 76 ASP cc_start: 0.8778 (t0) cc_final: 0.8053 (t0) REVERT: J 98 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.6958 (m-10) REVERT: K 7 LYS cc_start: 0.9494 (mtmt) cc_final: 0.9214 (mtmm) REVERT: K 76 ASP cc_start: 0.9272 (t0) cc_final: 0.8968 (t0) REVERT: K 81 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8907 (pp30) REVERT: K 85 ASP cc_start: 0.8927 (m-30) cc_final: 0.8440 (p0) REVERT: K 98 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: K 123 GLU cc_start: 0.8419 (mp0) cc_final: 0.8063 (mp0) REVERT: L 35 ASN cc_start: 0.9472 (OUTLIER) cc_final: 0.9151 (p0) REVERT: L 76 ASP cc_start: 0.8804 (t0) cc_final: 0.7908 (t0) REVERT: L 92 GLN cc_start: 0.9019 (tt0) cc_final: 0.8662 (tt0) REVERT: L 98 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: M 5 ASN cc_start: 0.8784 (t0) cc_final: 0.7948 (t0) REVERT: M 7 LYS cc_start: 0.9320 (mtpt) cc_final: 0.8946 (mtmm) REVERT: M 27 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8706 (tp) REVERT: M 51 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.7995 (ttp-170) REVERT: M 52 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7945 (mp0) REVERT: M 70 PHE cc_start: 0.9136 (t80) cc_final: 0.8529 (t80) REVERT: M 76 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: M 78 ARG cc_start: 0.9331 (tpp80) cc_final: 0.9107 (tpt-90) REVERT: M 87 GLU cc_start: 0.8935 (pm20) cc_final: 0.8307 (pp20) REVERT: N 8 ASP cc_start: 0.9013 (m-30) cc_final: 0.8779 (m-30) REVERT: N 74 ASP cc_start: 0.9112 (p0) cc_final: 0.8857 (p0) REVERT: N 76 ASP cc_start: 0.8664 (t0) cc_final: 0.7470 (t0) REVERT: N 98 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: O 20 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: O 70 PHE cc_start: 0.8472 (t80) cc_final: 0.6070 (t80) REVERT: O 76 ASP cc_start: 0.9263 (t0) cc_final: 0.8616 (t0) REVERT: O 98 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: P 20 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7576 (pp30) REVERT: P 70 PHE cc_start: 0.8711 (t80) cc_final: 0.8391 (t80) REVERT: P 71 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8324 (mtmm) REVERT: P 76 ASP cc_start: 0.9069 (t0) cc_final: 0.8799 (t0) REVERT: P 85 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8412 (p0) REVERT: P 92 GLN cc_start: 0.9118 (tt0) cc_final: 0.8834 (tt0) REVERT: P 98 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: P 100 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9197 (pt) REVERT: Q 5 ASN cc_start: 0.8835 (t0) cc_final: 0.8038 (t0) REVERT: Q 7 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9024 (mtmm) REVERT: Q 52 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: Q 70 PHE cc_start: 0.9133 (t80) cc_final: 0.8886 (t80) REVERT: Q 78 ARG cc_start: 0.9470 (tpp80) cc_final: 0.9144 (tpt-90) REVERT: Q 87 GLU cc_start: 0.8984 (pm20) cc_final: 0.8686 (pp20) REVERT: Q 98 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: R 20 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: R 74 ASP cc_start: 0.9193 (p0) cc_final: 0.8923 (p0) REVERT: R 76 ASP cc_start: 0.9040 (t0) cc_final: 0.8519 (t0) REVERT: R 98 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: S 70 PHE cc_start: 0.8707 (t80) cc_final: 0.6774 (t80) REVERT: S 71 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8574 (mtmm) REVERT: S 76 ASP cc_start: 0.9207 (t0) cc_final: 0.8938 (t0) REVERT: S 81 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8074 (tm-30) REVERT: S 82 ILE cc_start: 0.9466 (mt) cc_final: 0.9029 (mt) REVERT: S 85 ASP cc_start: 0.9010 (m-30) cc_final: 0.8422 (p0) REVERT: S 87 GLU cc_start: 0.8712 (mt-10) cc_final: 0.7120 (mt-10) REVERT: T 31 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8595 (ptm-80) REVERT: T 71 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8092 (mtmm) REVERT: T 76 ASP cc_start: 0.9119 (t0) cc_final: 0.8757 (t0) REVERT: T 85 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8581 (p0) REVERT: T 92 GLN cc_start: 0.9038 (tt0) cc_final: 0.8813 (tt0) REVERT: T 98 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: U 27 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8766 (tp) REVERT: U 51 ARG cc_start: 0.8963 (ttp-170) cc_final: 0.8124 (ttp-170) REVERT: U 52 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7448 (mt-10) REVERT: U 92 GLN cc_start: 0.8607 (tt0) cc_final: 0.8374 (tt0) REVERT: U 98 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: V 8 ASP cc_start: 0.8934 (m-30) cc_final: 0.8685 (m-30) REVERT: V 20 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7232 (pp30) REVERT: V 52 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8454 (mt-10) REVERT: V 59 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8385 (p) REVERT: V 70 PHE cc_start: 0.8574 (t80) cc_final: 0.7736 (t80) REVERT: V 74 ASP cc_start: 0.9113 (p0) cc_final: 0.8891 (p0) REVERT: V 76 ASP cc_start: 0.8785 (t0) cc_final: 0.8056 (t0) REVERT: V 98 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: W 7 LYS cc_start: 0.9486 (mtmt) cc_final: 0.9205 (mtmm) REVERT: W 76 ASP cc_start: 0.9265 (t0) cc_final: 0.8958 (t0) REVERT: W 81 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8911 (pp30) REVERT: W 85 ASP cc_start: 0.8916 (m-30) cc_final: 0.8438 (p0) REVERT: W 123 GLU cc_start: 0.8423 (mp0) cc_final: 0.8071 (mp0) REVERT: X 35 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9164 (p0) REVERT: X 76 ASP cc_start: 0.8822 (t0) cc_final: 0.7911 (t0) REVERT: X 92 GLN cc_start: 0.9055 (tt0) cc_final: 0.8688 (tt0) REVERT: X 98 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6435 (m-10) outliers start: 315 outliers final: 184 residues processed: 986 average time/residue: 0.3258 time to fit residues: 509.3684 Evaluate side-chains 975 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 747 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 D residue 126 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 GLN 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 94 ILE 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 B residue 132 LEU 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 30 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE 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 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE 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 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 98 PHE 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 35 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 LEU 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 108 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP 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 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 42 THR 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 J residue 9 LEU Chi-restraints excluded: chain J residue 20 GLN 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 44 LEU Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 94 ILE 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 81 GLN 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 30 THR 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 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 32 ILE 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 126 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 20 GLN 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 94 ILE 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 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 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE 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 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 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 100 ILE 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 32 ILE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 GLN Chi-restraints excluded: chain Q residue 98 PHE 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 20 GLN Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 44 LEU 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 24 ILE 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 110 ILE Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 14 ASP 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 85 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 42 THR 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 20 GLN 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 44 LEU Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 94 ILE 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 81 GLN 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 11 ILE Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 32 ILE 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 209 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN E 20 GLN F 102 GLN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN Q 20 GLN R 102 GLN ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 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 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 = 0.3034 r_free = 0.3034 target = 0.054502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.046884 restraints weight = 110459.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048515 restraints weight = 58231.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049669 restraints weight = 35913.656| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23688 Z= 0.168 Angle : 0.854 10.938 31968 Z= 0.419 Chirality : 0.053 0.235 3576 Planarity : 0.004 0.035 4248 Dihedral : 5.833 24.528 3264 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 11.03 % Allowed : 24.41 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.13), residues: 3024 helix: -1.21 (0.22), residues: 456 sheet: -1.46 (0.13), residues: 1224 loop : -3.47 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 50 HIS 0.001 0.001 HIS G 116 PHE 0.023 0.002 PHE F 91 TYR 0.016 0.001 TYR E 122 ARG 0.008 0.001 ARG O 31 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 816) hydrogen bonds : angle 5.87716 ( 2232) covalent geometry : bond 0.00374 (23688) covalent geometry : angle 0.85444 (31968) *********************** 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 1112 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 850 time to evaluate : 2.609 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: D 5 ASN cc_start: 0.8810 (t0) cc_final: 0.7960 (t0) REVERT: D 7 LYS cc_start: 0.9292 (mtpt) cc_final: 0.8886 (mtmm) REVERT: D 27 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8733 (tp) REVERT: D 51 ARG cc_start: 0.8853 (ttp-170) cc_final: 0.7956 (ttp-170) REVERT: D 52 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7953 (mp0) REVERT: D 70 PHE cc_start: 0.9027 (t80) cc_final: 0.8647 (t80) REVERT: D 85 ASP cc_start: 0.8898 (m-30) cc_final: 0.8691 (m-30) REVERT: D 87 GLU cc_start: 0.8953 (pm20) cc_final: 0.8354 (pp20) REVERT: B 8 ASP cc_start: 0.8942 (m-30) cc_final: 0.8694 (m-30) REVERT: B 74 ASP cc_start: 0.9063 (p0) cc_final: 0.8787 (p0) REVERT: B 76 ASP cc_start: 0.8514 (t0) cc_final: 0.7334 (t0) REVERT: B 92 GLN cc_start: 0.9035 (tt0) cc_final: 0.8534 (tt0) REVERT: B 98 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: B 111 ASP cc_start: 0.8884 (p0) cc_final: 0.8640 (p0) REVERT: B 123 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8465 (mt-10) REVERT: C 81 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8205 (pp30) REVERT: C 87 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8506 (mt-10) REVERT: C 92 GLN cc_start: 0.9112 (tt0) cc_final: 0.8862 (tt0) REVERT: C 98 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7069 (m-10) REVERT: A 20 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7280 (pp30) REVERT: A 70 PHE cc_start: 0.8631 (t80) cc_final: 0.7236 (t80) REVERT: A 71 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8218 (mtmm) REVERT: A 76 ASP cc_start: 0.8984 (t0) cc_final: 0.8332 (t0) REVERT: A 85 ASP cc_start: 0.9035 (m-30) cc_final: 0.8458 (p0) REVERT: A 98 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: E 5 ASN cc_start: 0.8818 (t0) cc_final: 0.7966 (t0) REVERT: E 7 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8963 (mtmm) REVERT: E 52 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: E 70 PHE cc_start: 0.8984 (t80) cc_final: 0.8412 (t80) REVERT: F 74 ASP cc_start: 0.9120 (p0) cc_final: 0.8881 (p0) REVERT: F 76 ASP cc_start: 0.8975 (t0) cc_final: 0.8427 (t0) REVERT: F 98 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: F 111 ASP cc_start: 0.8769 (p0) cc_final: 0.8527 (p0) REVERT: G 70 PHE cc_start: 0.8504 (t80) cc_final: 0.6323 (t80) REVERT: G 71 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8354 (mtmm) REVERT: G 76 ASP cc_start: 0.9182 (t0) cc_final: 0.8865 (t0) REVERT: G 81 GLN cc_start: 0.9107 (tm-30) cc_final: 0.7874 (tm-30) REVERT: G 82 ILE cc_start: 0.9488 (mt) cc_final: 0.8286 (mt) REVERT: G 85 ASP cc_start: 0.8914 (m-30) cc_final: 0.8046 (p0) REVERT: G 87 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7684 (mp0) REVERT: H 31 ARG cc_start: 0.9213 (ptm-80) cc_final: 0.8557 (ptm-80) REVERT: H 76 ASP cc_start: 0.9024 (t0) cc_final: 0.8771 (t0) REVERT: H 85 ASP cc_start: 0.9065 (m-30) cc_final: 0.8552 (p0) REVERT: H 92 GLN cc_start: 0.9152 (tt0) cc_final: 0.8940 (tt0) REVERT: H 98 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7699 (m-10) REVERT: I 51 ARG cc_start: 0.9001 (ttp-170) cc_final: 0.8555 (ttp-170) REVERT: J 4 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8409 (mm-40) REVERT: J 70 PHE cc_start: 0.8370 (t80) cc_final: 0.5308 (t80) REVERT: J 74 ASP cc_start: 0.9054 (p0) cc_final: 0.8785 (p0) REVERT: J 76 ASP cc_start: 0.8677 (t0) cc_final: 0.7569 (t0) REVERT: J 98 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: J 126 MET cc_start: 0.8201 (mtp) cc_final: 0.7959 (mmm) REVERT: K 81 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8734 (pp30) REVERT: K 82 ILE cc_start: 0.9422 (mt) cc_final: 0.8469 (mt) REVERT: K 85 ASP cc_start: 0.8874 (m-30) cc_final: 0.7905 (p0) REVERT: K 87 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8031 (mp0) REVERT: K 98 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: K 123 GLU cc_start: 0.8419 (mp0) cc_final: 0.8023 (mp0) REVERT: L 35 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9082 (p0) REVERT: L 71 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8301 (mtmm) REVERT: L 76 ASP cc_start: 0.8856 (t0) cc_final: 0.7774 (t0) REVERT: L 98 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: M 5 ASN cc_start: 0.8785 (t0) cc_final: 0.7945 (t0) REVERT: M 7 LYS cc_start: 0.9285 (mtpt) cc_final: 0.8879 (mtmm) REVERT: M 27 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8722 (tp) REVERT: M 51 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.7950 (ttp-170) REVERT: M 52 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7960 (mp0) REVERT: M 60 ARG cc_start: 0.9111 (ptp-110) cc_final: 0.8838 (ptp90) REVERT: M 70 PHE cc_start: 0.9040 (t80) cc_final: 0.8662 (t80) REVERT: M 85 ASP cc_start: 0.8913 (m-30) cc_final: 0.8708 (m-30) REVERT: M 87 GLU cc_start: 0.8963 (pm20) cc_final: 0.8328 (pp20) REVERT: M 98 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: N 8 ASP cc_start: 0.8930 (m-30) cc_final: 0.8683 (m-30) REVERT: N 74 ASP cc_start: 0.9049 (p0) cc_final: 0.8767 (p0) REVERT: N 76 ASP cc_start: 0.8491 (t0) cc_final: 0.7311 (t0) REVERT: N 92 GLN cc_start: 0.9009 (tt0) cc_final: 0.8507 (tt0) REVERT: N 98 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.6446 (m-10) REVERT: O 70 PHE cc_start: 0.8157 (t80) cc_final: 0.5840 (t80) REVERT: O 76 ASP cc_start: 0.9214 (t0) cc_final: 0.8801 (t0) REVERT: O 81 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: O 87 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8594 (mt-10) REVERT: O 98 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: P 20 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7279 (pp30) REVERT: P 70 PHE cc_start: 0.8642 (t80) cc_final: 0.8407 (t80) REVERT: P 71 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8297 (mtmm) REVERT: P 85 ASP cc_start: 0.9028 (m-30) cc_final: 0.8179 (p0) REVERT: P 87 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: P 92 GLN cc_start: 0.9115 (tt0) cc_final: 0.8885 (tp-100) REVERT: P 98 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: Q 5 ASN cc_start: 0.8811 (t0) cc_final: 0.7966 (t0) REVERT: Q 7 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8961 (mtmm) REVERT: Q 52 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: Q 70 PHE cc_start: 0.9014 (t80) cc_final: 0.8411 (t80) REVERT: R 74 ASP cc_start: 0.9098 (p0) cc_final: 0.8863 (p0) REVERT: R 76 ASP cc_start: 0.9021 (t0) cc_final: 0.8440 (t0) REVERT: R 98 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.5842 (m-10) REVERT: R 111 ASP cc_start: 0.8768 (p0) cc_final: 0.8515 (p0) REVERT: S 70 PHE cc_start: 0.8515 (t80) cc_final: 0.6338 (t80) REVERT: S 71 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8367 (mtmm) REVERT: S 76 ASP cc_start: 0.9187 (t0) cc_final: 0.8884 (t0) REVERT: S 81 GLN cc_start: 0.9105 (tm-30) cc_final: 0.7869 (tm-30) REVERT: S 82 ILE cc_start: 0.9489 (mt) cc_final: 0.8280 (mt) REVERT: S 85 ASP cc_start: 0.8919 (m-30) cc_final: 0.8048 (p0) REVERT: S 87 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7676 (mp0) REVERT: T 31 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8549 (ptm-80) REVERT: T 76 ASP cc_start: 0.9016 (t0) cc_final: 0.8774 (t0) REVERT: T 85 ASP cc_start: 0.9037 (m-30) cc_final: 0.8444 (p0) REVERT: T 92 GLN cc_start: 0.9173 (tt0) cc_final: 0.8945 (tt0) REVERT: T 98 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: U 51 ARG cc_start: 0.8999 (ttp-170) cc_final: 0.8314 (ttp-170) REVERT: V 70 PHE cc_start: 0.8364 (t80) cc_final: 0.5347 (t80) REVERT: V 74 ASP cc_start: 0.9066 (p0) cc_final: 0.8801 (p0) REVERT: V 76 ASP cc_start: 0.8687 (t0) cc_final: 0.7578 (t0) REVERT: V 98 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6542 (m-10) REVERT: V 126 MET cc_start: 0.8194 (mtp) cc_final: 0.7921 (mmm) REVERT: W 81 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8738 (pp30) REVERT: W 82 ILE cc_start: 0.9425 (mt) cc_final: 0.8434 (mt) REVERT: W 85 ASP cc_start: 0.8861 (m-30) cc_final: 0.7906 (p0) REVERT: W 87 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8019 (mp0) REVERT: W 123 GLU cc_start: 0.8426 (mp0) cc_final: 0.8133 (mp0) REVERT: X 35 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9147 (p0) REVERT: X 71 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8299 (mtmm) REVERT: X 76 ASP cc_start: 0.8858 (t0) cc_final: 0.7740 (t0) REVERT: X 98 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.6303 (m-10) outliers start: 262 outliers final: 160 residues processed: 1010 average time/residue: 0.3302 time to fit residues: 519.1352 Evaluate side-chains 956 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 765 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 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 20 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 87 GLU 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 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE 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 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 7 LYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 52 GLU 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 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 G residue 9 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP 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 98 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 42 THR 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 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 87 GLU 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 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 81 GLN 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 20 GLN 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 98 PHE 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 32 ILE Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 98 PHE 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 20 GLN Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 87 GLU Chi-restraints excluded: chain N residue 94 ILE 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 110 ILE 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 63 SER Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE 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 14 ASP Chi-restraints excluded: chain P residue 20 GLN 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 87 GLU 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 Q residue 7 LYS Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 52 GLU 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 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 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 14 ASP 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 U residue 42 THR 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 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 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 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 81 GLN 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 32 ILE Chi-restraints excluded: chain X residue 35 ASN 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 93 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** 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 E 20 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN J 20 GLN J 92 GLN K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 102 GLN M 20 GLN N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** 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 Q 20 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN V 20 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 102 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.043285 restraints weight = 115573.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.044791 restraints weight = 61533.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.045873 restraints weight = 37797.031| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 23688 Z= 0.360 Angle : 0.929 9.956 31968 Z= 0.474 Chirality : 0.053 0.234 3576 Planarity : 0.005 0.044 4248 Dihedral : 6.191 27.421 3264 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 12.58 % Allowed : 25.25 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.14), residues: 3024 helix: -1.16 (0.22), residues: 456 sheet: -1.33 (0.13), residues: 1224 loop : -3.51 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 50 HIS 0.004 0.001 HIS M 116 PHE 0.029 0.003 PHE D 98 TYR 0.015 0.002 TYR E 122 ARG 0.010 0.001 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 816) hydrogen bonds : angle 5.97330 ( 2232) covalent geometry : bond 0.00774 (23688) covalent geometry : angle 0.92908 (31968) *********************** 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: 299 poor density : 749 time to evaluate : 2.747 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 5 ASN cc_start: 0.8827 (t0) cc_final: 0.8511 (t0) REVERT: D 27 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8810 (tt) REVERT: D 51 ARG cc_start: 0.8788 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: D 70 PHE cc_start: 0.9172 (t80) cc_final: 0.8944 (t80) REVERT: D 77 GLU cc_start: 0.9528 (tm-30) cc_final: 0.9152 (tp30) REVERT: B 8 ASP cc_start: 0.8969 (m-30) cc_final: 0.8706 (m-30) REVERT: B 74 ASP cc_start: 0.9127 (p0) cc_final: 0.8875 (p0) REVERT: B 76 ASP cc_start: 0.8619 (t0) cc_final: 0.7126 (t0) REVERT: B 98 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: C 98 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: A 76 ASP cc_start: 0.9087 (t0) cc_final: 0.8310 (t0) REVERT: A 85 ASP cc_start: 0.9138 (m-30) cc_final: 0.8497 (p0) REVERT: A 98 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: A 123 GLU cc_start: 0.8779 (tt0) cc_final: 0.8424 (tp30) REVERT: E 5 ASN cc_start: 0.8829 (t0) cc_final: 0.8146 (t0) REVERT: E 7 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9039 (mtmm) REVERT: E 52 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: F 8 ASP cc_start: 0.8894 (m-30) cc_final: 0.8612 (m-30) REVERT: F 74 ASP cc_start: 0.9240 (p0) cc_final: 0.8987 (p0) REVERT: F 76 ASP cc_start: 0.9054 (t0) cc_final: 0.8515 (t0) REVERT: F 92 GLN cc_start: 0.9080 (tt0) cc_final: 0.8674 (tt0) REVERT: F 98 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: G 70 PHE cc_start: 0.8703 (t80) cc_final: 0.6999 (t80) REVERT: G 71 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8739 (mtmm) REVERT: G 76 ASP cc_start: 0.9293 (t0) cc_final: 0.8930 (t0) REVERT: G 81 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8041 (tm-30) REVERT: G 82 ILE cc_start: 0.9451 (mt) cc_final: 0.9106 (mt) REVERT: G 85 ASP cc_start: 0.9013 (m-30) cc_final: 0.8444 (p0) REVERT: G 87 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7126 (mt-10) REVERT: G 98 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: H 31 ARG cc_start: 0.9294 (ptm-80) cc_final: 0.8553 (ptm-80) REVERT: H 76 ASP cc_start: 0.9018 (t0) cc_final: 0.8789 (t0) REVERT: H 85 ASP cc_start: 0.9169 (m-30) cc_final: 0.8731 (p0) REVERT: H 92 GLN cc_start: 0.9043 (tt0) cc_final: 0.8661 (tt0) REVERT: H 98 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: H 119 GLU cc_start: 0.9129 (pm20) cc_final: 0.8801 (pm20) REVERT: I 51 ARG cc_start: 0.8919 (ttp-170) cc_final: 0.8407 (ttp-170) REVERT: I 52 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7353 (mp0) REVERT: J 4 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8451 (mm-40) REVERT: J 8 ASP cc_start: 0.9030 (m-30) cc_final: 0.8745 (m-30) REVERT: J 20 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7203 (pp30) REVERT: J 60 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: J 70 PHE cc_start: 0.8742 (t80) cc_final: 0.5714 (t80) REVERT: J 74 ASP cc_start: 0.9184 (p0) cc_final: 0.8899 (p0) REVERT: J 76 ASP cc_start: 0.8863 (t0) cc_final: 0.7749 (t0) REVERT: J 98 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.6869 (m-10) REVERT: K 76 ASP cc_start: 0.9210 (t0) cc_final: 0.8826 (t0) REVERT: K 81 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8776 (pp30) REVERT: K 82 ILE cc_start: 0.9447 (mt) cc_final: 0.8486 (mt) REVERT: K 85 ASP cc_start: 0.8954 (m-30) cc_final: 0.7890 (p0) REVERT: K 87 GLU cc_start: 0.8870 (mt-10) cc_final: 0.7566 (mp0) REVERT: K 98 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: L 71 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7912 (mtmm) REVERT: L 76 ASP cc_start: 0.8908 (t0) cc_final: 0.7818 (t0) REVERT: L 98 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: M 5 ASN cc_start: 0.8821 (t0) cc_final: 0.8509 (t0) REVERT: M 27 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8802 (tt) REVERT: M 51 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.7852 (ttp-170) REVERT: M 70 PHE cc_start: 0.9162 (t80) cc_final: 0.8938 (t80) REVERT: M 98 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: N 8 ASP cc_start: 0.8967 (m-30) cc_final: 0.8704 (m-30) REVERT: N 74 ASP cc_start: 0.9121 (p0) cc_final: 0.8869 (p0) REVERT: N 76 ASP cc_start: 0.8630 (t0) cc_final: 0.7176 (t0) REVERT: N 98 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: O 70 PHE cc_start: 0.8447 (t80) cc_final: 0.6467 (t80) REVERT: O 76 ASP cc_start: 0.9336 (t0) cc_final: 0.9006 (t0) REVERT: O 98 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: P 71 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8181 (mtmm) REVERT: P 76 ASP cc_start: 0.8913 (t0) cc_final: 0.8627 (t0) REVERT: P 85 ASP cc_start: 0.9155 (m-30) cc_final: 0.8263 (p0) REVERT: P 87 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: P 92 GLN cc_start: 0.9186 (tt0) cc_final: 0.8836 (tt0) REVERT: P 98 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: Q 5 ASN cc_start: 0.8827 (t0) cc_final: 0.8150 (t0) REVERT: Q 7 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9038 (mtmm) REVERT: Q 52 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: Q 70 PHE cc_start: 0.9169 (t80) cc_final: 0.8520 (t80) REVERT: R 8 ASP cc_start: 0.8914 (m-30) cc_final: 0.8634 (m-30) REVERT: R 74 ASP cc_start: 0.9243 (p0) cc_final: 0.9012 (p0) REVERT: R 76 ASP cc_start: 0.9118 (t0) cc_final: 0.8564 (t0) REVERT: R 92 GLN cc_start: 0.9104 (tt0) cc_final: 0.8693 (tt0) REVERT: R 98 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: S 70 PHE cc_start: 0.8708 (t80) cc_final: 0.7055 (t80) REVERT: S 71 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8731 (mtmm) REVERT: S 76 ASP cc_start: 0.9293 (t0) cc_final: 0.8927 (t0) REVERT: S 81 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8056 (tm-30) REVERT: S 82 ILE cc_start: 0.9452 (mt) cc_final: 0.9106 (mt) REVERT: S 85 ASP cc_start: 0.9025 (m-30) cc_final: 0.8460 (p0) REVERT: S 87 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7130 (mt-10) REVERT: T 31 ARG cc_start: 0.9296 (ptm-80) cc_final: 0.8545 (ptm-80) REVERT: T 76 ASP cc_start: 0.9013 (t0) cc_final: 0.8789 (t0) REVERT: T 85 ASP cc_start: 0.9140 (m-30) cc_final: 0.8877 (p0) REVERT: T 92 GLN cc_start: 0.9069 (tt0) cc_final: 0.8673 (tt0) REVERT: T 98 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: T 119 GLU cc_start: 0.9112 (pm20) cc_final: 0.8801 (pm20) REVERT: U 51 ARG cc_start: 0.8941 (ttp-170) cc_final: 0.8207 (ttp-170) REVERT: U 52 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7333 (mp0) REVERT: V 8 ASP cc_start: 0.9037 (m-30) cc_final: 0.8761 (m-30) REVERT: V 20 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7133 (pp30) REVERT: V 60 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: V 70 PHE cc_start: 0.8744 (t80) cc_final: 0.5760 (t80) REVERT: V 74 ASP cc_start: 0.9214 (p0) cc_final: 0.8929 (p0) REVERT: V 76 ASP cc_start: 0.8886 (t0) cc_final: 0.7760 (t0) REVERT: V 98 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.6863 (m-10) REVERT: W 76 ASP cc_start: 0.9227 (t0) cc_final: 0.8816 (t0) REVERT: W 81 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8785 (pp30) REVERT: W 82 ILE cc_start: 0.9441 (mt) cc_final: 0.8494 (mt) REVERT: W 85 ASP cc_start: 0.8958 (m-30) cc_final: 0.7893 (p0) REVERT: W 87 GLU cc_start: 0.8869 (mt-10) cc_final: 0.7560 (mp0) REVERT: X 71 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7914 (mtmm) REVERT: X 76 ASP cc_start: 0.8925 (t0) cc_final: 0.7825 (t0) REVERT: X 98 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.6426 (m-10) outliers start: 299 outliers final: 212 residues processed: 934 average time/residue: 0.3258 time to fit residues: 479.7218 Evaluate side-chains 951 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 709 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 92 GLN 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 20 GLN Chi-restraints excluded: chain B residue 30 THR 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 7 LYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 MET 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 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 10 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 64 ILE 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 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 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 30 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR 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 87 GLU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 98 PHE 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 7 LYS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 42 THR 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 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 20 GLN 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 44 LEU Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 94 ILE 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 65 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 81 GLN 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 K residue 132 LEU 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 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 98 PHE 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 32 ILE Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 20 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 7 LYS 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 63 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE 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 14 ASP 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 44 LEU Chi-restraints excluded: chain P residue 87 GLU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 100 ILE Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 64 ILE 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 69 VAL 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 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 30 THR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL 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 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 94 ILE 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 32 ILE Chi-restraints excluded: chain U residue 42 THR 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 20 GLN 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 44 LEU Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 100 ILE 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 11 ILE 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 81 GLN 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 11 ILE 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 94 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 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN I 20 GLN K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN M 20 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN Q 20 GLN R 117 ASN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN U 20 GLN V 92 GLN W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046317 restraints weight = 109803.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047972 restraints weight = 57572.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049141 restraints weight = 34990.870| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23688 Z= 0.169 Angle : 0.895 12.776 31968 Z= 0.438 Chirality : 0.052 0.217 3576 Planarity : 0.004 0.049 4248 Dihedral : 5.822 28.018 3264 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 11.41 % Allowed : 27.57 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.14), residues: 3024 helix: -0.71 (0.23), residues: 456 sheet: -1.21 (0.14), residues: 1224 loop : -3.26 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 50 HIS 0.001 0.001 HIS G 116 PHE 0.023 0.002 PHE D 98 TYR 0.015 0.001 TYR A 122 ARG 0.009 0.001 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 816) hydrogen bonds : angle 5.70502 ( 2232) covalent geometry : bond 0.00381 (23688) covalent geometry : angle 0.89472 (31968) *********************** 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 1107 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 836 time to evaluate : 2.728 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: D 5 ASN cc_start: 0.8782 (t0) cc_final: 0.7289 (t0) REVERT: D 7 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8698 (mtmm) REVERT: D 27 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (tp) REVERT: D 51 ARG cc_start: 0.8784 (ttp-170) cc_final: 0.7996 (ttp-170) REVERT: D 52 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: D 60 ARG cc_start: 0.9087 (ptp-110) cc_final: 0.8827 (ptp90) REVERT: D 70 PHE cc_start: 0.8989 (t80) cc_final: 0.8721 (t80) REVERT: B 8 ASP cc_start: 0.8907 (m-30) cc_final: 0.8696 (m-30) REVERT: B 74 ASP cc_start: 0.9052 (p0) cc_final: 0.8771 (p0) REVERT: B 76 ASP cc_start: 0.8478 (t0) cc_final: 0.6988 (t0) REVERT: B 98 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.6552 (m-10) REVERT: C 78 ARG cc_start: 0.9287 (tpt170) cc_final: 0.8942 (tpt-90) REVERT: C 81 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8345 (pp30) REVERT: C 98 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.6936 (m-10) REVERT: A 31 ARG cc_start: 0.9302 (ttm-80) cc_final: 0.8727 (ttm-80) REVERT: A 76 ASP cc_start: 0.8921 (t0) cc_final: 0.8047 (t0) REVERT: A 85 ASP cc_start: 0.9056 (m-30) cc_final: 0.8433 (p0) REVERT: A 98 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: A 119 GLU cc_start: 0.9088 (pm20) cc_final: 0.8859 (pm20) REVERT: A 123 GLU cc_start: 0.8757 (tt0) cc_final: 0.8470 (tp30) REVERT: E 52 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: E 60 ARG cc_start: 0.9088 (ptp-110) cc_final: 0.8815 (ptp90) REVERT: E 71 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7999 (mtmm) REVERT: E 78 ARG cc_start: 0.9441 (tpp80) cc_final: 0.9179 (tpp80) REVERT: F 4 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7737 (mp10) REVERT: F 74 ASP cc_start: 0.9159 (p0) cc_final: 0.8868 (p0) REVERT: F 76 ASP cc_start: 0.8978 (t0) cc_final: 0.8374 (t0) REVERT: F 92 GLN cc_start: 0.8990 (tt0) cc_final: 0.8593 (tt0) REVERT: F 98 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.5559 (m-10) REVERT: G 70 PHE cc_start: 0.8431 (t80) cc_final: 0.6717 (t80) REVERT: G 71 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8473 (mtmm) REVERT: G 76 ASP cc_start: 0.9218 (t0) cc_final: 0.8875 (t0) REVERT: G 81 GLN cc_start: 0.9046 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 82 ILE cc_start: 0.9488 (mt) cc_final: 0.8270 (mt) REVERT: G 85 ASP cc_start: 0.8854 (m-30) cc_final: 0.8086 (p0) REVERT: G 87 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7557 (mp0) REVERT: H 14 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7247 (t0) REVERT: H 20 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6869 (pp30) REVERT: H 31 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8701 (ptm-80) REVERT: H 71 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8093 (mtmm) REVERT: H 85 ASP cc_start: 0.9033 (m-30) cc_final: 0.8505 (p0) REVERT: H 87 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: H 98 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: H 119 GLU cc_start: 0.9051 (pm20) cc_final: 0.8835 (pm20) REVERT: H 122 TYR cc_start: 0.8217 (p90) cc_final: 0.7675 (p90) REVERT: I 51 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8373 (ttp-170) REVERT: I 52 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7828 (mt-10) REVERT: I 60 ARG cc_start: 0.9005 (ptp-110) cc_final: 0.8698 (ptp90) REVERT: I 76 ASP cc_start: 0.9037 (m-30) cc_final: 0.8543 (m-30) REVERT: I 87 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: J 8 ASP cc_start: 0.8958 (m-30) cc_final: 0.8749 (m-30) REVERT: J 44 LEU cc_start: 0.9393 (tt) cc_final: 0.9177 (tt) REVERT: J 60 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: J 70 PHE cc_start: 0.8477 (t80) cc_final: 0.5605 (t80) REVERT: J 74 ASP cc_start: 0.9101 (p0) cc_final: 0.8797 (p0) REVERT: J 76 ASP cc_start: 0.8788 (t0) cc_final: 0.7610 (t0) REVERT: J 98 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.6213 (m-10) REVERT: K 81 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: K 82 ILE cc_start: 0.9425 (mt) cc_final: 0.8564 (mt) REVERT: K 85 ASP cc_start: 0.8808 (m-30) cc_final: 0.7904 (p0) REVERT: K 87 GLU cc_start: 0.8798 (mt-10) cc_final: 0.7792 (mp0) REVERT: K 98 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: K 123 GLU cc_start: 0.8593 (mp0) cc_final: 0.8337 (mp0) REVERT: L 20 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7133 (pp30) REVERT: L 71 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7957 (mtmm) REVERT: L 98 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: M 5 ASN cc_start: 0.8785 (t0) cc_final: 0.8580 (t0) REVERT: M 27 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8725 (tp) REVERT: M 51 ARG cc_start: 0.8770 (ttp-170) cc_final: 0.7987 (ttp-170) REVERT: M 52 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: M 60 ARG cc_start: 0.9067 (ptp-110) cc_final: 0.8727 (ptp90) REVERT: M 70 PHE cc_start: 0.9000 (t80) cc_final: 0.8739 (t80) REVERT: M 77 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9175 (tm-30) REVERT: N 8 ASP cc_start: 0.8888 (m-30) cc_final: 0.8681 (m-30) REVERT: N 74 ASP cc_start: 0.9043 (p0) cc_final: 0.8762 (p0) REVERT: N 76 ASP cc_start: 0.8540 (t0) cc_final: 0.7282 (t0) REVERT: N 92 GLN cc_start: 0.8999 (tt0) cc_final: 0.8488 (tt0) REVERT: N 98 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: O 31 ARG cc_start: 0.8496 (ttt90) cc_final: 0.7775 (tpp80) REVERT: O 70 PHE cc_start: 0.7999 (t80) cc_final: 0.6137 (t80) REVERT: O 76 ASP cc_start: 0.9263 (t0) cc_final: 0.8937 (t0) REVERT: O 81 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8382 (pp30) REVERT: O 92 GLN cc_start: 0.9204 (tt0) cc_final: 0.8971 (tt0) REVERT: O 98 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: P 71 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8178 (mtmm) REVERT: P 76 ASP cc_start: 0.8796 (t0) cc_final: 0.8549 (t0) REVERT: P 85 ASP cc_start: 0.9074 (m-30) cc_final: 0.8188 (p0) REVERT: P 87 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: P 98 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: P 119 GLU cc_start: 0.9075 (pm20) cc_final: 0.8811 (pm20) REVERT: Q 52 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: Q 60 ARG cc_start: 0.9108 (ptp-110) cc_final: 0.8831 (ptp90) REVERT: Q 70 PHE cc_start: 0.8910 (t80) cc_final: 0.8413 (t80) REVERT: Q 78 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9195 (tpp80) REVERT: R 4 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7797 (mp10) REVERT: R 74 ASP cc_start: 0.9110 (p0) cc_final: 0.8853 (p0) REVERT: R 76 ASP cc_start: 0.9026 (t0) cc_final: 0.8442 (t0) REVERT: R 92 GLN cc_start: 0.8980 (tt0) cc_final: 0.8638 (tt0) REVERT: R 98 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: S 70 PHE cc_start: 0.8435 (t80) cc_final: 0.6710 (t80) REVERT: S 71 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8488 (mtmm) REVERT: S 76 ASP cc_start: 0.9214 (t0) cc_final: 0.8878 (t0) REVERT: S 81 GLN cc_start: 0.9039 (tm-30) cc_final: 0.7935 (tm-30) REVERT: S 82 ILE cc_start: 0.9483 (mt) cc_final: 0.8281 (mt) REVERT: S 85 ASP cc_start: 0.8845 (m-30) cc_final: 0.8104 (p0) REVERT: S 87 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7608 (mp0) REVERT: T 14 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7268 (t0) REVERT: T 20 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: T 31 ARG cc_start: 0.9220 (ptm-80) cc_final: 0.8707 (ptm-80) REVERT: T 71 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8086 (mtmm) REVERT: T 98 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: T 119 GLU cc_start: 0.9061 (pm20) cc_final: 0.8853 (pm20) REVERT: T 122 TYR cc_start: 0.8252 (p90) cc_final: 0.7620 (p90) REVERT: U 51 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8408 (ttp-170) REVERT: U 52 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7416 (mp0) REVERT: U 60 ARG cc_start: 0.9016 (ptp-110) cc_final: 0.8726 (ptp90) REVERT: U 87 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: V 8 ASP cc_start: 0.8946 (m-30) cc_final: 0.8738 (m-30) REVERT: V 44 LEU cc_start: 0.9389 (tt) cc_final: 0.9171 (tt) REVERT: V 60 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7859 (mtp85) REVERT: V 70 PHE cc_start: 0.8475 (t80) cc_final: 0.7549 (t80) REVERT: V 74 ASP cc_start: 0.9078 (p0) cc_final: 0.8770 (p0) REVERT: V 76 ASP cc_start: 0.8775 (t0) cc_final: 0.7984 (t0) REVERT: V 98 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.6178 (m-10) REVERT: W 76 ASP cc_start: 0.9134 (t0) cc_final: 0.8903 (t0) REVERT: W 81 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8749 (pp30) REVERT: W 82 ILE cc_start: 0.9421 (mt) cc_final: 0.8560 (mt) REVERT: W 85 ASP cc_start: 0.8834 (m-30) cc_final: 0.7913 (p0) REVERT: W 87 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7800 (mp0) REVERT: W 123 GLU cc_start: 0.8382 (mp0) cc_final: 0.7991 (mp0) REVERT: X 20 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7129 (pp30) REVERT: X 71 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7951 (mtmm) REVERT: X 98 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.6122 (m-10) outliers start: 271 outliers final: 160 residues processed: 1000 average time/residue: 0.3434 time to fit residues: 534.1627 Evaluate side-chains 964 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 767 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 92 GLN 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 D residue 132 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 108 THR 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 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 MET 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 39 VAL Chi-restraints excluded: chain A residue 41 VAL 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 E residue 10 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 52 GLU 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 33 SER 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 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 30 THR 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 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP 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 87 GLU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 87 GLU 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 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 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 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 81 GLN Chi-restraints excluded: chain K residue 98 PHE 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 20 GLN 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 98 PHE 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 32 ILE Chi-restraints excluded: chain M residue 52 GLU 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 94 ILE Chi-restraints excluded: chain N residue 98 PHE 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 63 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 98 PHE 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 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 87 GLU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 106 MET 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 10 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 52 GLU 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 33 SER 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 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 32 ILE Chi-restraints excluded: chain S residue 39 VAL 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 14 ASP 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 110 ILE Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 GLU 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 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 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 100 ILE Chi-restraints excluded: chain V residue 110 ILE 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 81 GLN 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 35 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 283 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN M 20 GLN N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043669 restraints weight = 114714.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.045224 restraints weight = 60919.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.046336 restraints weight = 37517.439| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 23688 Z= 0.312 Angle : 0.950 11.193 31968 Z= 0.478 Chirality : 0.053 0.247 3576 Planarity : 0.004 0.044 4248 Dihedral : 6.044 29.648 3264 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 11.41 % Allowed : 28.20 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 3024 helix: -0.85 (0.22), residues: 456 sheet: -1.17 (0.14), residues: 1224 loop : -3.28 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 50 HIS 0.003 0.001 HIS D 116 PHE 0.032 0.003 PHE V 91 TYR 0.020 0.002 TYR I 112 ARG 0.012 0.001 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 816) hydrogen bonds : angle 5.88169 ( 2232) covalent geometry : bond 0.00680 (23688) covalent geometry : angle 0.94951 (31968) *********************** 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 1020 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 749 time to evaluate : 2.693 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: D 27 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8826 (tt) REVERT: D 51 ARG cc_start: 0.8753 (ttp-170) cc_final: 0.7989 (ttp-170) REVERT: D 52 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 91 PHE cc_start: 0.8906 (m-80) cc_final: 0.8704 (m-10) REVERT: B 8 ASP cc_start: 0.8926 (m-30) cc_final: 0.8671 (m-30) REVERT: B 74 ASP cc_start: 0.9105 (p0) cc_final: 0.8855 (p0) REVERT: B 76 ASP cc_start: 0.8626 (t0) cc_final: 0.7187 (t0) REVERT: B 92 GLN cc_start: 0.9058 (tt0) cc_final: 0.8567 (tt0) REVERT: B 98 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.6938 (m-10) REVERT: B 123 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8346 (mp0) REVERT: C 98 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: A 76 ASP cc_start: 0.8997 (t0) cc_final: 0.8404 (t0) REVERT: A 85 ASP cc_start: 0.9147 (m-30) cc_final: 0.8496 (p0) REVERT: A 119 GLU cc_start: 0.9143 (pm20) cc_final: 0.8932 (pm20) REVERT: A 123 GLU cc_start: 0.8790 (tt0) cc_final: 0.8429 (tp30) REVERT: E 7 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8895 (mtmm) REVERT: E 51 ARG cc_start: 0.8911 (ttp-170) cc_final: 0.8442 (ttp-170) REVERT: E 52 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: F 8 ASP cc_start: 0.8907 (m-30) cc_final: 0.8633 (m-30) REVERT: F 74 ASP cc_start: 0.9213 (p0) cc_final: 0.8959 (p0) REVERT: F 76 ASP cc_start: 0.9044 (t0) cc_final: 0.8497 (t0) REVERT: F 92 GLN cc_start: 0.9036 (tt0) cc_final: 0.8585 (tt0) REVERT: F 98 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: G 70 PHE cc_start: 0.8640 (t80) cc_final: 0.6752 (t80) REVERT: G 71 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8429 (mtmm) REVERT: G 76 ASP cc_start: 0.9287 (t0) cc_final: 0.8901 (t0) REVERT: G 81 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8392 (tm-30) REVERT: G 82 ILE cc_start: 0.9462 (mt) cc_final: 0.9024 (mt) REVERT: G 85 ASP cc_start: 0.9052 (m-30) cc_final: 0.8769 (p0) REVERT: G 98 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: H 31 ARG cc_start: 0.9320 (ptm-80) cc_final: 0.8592 (ptm-80) REVERT: I 51 ARG cc_start: 0.8918 (ttp-170) cc_final: 0.8337 (ttp-170) REVERT: I 52 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7338 (mp0) REVERT: J 8 ASP cc_start: 0.8969 (m-30) cc_final: 0.8761 (m-30) REVERT: J 60 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7901 (mtp85) REVERT: J 70 PHE cc_start: 0.8725 (t80) cc_final: 0.5569 (t80) REVERT: J 74 ASP cc_start: 0.9138 (p0) cc_final: 0.8753 (p0) REVERT: J 75 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8964 (p) REVERT: J 76 ASP cc_start: 0.8918 (t0) cc_final: 0.7783 (t0) REVERT: J 92 GLN cc_start: 0.9090 (tt0) cc_final: 0.8859 (tt0) REVERT: J 98 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.6330 (m-10) REVERT: J 126 MET cc_start: 0.8198 (mtp) cc_final: 0.7960 (mmm) REVERT: K 31 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8366 (mtp85) REVERT: K 76 ASP cc_start: 0.9166 (t0) cc_final: 0.8800 (t0) REVERT: K 81 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8776 (pp30) REVERT: K 82 ILE cc_start: 0.9432 (mt) cc_final: 0.8512 (mt) REVERT: K 85 ASP cc_start: 0.8933 (m-30) cc_final: 0.7885 (p0) REVERT: K 87 GLU cc_start: 0.8849 (mt-10) cc_final: 0.7623 (mp0) REVERT: K 98 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: K 123 GLU cc_start: 0.8653 (mp0) cc_final: 0.8395 (mp0) REVERT: L 35 ASN cc_start: 0.9523 (OUTLIER) cc_final: 0.9247 (p0) REVERT: L 71 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7959 (mtmm) REVERT: L 85 ASP cc_start: 0.9088 (m-30) cc_final: 0.8769 (p0) REVERT: L 87 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8478 (pt0) REVERT: L 98 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: M 27 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8819 (tt) REVERT: M 51 ARG cc_start: 0.8745 (ttp-170) cc_final: 0.7977 (ttp-170) REVERT: M 52 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: M 70 PHE cc_start: 0.9084 (t80) cc_final: 0.8796 (t80) REVERT: M 76 ASP cc_start: 0.9235 (m-30) cc_final: 0.8655 (m-30) REVERT: N 8 ASP cc_start: 0.8929 (m-30) cc_final: 0.8669 (m-30) REVERT: N 74 ASP cc_start: 0.9108 (p0) cc_final: 0.8849 (p0) REVERT: N 76 ASP cc_start: 0.8628 (t0) cc_final: 0.7104 (t0) REVERT: N 92 GLN cc_start: 0.9051 (tt0) cc_final: 0.8546 (tt0) REVERT: N 98 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: N 123 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8413 (mp0) REVERT: O 70 PHE cc_start: 0.8392 (t80) cc_final: 0.6462 (t80) REVERT: O 76 ASP cc_start: 0.9329 (t0) cc_final: 0.9043 (t0) REVERT: O 92 GLN cc_start: 0.9101 (tt0) cc_final: 0.8799 (tt0) REVERT: O 98 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: P 71 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8270 (mtmt) REVERT: P 76 ASP cc_start: 0.8782 (t0) cc_final: 0.8488 (t0) REVERT: P 85 ASP cc_start: 0.9174 (m-30) cc_final: 0.8260 (p0) REVERT: P 87 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: P 119 GLU cc_start: 0.9122 (pm20) cc_final: 0.8863 (pm20) REVERT: Q 7 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8895 (mtmm) REVERT: Q 52 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: R 8 ASP cc_start: 0.8917 (m-30) cc_final: 0.8645 (m-30) REVERT: R 74 ASP cc_start: 0.9194 (p0) cc_final: 0.8936 (p0) REVERT: R 76 ASP cc_start: 0.9061 (t0) cc_final: 0.8524 (t0) REVERT: R 92 GLN cc_start: 0.9067 (tt0) cc_final: 0.8651 (tt0) REVERT: R 98 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.6036 (m-10) REVERT: R 106 MET cc_start: 0.8304 (ttp) cc_final: 0.7711 (ttp) REVERT: S 70 PHE cc_start: 0.8680 (t80) cc_final: 0.7009 (t80) REVERT: S 71 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8453 (mtmm) REVERT: S 76 ASP cc_start: 0.9295 (t0) cc_final: 0.8915 (t0) REVERT: S 81 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8397 (tm-30) REVERT: S 82 ILE cc_start: 0.9449 (mt) cc_final: 0.9016 (mt) REVERT: S 85 ASP cc_start: 0.9041 (m-30) cc_final: 0.8765 (p0) REVERT: T 31 ARG cc_start: 0.9337 (ptm-80) cc_final: 0.8605 (ptm-80) REVERT: U 51 ARG cc_start: 0.8942 (ttp-170) cc_final: 0.8348 (ttp-170) REVERT: U 52 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7298 (mp0) REVERT: U 76 ASP cc_start: 0.9290 (m-30) cc_final: 0.8790 (m-30) REVERT: U 87 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8604 (pp20) REVERT: V 8 ASP cc_start: 0.9001 (m-30) cc_final: 0.8773 (m-30) REVERT: V 60 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: V 70 PHE cc_start: 0.8730 (t80) cc_final: 0.5535 (t80) REVERT: V 74 ASP cc_start: 0.9162 (p0) cc_final: 0.8789 (p0) REVERT: V 75 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8989 (p) REVERT: V 76 ASP cc_start: 0.8941 (t0) cc_final: 0.7779 (t0) REVERT: V 98 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: W 31 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8351 (tpt-90) REVERT: W 76 ASP cc_start: 0.9217 (t0) cc_final: 0.8991 (t0) REVERT: W 81 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8781 (pp30) REVERT: W 82 ILE cc_start: 0.9441 (mt) cc_final: 0.8538 (mt) REVERT: W 85 ASP cc_start: 0.8935 (m-30) cc_final: 0.7890 (p0) REVERT: W 87 GLU cc_start: 0.8852 (mt-10) cc_final: 0.7628 (mp0) REVERT: W 123 GLU cc_start: 0.8474 (mp0) cc_final: 0.8185 (mp0) REVERT: X 35 ASN cc_start: 0.9527 (OUTLIER) cc_final: 0.9253 (p0) REVERT: X 71 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7963 (mtmm) REVERT: X 85 ASP cc_start: 0.9115 (m-30) cc_final: 0.8768 (p0) REVERT: X 87 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8479 (pt0) REVERT: X 98 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.6408 (m-10) outliers start: 271 outliers final: 190 residues processed: 936 average time/residue: 0.3734 time to fit residues: 558.4410 Evaluate side-chains 931 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 711 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 69 VAL 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 20 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 LEU 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 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 30 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 MET 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 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 52 GLU 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 33 SER Chi-restraints excluded: chain F residue 41 VAL 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 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 PHE 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 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 42 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 87 GLU 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 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 60 ARG Chi-restraints excluded: chain J residue 75 THR 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 81 GLN Chi-restraints excluded: chain K residue 98 PHE 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 20 GLN 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 98 PHE 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 32 ILE Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 20 GLN Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 94 ILE 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 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE 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 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 87 GLU Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 108 THR 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 32 ILE Chi-restraints excluded: chain Q residue 52 GLU 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 33 SER Chi-restraints excluded: chain R residue 41 VAL 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 121 SER 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 30 THR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 98 PHE 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 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 T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 GLU 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 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 75 THR Chi-restraints excluded: chain V residue 94 ILE 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 W residue 9 LEU Chi-restraints excluded: chain W residue 11 ILE 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 81 GLN 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 11 ILE 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 94 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 Chi-restraints excluded: chain X residue 132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 211 optimal weight: 7.9990 chunk 4 optimal weight: 0.0020 chunk 291 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 154 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 117 ASN ** 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN G 92 GLN H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN J 92 GLN K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN M 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.046849 restraints weight = 108833.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.048517 restraints weight = 56788.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049686 restraints weight = 34385.414| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23688 Z= 0.165 Angle : 0.961 15.152 31968 Z= 0.470 Chirality : 0.053 0.232 3576 Planarity : 0.004 0.041 4248 Dihedral : 5.826 32.830 3264 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 10.06 % Allowed : 29.63 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.14), residues: 3024 helix: -0.66 (0.22), residues: 480 sheet: -1.12 (0.14), residues: 1224 loop : -3.05 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 50 HIS 0.001 0.001 HIS W 116 PHE 0.032 0.002 PHE M 91 TYR 0.019 0.001 TYR I 112 ARG 0.009 0.001 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 816) hydrogen bonds : angle 5.71424 ( 2232) covalent geometry : bond 0.00385 (23688) covalent geometry : angle 0.96092 (31968) *********************** 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 1045 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 806 time to evaluate : 2.686 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: 0.8971 (OUTLIER) cc_final: 0.8666 (tp) REVERT: D 51 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.7925 (ttp-170) REVERT: D 52 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: D 77 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9118 (tp30) REVERT: B 8 ASP cc_start: 0.8897 (m-30) cc_final: 0.8679 (m-30) REVERT: B 74 ASP cc_start: 0.9071 (p0) cc_final: 0.8790 (p0) REVERT: B 76 ASP cc_start: 0.8454 (t0) cc_final: 0.6983 (t0) REVERT: B 98 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.6432 (m-10) REVERT: B 123 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8387 (mp0) REVERT: C 51 ARG cc_start: 0.8794 (ttp-110) cc_final: 0.8592 (ttp-110) REVERT: C 98 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.6874 (m-10) REVERT: A 20 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7001 (pp30) REVERT: A 76 ASP cc_start: 0.8859 (t0) cc_final: 0.8173 (t0) REVERT: A 85 ASP cc_start: 0.9062 (m-30) cc_final: 0.8434 (p0) REVERT: A 119 GLU cc_start: 0.9088 (pm20) cc_final: 0.8787 (pm20) REVERT: A 123 GLU cc_start: 0.8731 (tt0) cc_final: 0.8439 (tp30) REVERT: E 31 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8627 (mmm-85) REVERT: E 51 ARG cc_start: 0.8820 (ttp-170) cc_final: 0.8219 (ttp-170) REVERT: E 52 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: E 60 ARG cc_start: 0.9092 (ptp-110) cc_final: 0.8740 (ptp90) REVERT: E 71 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7967 (mtmm) REVERT: E 102 GLN cc_start: 0.8681 (tp40) cc_final: 0.8257 (tp-100) REVERT: F 4 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7760 (mp10) REVERT: F 74 ASP cc_start: 0.9115 (p0) cc_final: 0.8853 (p0) REVERT: F 76 ASP cc_start: 0.8920 (t0) cc_final: 0.8491 (t0) REVERT: F 92 GLN cc_start: 0.9036 (tt0) cc_final: 0.8630 (tt0) REVERT: F 98 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: G 70 PHE cc_start: 0.8379 (t80) cc_final: 0.6342 (t80) REVERT: G 76 ASP cc_start: 0.9196 (t0) cc_final: 0.8875 (t0) REVERT: G 81 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8631 (tm-30) REVERT: G 82 ILE cc_start: 0.9520 (mt) cc_final: 0.8952 (mt) REVERT: G 92 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: H 20 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6604 (pp30) REVERT: H 31 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8738 (ptm-80) REVERT: H 71 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8097 (mtmm) REVERT: I 51 ARG cc_start: 0.8927 (ttp-170) cc_final: 0.8555 (ttp-170) REVERT: I 52 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7431 (mp0) REVERT: I 60 ARG cc_start: 0.9056 (ptp-110) cc_final: 0.8739 (ptp90) REVERT: I 76 ASP cc_start: 0.9078 (m-30) cc_final: 0.8607 (m-30) REVERT: I 87 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: I 92 GLN cc_start: 0.8874 (mt0) cc_final: 0.8610 (mt0) REVERT: I 111 ASP cc_start: 0.8009 (p0) cc_final: 0.7805 (p0) REVERT: J 4 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8097 (mp10) REVERT: J 8 ASP cc_start: 0.8935 (m-30) cc_final: 0.8727 (m-30) REVERT: J 60 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7851 (mtp85) REVERT: J 70 PHE cc_start: 0.8496 (t80) cc_final: 0.7507 (t80) REVERT: J 74 ASP cc_start: 0.9080 (p0) cc_final: 0.8807 (p0) REVERT: J 76 ASP cc_start: 0.8755 (t0) cc_final: 0.7952 (t0) REVERT: J 98 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6050 (m-10) REVERT: K 81 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8772 (pp30) REVERT: K 82 ILE cc_start: 0.9401 (mt) cc_final: 0.8606 (mt) REVERT: K 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.7873 (p0) REVERT: K 87 GLU cc_start: 0.8812 (mt-10) cc_final: 0.7748 (mp0) REVERT: K 92 GLN cc_start: 0.9169 (tt0) cc_final: 0.8897 (tt0) REVERT: K 98 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: K 106 MET cc_start: 0.8480 (tpp) cc_final: 0.8247 (tpp) REVERT: L 20 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: L 35 ASN cc_start: 0.9436 (OUTLIER) cc_final: 0.9177 (p0) REVERT: L 71 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7869 (mtmm) REVERT: L 85 ASP cc_start: 0.9020 (m-30) cc_final: 0.8672 (p0) REVERT: L 87 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8303 (pt0) REVERT: L 98 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: M 51 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.7918 (ttp-170) REVERT: M 52 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: M 77 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9207 (tm-30) REVERT: N 8 ASP cc_start: 0.8884 (m-30) cc_final: 0.8682 (m-30) REVERT: N 31 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8217 (ttm-80) REVERT: N 52 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8338 (mt-10) REVERT: N 74 ASP cc_start: 0.9051 (p0) cc_final: 0.8781 (p0) REVERT: N 76 ASP cc_start: 0.8450 (t0) cc_final: 0.6970 (t0) REVERT: N 92 GLN cc_start: 0.8911 (tt0) cc_final: 0.8397 (tt0) REVERT: N 98 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.6433 (m-10) REVERT: N 123 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8409 (mp0) REVERT: O 51 ARG cc_start: 0.8799 (ttp-110) cc_final: 0.8572 (ttp-110) REVERT: O 70 PHE cc_start: 0.8027 (t80) cc_final: 0.6280 (t80) REVERT: O 76 ASP cc_start: 0.9256 (t0) cc_final: 0.8944 (t0) REVERT: O 82 ILE cc_start: 0.9501 (mt) cc_final: 0.9299 (tp) REVERT: O 98 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: P 20 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: P 71 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8137 (mtmm) REVERT: P 76 ASP cc_start: 0.8764 (t0) cc_final: 0.8529 (t0) REVERT: P 85 ASP cc_start: 0.9093 (m-30) cc_final: 0.8195 (p0) REVERT: P 87 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: P 119 GLU cc_start: 0.9074 (pm20) cc_final: 0.8801 (pm20) REVERT: Q 52 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: Q 60 ARG cc_start: 0.9107 (ptp-110) cc_final: 0.8754 (ptp90) REVERT: Q 71 LYS cc_start: 0.8384 (mtmm) cc_final: 0.7995 (mtmm) REVERT: Q 87 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: Q 102 GLN cc_start: 0.8697 (tp40) cc_final: 0.8262 (tp-100) REVERT: R 4 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7767 (mp10) REVERT: R 74 ASP cc_start: 0.9107 (p0) cc_final: 0.8836 (p0) REVERT: R 76 ASP cc_start: 0.8958 (t0) cc_final: 0.8510 (t0) REVERT: R 92 GLN cc_start: 0.9074 (tt0) cc_final: 0.8667 (tt0) REVERT: R 98 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: S 70 PHE cc_start: 0.8414 (t80) cc_final: 0.6675 (t80) REVERT: S 71 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8127 (mtmm) REVERT: S 76 ASP cc_start: 0.9184 (t0) cc_final: 0.8863 (t0) REVERT: S 81 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8634 (tm-30) REVERT: S 82 ILE cc_start: 0.9502 (mt) cc_final: 0.8844 (mt) REVERT: S 123 GLU cc_start: 0.8562 (mp0) cc_final: 0.7877 (mp0) REVERT: T 31 ARG cc_start: 0.9246 (ptm-80) cc_final: 0.8765 (ptm-80) REVERT: T 71 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8125 (mtmm) REVERT: T 85 ASP cc_start: 0.8606 (p0) cc_final: 0.8360 (p0) REVERT: T 122 TYR cc_start: 0.8234 (p90) cc_final: 0.7790 (p90) REVERT: U 51 ARG cc_start: 0.8950 (ttp-170) cc_final: 0.8549 (ttp-170) REVERT: U 52 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7395 (mp0) REVERT: U 60 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8882 (ptp90) REVERT: U 76 ASP cc_start: 0.9189 (m-30) cc_final: 0.8807 (m-30) REVERT: U 82 ILE cc_start: 0.9403 (mm) cc_final: 0.9190 (mm) REVERT: U 87 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: V 70 PHE cc_start: 0.8482 (t80) cc_final: 0.7478 (t80) REVERT: V 74 ASP cc_start: 0.9104 (p0) cc_final: 0.8825 (p0) REVERT: V 76 ASP cc_start: 0.8764 (t0) cc_final: 0.7922 (t0) REVERT: V 98 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6229 (m-10) REVERT: V 119 GLU cc_start: 0.8934 (pm20) cc_final: 0.8709 (pm20) REVERT: W 76 ASP cc_start: 0.9096 (t0) cc_final: 0.8834 (t0) REVERT: W 81 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8761 (pp30) REVERT: W 82 ILE cc_start: 0.9429 (mt) cc_final: 0.8592 (mt) REVERT: W 85 ASP cc_start: 0.8823 (m-30) cc_final: 0.7874 (p0) REVERT: W 87 GLU cc_start: 0.8812 (mt-10) cc_final: 0.7745 (mp0) REVERT: W 92 GLN cc_start: 0.9117 (tt0) cc_final: 0.8887 (tt0) REVERT: W 106 MET cc_start: 0.8488 (tpp) cc_final: 0.8264 (tpp) REVERT: X 20 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7170 (pp30) REVERT: X 35 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9178 (p0) REVERT: X 71 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7863 (mtmm) REVERT: X 85 ASP cc_start: 0.9012 (m-30) cc_final: 0.8668 (p0) REVERT: X 87 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8301 (pt0) REVERT: X 98 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.6167 (m-10) outliers start: 239 outliers final: 169 residues processed: 959 average time/residue: 0.3346 time to fit residues: 499.7157 Evaluate side-chains 968 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 768 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 87 GLU 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 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 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 MET 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 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 52 GLU 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 33 SER Chi-restraints excluded: chain F residue 41 VAL 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 121 SER 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 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 108 THR 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 69 VAL Chi-restraints excluded: chain I residue 87 GLU 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 60 ARG Chi-restraints excluded: chain J residue 92 GLN 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 81 GLN Chi-restraints excluded: chain K residue 98 PHE 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 20 GLN 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 98 PHE 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 52 GLU 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 94 ILE 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 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE 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 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 87 GLU Chi-restraints excluded: chain P residue 106 MET Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 87 GLU 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 33 SER Chi-restraints excluded: chain R residue 41 VAL 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 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 30 THR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 98 PHE 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 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 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 GLU 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 94 ILE Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE 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 81 GLN 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 35 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 278 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN G 92 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN M 20 GLN N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.044259 restraints weight = 114591.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045801 restraints weight = 60611.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046905 restraints weight = 37612.457| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23688 Z= 0.293 Angle : 0.987 15.420 31968 Z= 0.494 Chirality : 0.054 0.241 3576 Planarity : 0.004 0.046 4248 Dihedral : 6.049 30.740 3264 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 9.47 % Allowed : 31.02 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 3024 helix: -0.72 (0.23), residues: 456 sheet: -1.15 (0.14), residues: 1224 loop : -3.07 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 50 HIS 0.002 0.001 HIS D 116 PHE 0.029 0.002 PHE V 91 TYR 0.018 0.002 TYR I 112 ARG 0.011 0.001 ARG O 31 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 816) hydrogen bonds : angle 5.90921 ( 2232) covalent geometry : bond 0.00649 (23688) covalent geometry : angle 0.98659 (31968) ********************** 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 973 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 748 time to evaluate : 2.860 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: D 27 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8892 (tt) REVERT: D 51 ARG cc_start: 0.8740 (ttp-170) cc_final: 0.7985 (ttp-170) REVERT: B 8 ASP cc_start: 0.8920 (m-30) cc_final: 0.8672 (m-30) REVERT: B 74 ASP cc_start: 0.9109 (p0) cc_final: 0.8864 (p0) REVERT: B 76 ASP cc_start: 0.8600 (t0) cc_final: 0.7173 (t0) REVERT: B 92 GLN cc_start: 0.9023 (tt0) cc_final: 0.8514 (tt0) REVERT: B 98 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.6832 (m-10) REVERT: B 123 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8444 (mp0) REVERT: C 76 ASP cc_start: 0.9144 (t0) cc_final: 0.8814 (t0) REVERT: C 98 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.6667 (m-10) REVERT: A 76 ASP cc_start: 0.8946 (t0) cc_final: 0.8407 (t0) REVERT: A 85 ASP cc_start: 0.9161 (m-30) cc_final: 0.8505 (p0) REVERT: A 119 GLU cc_start: 0.9141 (pm20) cc_final: 0.8844 (pm20) REVERT: A 123 GLU cc_start: 0.8781 (tt0) cc_final: 0.8453 (tp30) REVERT: E 51 ARG cc_start: 0.8847 (ttp-170) cc_final: 0.8211 (ttp-170) REVERT: E 52 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: E 60 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8855 (ptp90) REVERT: E 87 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: F 4 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7821 (mp10) REVERT: F 8 ASP cc_start: 0.8984 (m-30) cc_final: 0.8735 (m-30) REVERT: F 74 ASP cc_start: 0.9221 (p0) cc_final: 0.8935 (p0) REVERT: F 76 ASP cc_start: 0.9045 (t0) cc_final: 0.8553 (t0) REVERT: F 92 GLN cc_start: 0.9074 (tt0) cc_final: 0.8574 (tt0) REVERT: F 98 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: F 123 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8274 (mp0) REVERT: G 70 PHE cc_start: 0.8571 (t80) cc_final: 0.6632 (t80) REVERT: G 71 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8551 (mtmm) REVERT: G 76 ASP cc_start: 0.9262 (t0) cc_final: 0.8875 (t0) REVERT: G 82 ILE cc_start: 0.9372 (mt) cc_final: 0.9123 (mt) REVERT: G 92 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: G 94 ILE cc_start: 0.9472 (mt) cc_final: 0.9267 (mm) REVERT: G 98 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: H 31 ARG cc_start: 0.9326 (ptm-80) cc_final: 0.8617 (ptm-80) REVERT: H 71 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8260 (mtmm) REVERT: H 85 ASP cc_start: 0.8763 (p0) cc_final: 0.8453 (p0) REVERT: I 51 ARG cc_start: 0.8982 (ttp-170) cc_final: 0.8506 (ttp-170) REVERT: I 52 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7359 (mp0) REVERT: J 8 ASP cc_start: 0.8996 (m-30) cc_final: 0.8783 (m-30) REVERT: J 60 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7908 (mtp85) REVERT: J 70 PHE cc_start: 0.8748 (t80) cc_final: 0.7986 (t80) REVERT: J 74 ASP cc_start: 0.9193 (p0) cc_final: 0.8848 (p0) REVERT: J 76 ASP cc_start: 0.8905 (t0) cc_final: 0.8326 (t0) REVERT: J 92 GLN cc_start: 0.9058 (tt0) cc_final: 0.8773 (tt0) REVERT: J 98 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.6271 (m-10) REVERT: K 76 ASP cc_start: 0.9118 (t0) cc_final: 0.8730 (t0) REVERT: K 81 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8790 (pp30) REVERT: K 82 ILE cc_start: 0.9414 (mt) cc_final: 0.8561 (mt) REVERT: K 85 ASP cc_start: 0.8932 (m-30) cc_final: 0.7880 (p0) REVERT: K 87 GLU cc_start: 0.8851 (mt-10) cc_final: 0.7576 (mp0) REVERT: K 98 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: K 106 MET cc_start: 0.8501 (tpp) cc_final: 0.8292 (tpp) REVERT: K 117 ASN cc_start: 0.9413 (p0) cc_final: 0.9137 (p0) REVERT: L 35 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.9292 (p0) REVERT: L 71 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7925 (mtmm) REVERT: L 85 ASP cc_start: 0.9121 (m-30) cc_final: 0.8780 (p0) REVERT: L 87 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8478 (pt0) REVERT: L 98 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: M 5 ASN cc_start: 0.9204 (t0) cc_final: 0.8793 (t0) REVERT: M 51 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.7962 (ttp-170) REVERT: M 76 ASP cc_start: 0.9238 (m-30) cc_final: 0.8640 (m-30) REVERT: M 78 ARG cc_start: 0.9376 (tpp80) cc_final: 0.9057 (tpt-90) REVERT: N 8 ASP cc_start: 0.8926 (m-30) cc_final: 0.8679 (m-30) REVERT: N 74 ASP cc_start: 0.9086 (p0) cc_final: 0.8817 (p0) REVERT: N 76 ASP cc_start: 0.8600 (t0) cc_final: 0.7108 (t0) REVERT: N 92 GLN cc_start: 0.9050 (tt0) cc_final: 0.8567 (tt0) REVERT: N 98 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: N 123 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8452 (mp0) REVERT: O 31 ARG cc_start: 0.8410 (ttt90) cc_final: 0.8193 (tpp80) REVERT: O 70 PHE cc_start: 0.8316 (t80) cc_final: 0.6543 (t80) REVERT: O 76 ASP cc_start: 0.9320 (t0) cc_final: 0.9030 (t0) REVERT: O 98 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7036 (m-10) REVERT: P 71 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8146 (mtmm) REVERT: P 76 ASP cc_start: 0.8813 (t0) cc_final: 0.8577 (t0) REVERT: P 85 ASP cc_start: 0.9194 (m-30) cc_final: 0.8275 (p0) REVERT: P 87 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: P 119 GLU cc_start: 0.9102 (pm20) cc_final: 0.8802 (pm20) REVERT: Q 52 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: Q 87 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: R 4 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7817 (mp10) REVERT: R 8 ASP cc_start: 0.8961 (m-30) cc_final: 0.8720 (m-30) REVERT: R 74 ASP cc_start: 0.9203 (p0) cc_final: 0.8948 (p0) REVERT: R 76 ASP cc_start: 0.9111 (t0) cc_final: 0.8660 (t0) REVERT: R 92 GLN cc_start: 0.9137 (tt0) cc_final: 0.8685 (tt0) REVERT: R 98 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: S 31 ARG cc_start: 0.8266 (ttt90) cc_final: 0.7970 (ttt90) REVERT: S 70 PHE cc_start: 0.8620 (t80) cc_final: 0.6534 (t80) REVERT: S 71 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8382 (mtmm) REVERT: S 76 ASP cc_start: 0.9278 (t0) cc_final: 0.8940 (t0) REVERT: S 82 ILE cc_start: 0.9349 (mt) cc_final: 0.8794 (mt) REVERT: S 123 GLU cc_start: 0.8597 (mp0) cc_final: 0.7977 (mp0) REVERT: T 31 ARG cc_start: 0.9326 (ptm-80) cc_final: 0.8635 (ptm-80) REVERT: T 85 ASP cc_start: 0.8810 (p0) cc_final: 0.8477 (p0) REVERT: U 22 GLU cc_start: 0.8254 (mp0) cc_final: 0.7869 (pm20) REVERT: U 31 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8827 (ttm-80) REVERT: U 51 ARG cc_start: 0.8977 (ttp-170) cc_final: 0.8508 (ttp-170) REVERT: U 52 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7279 (mp0) REVERT: U 76 ASP cc_start: 0.9287 (m-30) cc_final: 0.8788 (m-30) REVERT: V 70 PHE cc_start: 0.8748 (t80) cc_final: 0.7942 (t80) REVERT: V 74 ASP cc_start: 0.9207 (p0) cc_final: 0.8850 (p0) REVERT: V 76 ASP cc_start: 0.8944 (t0) cc_final: 0.8330 (t0) REVERT: V 98 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6401 (m-10) REVERT: V 126 MET cc_start: 0.8147 (mtp) cc_final: 0.7920 (mmm) REVERT: W 31 ARG cc_start: 0.8496 (tpt-90) cc_final: 0.8126 (mmm160) REVERT: W 76 ASP cc_start: 0.9217 (t0) cc_final: 0.8795 (t0) REVERT: W 81 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8788 (pp30) REVERT: W 82 ILE cc_start: 0.9446 (mt) cc_final: 0.8545 (mt) REVERT: W 85 ASP cc_start: 0.8926 (m-30) cc_final: 0.7880 (p0) REVERT: W 87 GLU cc_start: 0.8805 (mt-10) cc_final: 0.7611 (mp0) REVERT: W 117 ASN cc_start: 0.9383 (p0) cc_final: 0.9125 (p0) REVERT: W 123 GLU cc_start: 0.8571 (mp0) cc_final: 0.8360 (mp0) REVERT: X 35 ASN cc_start: 0.9512 (OUTLIER) cc_final: 0.9288 (p0) REVERT: X 71 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7982 (mtmm) REVERT: X 85 ASP cc_start: 0.9104 (m-30) cc_final: 0.8781 (p0) REVERT: X 87 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8469 (pt0) REVERT: X 98 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.6275 (m-10) outliers start: 225 outliers final: 174 residues processed: 912 average time/residue: 0.4267 time to fit residues: 623.5953 Evaluate side-chains 926 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 728 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 87 GLU 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 20 GLN 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 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 126 MET 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 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 87 GLU 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 33 SER Chi-restraints excluded: chain F residue 41 VAL 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 121 SER 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 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU 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 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 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 94 ILE 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 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 81 GLN Chi-restraints excluded: chain K residue 98 PHE 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 20 GLN 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 98 PHE 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 24 ILE 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 20 GLN 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 94 ILE 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 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 98 PHE 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 32 ILE 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 106 MET Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 87 GLU 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 33 SER Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 64 ILE 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 121 SER 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 30 THR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 98 PHE 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 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 T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS 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 94 ILE 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 20 GLN 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 81 GLN 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 35 ASN Chi-restraints excluded: chain X residue 94 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** W 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.043584 restraints weight = 113348.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045121 restraints weight = 59875.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.046214 restraints weight = 36789.323| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.267 23688 Z= 0.428 Angle : 1.450 59.200 31968 Z= 0.823 Chirality : 0.055 0.490 3576 Planarity : 0.007 0.161 4248 Dihedral : 6.047 30.250 3264 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 33.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 9.01 % Allowed : 31.27 % Favored : 59.72 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 3024 helix: -0.67 (0.23), residues: 456 sheet: -1.14 (0.14), residues: 1224 loop : -3.07 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 50 HIS 0.002 0.001 HIS D 116 PHE 0.025 0.002 PHE V 91 TYR 0.015 0.002 TYR I 112 ARG 0.010 0.001 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 816) hydrogen bonds : angle 5.92080 ( 2232) covalent geometry : bond 0.00966 (23688) covalent geometry : angle 1.44956 (31968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9885.93 seconds wall clock time: 174 minutes 33.91 seconds (10473.91 seconds total)