Starting phenix.real_space_refine on Fri Sep 19 04:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tea_10478/09_2025/6tea_10478.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tea_10478/09_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_10478/09_2025/6tea_10478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tea_10478/09_2025/6tea_10478.map" model { file = "/net/cci-nas-00/data/ceres_data/6tea_10478/09_2025/6tea_10478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tea_10478/09_2025/6tea_10478.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 14688 2.51 5 N 3912 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Restraints were copied for chains: B, C, A, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 1.46, per 1000 atoms: 0.06 Number of scatterers: 23328 At special positions: 0 Unit cell: (98.859, 98.859, 170.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4680 8.00 N 3912 7.00 C 14688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 24 sheets defined 10.0% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA L 79 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG M 80 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG O 80 " --> pdb=" O ASP O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA P 79 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 80 " --> pdb=" O ASP P 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA Q 79 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 80 " --> pdb=" O ASP Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA S 79 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG S 80 " --> pdb=" O ASP S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA T 79 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG T 80 " --> pdb=" O ASP T 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.561A pdb=" N ALA U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA V 79 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 80 " --> pdb=" O ASP V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG W 80 " --> pdb=" O ASP W 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 85 removed outlier: 3.560A pdb=" N ALA X 79 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG X 80 " --> pdb=" O ASP X 76 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE D 107 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA D 62 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE C 107 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA C 127 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA C 62 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'F' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE H 107 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA H 127 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA H 62 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE K 107 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA K 127 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA K 62 " --> pdb=" O SER K 128 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE L 107 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA L 127 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA L 62 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE M 107 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA M 127 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA M 62 " --> pdb=" O SER M 128 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'N' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'O' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE O 107 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA O 127 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA O 62 " --> pdb=" O SER O 128 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'P' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE P 107 " --> pdb=" O ALA P 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA P 127 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA P 62 " --> pdb=" O SER P 128 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Q' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE Q 107 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA Q 127 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA Q 62 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'R' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE R 107 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA R 127 " --> pdb=" O ILE R 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA R 62 " --> pdb=" O SER R 128 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'S' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE S 107 " --> pdb=" O ALA S 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA S 127 " --> pdb=" O ILE S 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA S 62 " --> pdb=" O SER S 128 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'T' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE T 107 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA T 127 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA T 62 " --> pdb=" O SER T 128 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'U' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'V' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE V 107 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA V 127 " --> pdb=" O ILE V 107 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA V 62 " --> pdb=" O SER V 128 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'W' and resid 22 through 23 removed outlier: 5.685A pdb=" N ILE W 107 " --> pdb=" O ALA W 127 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA W 127 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA W 62 " --> pdb=" O SER W 128 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'X' and resid 22 through 23 removed outlier: 5.684A pdb=" N ILE X 107 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA X 127 " --> pdb=" O ILE X 107 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA X 62 " --> pdb=" O SER X 128 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.46 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: 0.09 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.950 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 23688 Z= 0.383 Angle : 1.337 15.408 31968 Z= 0.686 Chirality : 0.085 0.460 3576 Planarity : 0.006 0.047 4248 Dihedral : 12.642 77.473 8328 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.86 (0.12), residues: 3024 helix: -3.41 (0.16), residues: 456 sheet: -2.70 (0.13), residues: 1056 loop : -3.57 (0.12), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG R 60 TYR 0.008 0.002 TYR B 122 PHE 0.022 0.004 PHE J 98 TRP 0.007 0.002 TRP U 50 HIS 0.004 0.002 HIS L 116 Details of bonding type rmsd covalent geometry : bond 0.00835 (23688) covalent geometry : angle 1.33684 (31968) hydrogen bonds : bond 0.27868 ( 816) hydrogen bonds : angle 9.94326 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1414 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 ASN cc_start: 0.8345 (t0) cc_final: 0.8124 (t0) REVERT: D 24 ILE cc_start: 0.9006 (pt) cc_final: 0.8752 (tp) REVERT: D 51 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8278 (ttp-170) REVERT: D 77 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9095 (tm-30) REVERT: D 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8918 (tp) REVERT: D 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.8824 (m-30) REVERT: D 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8917 (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: 0.8501 (m-30) REVERT: B 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8930 (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: 0.9155 (m-80) REVERT: C 35 ASN cc_start: 0.9193 (m-40) cc_final: 0.8957 (m-40) REVERT: C 76 ASP cc_start: 0.9154 (t0) cc_final: 0.8919 (t0) REVERT: C 82 ILE cc_start: 0.9562 (mt) cc_final: 0.9238 (mt) REVERT: C 111 ASP cc_start: 0.8490 (p0) cc_final: 0.7905 (p0) REVERT: A 60 ARG cc_start: 0.8918 (ptp-110) cc_final: 0.8519 (mtm-85) REVERT: A 91 PHE cc_start: 0.8798 (m-80) cc_final: 0.8416 (m-80) REVERT: A 92 GLN cc_start: 0.9203 (tt0) cc_final: 0.8854 (tt0) REVERT: A 106 MET cc_start: 0.8571 (ptp) cc_final: 0.8306 (ptp) REVERT: A 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9190 (tp) REVERT: A 111 ASP cc_start: 0.8489 (p0) cc_final: 0.8144 (p0) 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: 0.7971 (ttp-170) REVERT: E 53 LEU cc_start: 0.8520 (mm) cc_final: 0.8287 (mm) REVERT: E 77 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9183 (tm-30) REVERT: E 82 ILE cc_start: 0.9499 (mt) cc_final: 0.8846 (tp) REVERT: E 85 ASP cc_start: 0.9223 (m-30) cc_final: 0.8848 (m-30) REVERT: E 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8883 (tt) REVERT: F 4 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8212 (mp10) REVERT: F 8 ASP cc_start: 0.8980 (m-30) cc_final: 0.8540 (m-30) REVERT: F 60 ARG cc_start: 0.8871 (ptp-110) cc_final: 0.8551 (mpp80) REVERT: F 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8205 (t80) REVERT: F 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8874 (t0) REVERT: F 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8723 (mm-30) REVERT: G 35 ASN cc_start: 0.9207 (m-40) cc_final: 0.8930 (m-40) REVERT: G 70 PHE cc_start: 0.8726 (t80) cc_final: 0.8494 (t80) REVERT: G 76 ASP cc_start: 0.9190 (t0) cc_final: 0.8973 (t0) REVERT: G 81 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8615 (tm-30) REVERT: G 82 ILE cc_start: 0.9555 (mt) cc_final: 0.9112 (mm) REVERT: G 85 ASP cc_start: 0.8994 (m-30) cc_final: 0.8780 (m-30) REVERT: G 87 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8664 (mt-10) REVERT: G 111 ASP cc_start: 0.8379 (p0) cc_final: 0.8106 (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: 0.8705 (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: 0.8856 (tt0) REVERT: H 124 LEU cc_start: 0.9022 (tt) cc_final: 0.8280 (tt) REVERT: I 22 GLU cc_start: 0.7843 (mp0) cc_final: 0.7601 (mp0) REVERT: I 24 ILE cc_start: 0.8957 (pt) cc_final: 0.8730 (tp) REVERT: I 51 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8061 (ttp-110) REVERT: I 77 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9125 (tm-30) REVERT: I 82 ILE cc_start: 0.9512 (mt) cc_final: 0.8924 (tp) REVERT: I 85 ASP cc_start: 0.9199 (m-30) cc_final: 0.8895 (m-30) REVERT: I 124 LEU cc_start: 0.9209 (tt) cc_final: 0.8841 (tp) REVERT: J 4 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8228 (mp10) REVERT: J 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8546 (m-30) REVERT: J 35 ASN cc_start: 0.9011 (m-40) cc_final: 0.8801 (m-40) REVERT: J 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8671 (mpp80) REVERT: J 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7928 (t80) REVERT: J 76 ASP cc_start: 0.9134 (t0) cc_final: 0.8882 (t0) REVERT: J 112 TYR cc_start: 0.9385 (m-80) cc_final: 0.9154 (m-80) REVERT: K 70 PHE cc_start: 0.8833 (t80) cc_final: 0.8470 (t80) REVERT: K 76 ASP cc_start: 0.9200 (t0) cc_final: 0.8986 (t0) REVERT: K 81 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8487 (pp30) REVERT: K 82 ILE cc_start: 0.9580 (mt) cc_final: 0.9221 (mt) REVERT: K 85 ASP cc_start: 0.8989 (m-30) cc_final: 0.8756 (m-30) REVERT: K 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8780 (mt-10) REVERT: K 111 ASP cc_start: 0.8467 (p0) cc_final: 0.7477 (p0) REVERT: L 60 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8602 (mtm-85) REVERT: L 70 PHE cc_start: 0.9057 (t80) cc_final: 0.8666 (t80) REVERT: L 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8279 (m-80) REVERT: L 92 GLN cc_start: 0.9213 (tt0) cc_final: 0.8979 (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: 0.8748 (tp) REVERT: M 51 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8276 (ttp-170) REVERT: M 77 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9095 (tm-30) REVERT: M 82 ILE cc_start: 0.9530 (mt) cc_final: 0.8913 (tp) REVERT: M 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.8823 (m-30) REVERT: M 124 LEU cc_start: 0.9292 (tt) cc_final: 0.8917 (tt) REVERT: N 4 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8049 (mp10) REVERT: N 8 ASP cc_start: 0.8896 (m-30) cc_final: 0.8503 (m-30) REVERT: N 24 ILE cc_start: 0.9182 (pt) cc_final: 0.8937 (mp) REVERT: N 70 PHE cc_start: 0.8541 (t80) cc_final: 0.7781 (t80) REVERT: N 112 TYR cc_start: 0.9384 (m-80) cc_final: 0.9180 (m-80) REVERT: O 35 ASN cc_start: 0.9191 (m-40) cc_final: 0.8954 (m-40) REVERT: O 76 ASP cc_start: 0.9153 (t0) cc_final: 0.8914 (t0) REVERT: O 82 ILE cc_start: 0.9561 (mt) cc_final: 0.9236 (mt) REVERT: P 60 ARG cc_start: 0.8917 (ptp-110) cc_final: 0.8522 (mtm-85) REVERT: P 91 PHE cc_start: 0.8797 (m-80) cc_final: 0.8415 (m-80) REVERT: P 92 GLN cc_start: 0.9197 (tt0) cc_final: 0.8851 (tt0) REVERT: P 106 MET cc_start: 0.8578 (ptp) cc_final: 0.8307 (ptp) REVERT: P 107 ILE cc_start: 0.9675 (tp) cc_final: 0.9192 (tp) REVERT: P 124 LEU cc_start: 0.9164 (tt) cc_final: 0.8555 (tt) REVERT: Q 24 ILE cc_start: 0.9123 (pt) cc_final: 0.8856 (tp) REVERT: Q 51 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.7972 (ttp-170) REVERT: Q 53 LEU cc_start: 0.8519 (mm) cc_final: 0.8284 (mm) REVERT: Q 77 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9181 (tm-30) REVERT: Q 82 ILE cc_start: 0.9501 (mt) cc_final: 0.8848 (tp) REVERT: Q 85 ASP cc_start: 0.9219 (m-30) cc_final: 0.8850 (m-30) REVERT: Q 124 LEU cc_start: 0.9225 (tt) cc_final: 0.8881 (tt) REVERT: R 4 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8214 (mp10) REVERT: R 8 ASP cc_start: 0.8981 (m-30) cc_final: 0.8541 (m-30) REVERT: R 60 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8550 (mpp80) REVERT: R 70 PHE cc_start: 0.8594 (t80) cc_final: 0.8200 (t80) REVERT: R 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8872 (t0) REVERT: R 90 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8724 (mm-30) REVERT: S 35 ASN cc_start: 0.9209 (m-40) cc_final: 0.8935 (m-40) REVERT: S 70 PHE cc_start: 0.8728 (t80) cc_final: 0.8495 (t80) REVERT: S 76 ASP cc_start: 0.9188 (t0) cc_final: 0.8971 (t0) REVERT: S 81 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8615 (tm-30) REVERT: S 82 ILE cc_start: 0.9550 (mt) cc_final: 0.9108 (mm) REVERT: S 85 ASP cc_start: 0.8995 (m-30) cc_final: 0.8778 (m-30) REVERT: S 87 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8662 (mt-10) REVERT: S 111 ASP cc_start: 0.8378 (p0) cc_final: 0.8100 (p0) REVERT: T 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8953 (pt) REVERT: T 60 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8581 (mtm-85) REVERT: T 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8705 (t80) REVERT: T 91 PHE cc_start: 0.8826 (m-80) cc_final: 0.8563 (m-80) REVERT: T 92 GLN cc_start: 0.9125 (tt0) cc_final: 0.8847 (tt0) REVERT: T 124 LEU cc_start: 0.9019 (tt) cc_final: 0.8276 (tt) REVERT: U 22 GLU cc_start: 0.7839 (mp0) cc_final: 0.7599 (mp0) REVERT: U 24 ILE cc_start: 0.8953 (pt) cc_final: 0.8730 (tp) REVERT: U 51 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8055 (ttp-110) REVERT: U 77 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9123 (tm-30) REVERT: U 82 ILE cc_start: 0.9511 (mt) cc_final: 0.8924 (tp) REVERT: U 85 ASP cc_start: 0.9197 (m-30) cc_final: 0.8893 (m-30) REVERT: U 124 LEU cc_start: 0.9206 (tt) cc_final: 0.8844 (tp) REVERT: V 8 ASP cc_start: 0.8922 (m-30) cc_final: 0.8533 (m-30) REVERT: V 35 ASN cc_start: 0.9013 (m-40) cc_final: 0.8800 (m-40) REVERT: V 60 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8676 (mpp80) REVERT: V 70 PHE cc_start: 0.8523 (t80) cc_final: 0.7924 (t80) REVERT: V 76 ASP cc_start: 0.9133 (t0) cc_final: 0.8881 (t0) REVERT: V 112 TYR cc_start: 0.9387 (m-80) cc_final: 0.9148 (m-80) REVERT: W 70 PHE cc_start: 0.8834 (t80) cc_final: 0.8467 (t80) REVERT: W 76 ASP cc_start: 0.9196 (t0) cc_final: 0.8982 (t0) REVERT: W 81 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8487 (pp30) REVERT: W 82 ILE cc_start: 0.9576 (mt) cc_final: 0.9218 (mt) REVERT: W 85 ASP cc_start: 0.8985 (m-30) cc_final: 0.8754 (m-30) REVERT: W 87 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8777 (mt-10) REVERT: W 111 ASP cc_start: 0.8460 (p0) cc_final: 0.7475 (p0) REVERT: X 60 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8599 (mtm-85) REVERT: X 70 PHE cc_start: 0.9058 (t80) cc_final: 0.8664 (t80) REVERT: X 91 PHE cc_start: 0.8713 (m-80) cc_final: 0.8273 (m-80) REVERT: X 92 GLN cc_start: 0.9210 (tt0) cc_final: 0.8976 (tt0) REVERT: X 112 TYR cc_start: 0.9080 (m-80) cc_final: 0.8854 (m-10) REVERT: X 124 LEU cc_start: 0.9048 (tt) cc_final: 0.8287 (tt) outliers start: 0 outliers final: 0 residues processed: 1414 average time/residue: 0.1658 time to fit residues: 355.8755 Evaluate side-chains 878 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 878 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN D 92 GLN D 102 GLN D 116 HIS B 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN A 102 GLN A 116 HIS E 20 GLN E 92 GLN E 102 GLN E 116 HIS F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS I 20 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 116 HIS J 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 HIS M 20 GLN M 92 GLN M 102 GLN M 116 HIS N 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN P 102 GLN P 116 HIS Q 20 GLN Q 92 GLN Q 102 GLN Q 116 HIS R 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 HIS U 20 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 102 GLN U 116 HIS V 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 116 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.048701 restraints weight = 106986.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050390 restraints weight = 58392.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051569 restraints weight = 36291.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052345 restraints weight = 24578.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053018 restraints weight = 18116.150| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23688 Z= 0.207 Angle : 0.834 9.220 31968 Z= 0.430 Chirality : 0.053 0.257 3576 Planarity : 0.005 0.038 4248 Dihedral : 6.626 23.967 3264 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 8.63 % Allowed : 21.25 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.13 (0.13), residues: 3024 helix: -2.52 (0.18), residues: 480 sheet: -1.94 (0.14), residues: 1104 loop : -3.49 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 78 TYR 0.010 0.001 TYR M 112 PHE 0.032 0.002 PHE E 70 TRP 0.014 0.002 TRP P 50 HIS 0.007 0.002 HIS I 116 Details of bonding type rmsd covalent geometry : bond 0.00447 (23688) covalent geometry : angle 0.83395 (31968) hydrogen bonds : bond 0.04278 ( 816) hydrogen bonds : angle 7.00056 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 965 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 ILE cc_start: 0.8982 (pt) cc_final: 0.8732 (tp) REVERT: D 30 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8512 (t) REVERT: D 51 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8261 (ttp-170) REVERT: D 52 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8145 (mp0) REVERT: D 53 LEU cc_start: 0.8855 (mm) cc_final: 0.8535 (mm) REVERT: D 70 PHE cc_start: 0.8901 (t80) cc_final: 0.8470 (t80) REVERT: D 78 ARG cc_start: 0.9315 (tpp80) cc_final: 0.8914 (tpt-90) REVERT: D 82 ILE cc_start: 0.9370 (mt) cc_final: 0.8914 (mm) REVERT: B 20 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6736 (pp30) REVERT: B 74 ASP cc_start: 0.8901 (p0) cc_final: 0.8589 (p0) REVERT: B 92 GLN cc_start: 0.9140 (tt0) cc_final: 0.8785 (tt0) REVERT: B 111 ASP cc_start: 0.8867 (p0) cc_final: 0.8658 (p0) REVERT: B 124 LEU cc_start: 0.9660 (tt) cc_final: 0.8911 (tt) REVERT: C 52 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8491 (mt-10) REVERT: C 53 LEU cc_start: 0.9446 (mm) cc_final: 0.9135 (mt) REVERT: C 81 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8411 (pp30) REVERT: C 82 ILE cc_start: 0.9495 (mt) cc_final: 0.9243 (mt) REVERT: A 60 ARG cc_start: 0.8963 (ptp-110) cc_final: 0.8667 (mpp80) REVERT: A 76 ASP cc_start: 0.8951 (t0) cc_final: 0.8608 (t0) REVERT: A 85 ASP cc_start: 0.8977 (m-30) cc_final: 0.8291 (p0) REVERT: A 87 GLU cc_start: 0.8823 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 92 GLN cc_start: 0.9138 (tt0) cc_final: 0.8709 (tt0) REVERT: E 24 ILE cc_start: 0.9163 (pt) cc_final: 0.8937 (tp) REVERT: E 31 ARG cc_start: 0.8759 (mtp-110) cc_final: 0.8387 (tpp80) REVERT: E 52 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7668 (mp0) REVERT: E 70 PHE cc_start: 0.9166 (t80) cc_final: 0.8902 (t80) REVERT: E 78 ARG cc_start: 0.9364 (tpp80) cc_final: 0.9125 (mmm160) REVERT: E 82 ILE cc_start: 0.9401 (mt) cc_final: 0.8956 (mm) REVERT: F 4 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8136 (mp10) REVERT: F 20 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6801 (pp30) REVERT: F 70 PHE cc_start: 0.8525 (t80) cc_final: 0.8245 (t80) REVERT: F 90 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8535 (mm-30) REVERT: G 31 ARG cc_start: 0.8539 (ttt90) cc_final: 0.7489 (ttt90) REVERT: G 51 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8579 (ttp-110) REVERT: G 52 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 78 ARG cc_start: 0.9350 (tpp80) cc_final: 0.8612 (tpp80) REVERT: G 81 GLN cc_start: 0.8990 (tm-30) cc_final: 0.7327 (tm-30) REVERT: G 82 ILE cc_start: 0.9518 (mt) cc_final: 0.8879 (mm) REVERT: G 85 ASP cc_start: 0.8931 (m-30) cc_final: 0.8235 (p0) REVERT: G 87 GLU cc_start: 0.8775 (mt-10) cc_final: 0.7436 (mt-10) REVERT: G 106 MET cc_start: 0.7590 (pmm) cc_final: 0.7063 (pmm) REVERT: H 14 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6995 (t70) REVERT: H 60 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8651 (ptp90) REVERT: H 76 ASP cc_start: 0.8977 (t0) cc_final: 0.8738 (t0) REVERT: H 92 GLN cc_start: 0.8974 (tt0) cc_final: 0.8651 (tt0) REVERT: I 5 ASN cc_start: 0.8476 (t0) cc_final: 0.7125 (t0) REVERT: I 7 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9088 (mtmt) REVERT: I 24 ILE cc_start: 0.8938 (pt) cc_final: 0.8694 (tp) REVERT: I 27 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8519 (tp) REVERT: I 31 ARG cc_start: 0.8805 (mtp-110) cc_final: 0.8563 (mtp-110) REVERT: I 51 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.7873 (ttp-170) REVERT: I 52 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7810 (mt-10) REVERT: I 53 LEU cc_start: 0.8925 (mm) cc_final: 0.8605 (mm) REVERT: I 78 ARG cc_start: 0.9327 (tpp80) cc_final: 0.9028 (tpt-90) REVERT: I 82 ILE cc_start: 0.9435 (mt) cc_final: 0.9080 (mm) REVERT: I 94 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9292 (tp) REVERT: J 4 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8212 (mp10) REVERT: J 20 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6695 (pp30) REVERT: J 31 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8547 (ttt90) REVERT: J 70 PHE cc_start: 0.8398 (t80) cc_final: 0.7878 (t80) REVERT: K 31 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8104 (mmm160) REVERT: K 47 GLN cc_start: 0.8477 (mp10) cc_final: 0.8197 (mp10) REVERT: K 51 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8746 (ttp80) REVERT: K 52 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8391 (mt-10) REVERT: K 81 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 82 ILE cc_start: 0.9469 (mt) cc_final: 0.9062 (mt) REVERT: K 85 ASP cc_start: 0.8925 (m-30) cc_final: 0.8462 (p0) REVERT: K 111 ASP cc_start: 0.7979 (p0) cc_final: 0.7736 (p0) REVERT: K 126 MET cc_start: 0.8423 (mtp) cc_final: 0.8174 (mtm) REVERT: L 20 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6958 (pp30) REVERT: L 60 ARG cc_start: 0.8931 (ptp-110) cc_final: 0.8640 (mpp80) REVERT: L 92 GLN cc_start: 0.9013 (tt0) cc_final: 0.8661 (tt0) REVERT: M 24 ILE cc_start: 0.8974 (pt) cc_final: 0.8726 (tp) REVERT: M 30 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8516 (t) REVERT: M 51 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8258 (ttp-170) REVERT: M 52 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8151 (mp0) REVERT: M 53 LEU cc_start: 0.8860 (mm) cc_final: 0.8538 (mm) REVERT: M 70 PHE cc_start: 0.8907 (t80) cc_final: 0.8480 (t80) REVERT: M 78 ARG cc_start: 0.9320 (tpp80) cc_final: 0.8919 (tpt-90) REVERT: M 82 ILE cc_start: 0.9364 (mt) cc_final: 0.8917 (mm) REVERT: N 20 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6731 (pp30) REVERT: N 70 PHE cc_start: 0.8285 (t80) cc_final: 0.8038 (t80) REVERT: N 74 ASP cc_start: 0.8899 (p0) cc_final: 0.8591 (p0) REVERT: N 92 GLN cc_start: 0.9147 (tt0) cc_final: 0.8786 (tt0) REVERT: N 111 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8652 (p0) REVERT: N 124 LEU cc_start: 0.9665 (tt) cc_final: 0.8892 (tt) REVERT: O 52 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8496 (mt-10) REVERT: O 53 LEU cc_start: 0.9445 (mm) cc_final: 0.9157 (mt) REVERT: O 81 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: O 82 ILE cc_start: 0.9492 (mt) cc_final: 0.9246 (mt) REVERT: P 60 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8671 (mpp80) REVERT: P 76 ASP cc_start: 0.8941 (t0) cc_final: 0.8588 (t0) REVERT: P 85 ASP cc_start: 0.8972 (m-30) cc_final: 0.8291 (p0) REVERT: P 87 GLU cc_start: 0.8829 (mt-10) cc_final: 0.7258 (mt-10) REVERT: P 92 GLN cc_start: 0.9133 (tt0) cc_final: 0.8702 (tt0) REVERT: Q 24 ILE cc_start: 0.9162 (pt) cc_final: 0.8940 (tp) REVERT: Q 31 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8381 (tpp80) REVERT: Q 52 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7675 (mp0) REVERT: Q 70 PHE cc_start: 0.9176 (t80) cc_final: 0.8911 (t80) REVERT: Q 78 ARG cc_start: 0.9366 (tpp80) cc_final: 0.9123 (mmm160) REVERT: Q 82 ILE cc_start: 0.9400 (mt) cc_final: 0.8958 (mm) REVERT: R 4 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8127 (mp10) REVERT: R 20 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: R 70 PHE cc_start: 0.8526 (t80) cc_final: 0.8252 (t80) REVERT: R 90 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8538 (mm-30) REVERT: R 92 GLN cc_start: 0.9090 (tt0) cc_final: 0.8885 (tt0) REVERT: S 31 ARG cc_start: 0.8536 (ttt90) cc_final: 0.7480 (ttt90) REVERT: S 51 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8579 (ttp-110) REVERT: S 52 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8442 (mt-10) REVERT: S 78 ARG cc_start: 0.9351 (tpp80) cc_final: 0.8614 (tpp80) REVERT: S 81 GLN cc_start: 0.8993 (tm-30) cc_final: 0.7311 (tm-30) REVERT: S 82 ILE cc_start: 0.9516 (mt) cc_final: 0.8880 (mm) REVERT: S 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8245 (p0) REVERT: S 87 GLU cc_start: 0.8786 (mt-10) cc_final: 0.7435 (mt-10) REVERT: S 106 MET cc_start: 0.7571 (pmm) cc_final: 0.7081 (pmm) REVERT: T 14 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6999 (t70) REVERT: T 60 ARG cc_start: 0.8873 (ptp-110) cc_final: 0.8649 (ptp90) REVERT: T 76 ASP cc_start: 0.8947 (t0) cc_final: 0.8681 (t0) REVERT: T 92 GLN cc_start: 0.8967 (tt0) cc_final: 0.8643 (tt0) REVERT: U 5 ASN cc_start: 0.8482 (t0) cc_final: 0.7855 (t0) REVERT: U 24 ILE cc_start: 0.8936 (pt) cc_final: 0.8695 (tp) REVERT: U 27 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8501 (tp) REVERT: U 51 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.7877 (ttp-170) REVERT: U 52 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7815 (mt-10) REVERT: U 53 LEU cc_start: 0.8920 (mm) cc_final: 0.8546 (mm) REVERT: U 78 ARG cc_start: 0.9329 (tpp80) cc_final: 0.9033 (tpt-90) REVERT: U 82 ILE cc_start: 0.9433 (mt) cc_final: 0.9081 (mm) REVERT: U 94 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9292 (tp) REVERT: V 20 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6706 (pp30) REVERT: V 70 PHE cc_start: 0.8408 (t80) cc_final: 0.7873 (t80) REVERT: W 47 GLN cc_start: 0.8486 (mp10) cc_final: 0.8205 (mp10) REVERT: W 51 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8760 (ttp80) REVERT: W 52 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8391 (mt-10) REVERT: W 81 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8060 (tm-30) REVERT: W 82 ILE cc_start: 0.9469 (mt) cc_final: 0.9065 (mt) REVERT: W 85 ASP cc_start: 0.8927 (m-30) cc_final: 0.8468 (p0) REVERT: W 111 ASP cc_start: 0.7956 (p0) cc_final: 0.7721 (p0) REVERT: W 126 MET cc_start: 0.8436 (mtp) cc_final: 0.8183 (mtm) REVERT: X 20 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6957 (pp30) REVERT: X 60 ARG cc_start: 0.8956 (ptp-110) cc_final: 0.8648 (mpp80) REVERT: X 92 GLN cc_start: 0.9017 (tt0) cc_final: 0.8658 (tt0) outliers start: 205 outliers final: 112 residues processed: 1035 average time/residue: 0.1499 time to fit residues: 243.9545 Evaluate side-chains 971 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 840 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 20 GLN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 20 GLN Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 35 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 228 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS C 20 GLN C 102 GLN A 20 GLN F 92 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN J 116 HIS K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 HIS O 20 GLN O 102 GLN P 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** T 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 GLN V 116 HIS W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045855 restraints weight = 111219.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.047480 restraints weight = 58605.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048599 restraints weight = 35766.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049395 restraints weight = 23961.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049980 restraints weight = 17140.763| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23688 Z= 0.227 Angle : 0.847 9.583 31968 Z= 0.421 Chirality : 0.052 0.271 3576 Planarity : 0.004 0.031 4248 Dihedral : 6.153 23.062 3264 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 10.44 % Allowed : 22.01 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.13), residues: 3024 helix: -1.92 (0.20), residues: 480 sheet: -1.70 (0.14), residues: 1104 loop : -3.43 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 31 TYR 0.015 0.001 TYR X 122 PHE 0.021 0.002 PHE K 70 TRP 0.011 0.002 TRP K 50 HIS 0.004 0.002 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00491 (23688) covalent geometry : angle 0.84663 (31968) hydrogen bonds : bond 0.03729 ( 816) hydrogen bonds : angle 6.25808 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 882 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8272 (ttp-170) REVERT: D 52 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8144 (mp0) REVERT: D 70 PHE cc_start: 0.8948 (t80) cc_final: 0.8355 (t80) REVERT: D 78 ARG cc_start: 0.9317 (tpp80) cc_final: 0.9054 (tpp80) REVERT: D 82 ILE cc_start: 0.9471 (mt) cc_final: 0.9216 (mm) REVERT: D 87 GLU cc_start: 0.8782 (pm20) cc_final: 0.8557 (pm20) REVERT: B 4 GLN cc_start: 0.8721 (mm-40) cc_final: 0.7963 (mp10) REVERT: B 74 ASP cc_start: 0.8931 (p0) cc_final: 0.8637 (p0) REVERT: B 76 ASP cc_start: 0.8577 (t0) cc_final: 0.7387 (t0) REVERT: B 98 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 111 ASP cc_start: 0.8829 (p0) cc_final: 0.8624 (p0) REVERT: C 81 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8587 (pp30) REVERT: C 82 ILE cc_start: 0.9488 (mt) cc_final: 0.9252 (mt) REVERT: A 35 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.9037 (p0) REVERT: A 70 PHE cc_start: 0.8709 (t80) cc_final: 0.7525 (t80) REVERT: A 76 ASP cc_start: 0.8961 (t0) cc_final: 0.8200 (t0) REVERT: A 85 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 87 GLU cc_start: 0.8731 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 92 GLN cc_start: 0.9017 (tt0) cc_final: 0.8735 (tt0) REVERT: A 98 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: A 119 GLU cc_start: 0.8699 (pm20) cc_final: 0.8480 (pm20) REVERT: A 126 MET cc_start: 0.8273 (mmm) cc_final: 0.7639 (mmt) REVERT: E 24 ILE cc_start: 0.9110 (pt) cc_final: 0.8767 (tp) REVERT: E 51 ARG cc_start: 0.8960 (ttp-110) cc_final: 0.8459 (ttp-170) REVERT: E 52 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7813 (mp0) REVERT: E 70 PHE cc_start: 0.9185 (t80) cc_final: 0.8834 (t80) REVERT: F 70 PHE cc_start: 0.8426 (t80) cc_final: 0.5865 (t80) REVERT: F 74 ASP cc_start: 0.9019 (p0) cc_final: 0.8795 (p0) REVERT: F 76 ASP cc_start: 0.8784 (t0) cc_final: 0.7973 (t0) REVERT: F 98 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: G 31 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7604 (ttt90) REVERT: G 51 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8641 (ttp-170) REVERT: G 78 ARG cc_start: 0.9306 (tpp80) cc_final: 0.8589 (tpp80) REVERT: G 81 GLN cc_start: 0.9001 (tm-30) cc_final: 0.7766 (tm-30) REVERT: G 82 ILE cc_start: 0.9510 (mt) cc_final: 0.8929 (mm) REVERT: G 85 ASP cc_start: 0.8849 (m-30) cc_final: 0.8457 (p0) REVERT: H 31 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8379 (ptm-80) REVERT: H 76 ASP cc_start: 0.8943 (t0) cc_final: 0.8596 (t0) REVERT: H 85 ASP cc_start: 0.8978 (m-30) cc_final: 0.8567 (p0) REVERT: H 87 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7860 (mt-10) REVERT: I 5 ASN cc_start: 0.8682 (t0) cc_final: 0.7394 (t0) REVERT: I 7 LYS cc_start: 0.9309 (mtpt) cc_final: 0.8982 (mtmm) REVERT: I 24 ILE cc_start: 0.8973 (pt) cc_final: 0.8568 (tp) REVERT: I 27 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8616 (tp) REVERT: I 51 ARG cc_start: 0.9004 (ttp-110) cc_final: 0.8204 (ttp-170) REVERT: I 52 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7679 (mt-10) REVERT: I 82 ILE cc_start: 0.9505 (mt) cc_final: 0.9112 (mm) REVERT: I 87 GLU cc_start: 0.8858 (pm20) cc_final: 0.8391 (pm20) REVERT: I 98 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: I 124 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.8786 (tt) REVERT: J 4 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8246 (mm-40) REVERT: J 70 PHE cc_start: 0.8297 (t80) cc_final: 0.5666 (t80) REVERT: J 76 ASP cc_start: 0.8523 (t0) cc_final: 0.7156 (t0) REVERT: J 98 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: K 7 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9085 (mtmm) REVERT: K 31 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8200 (mmm160) REVERT: K 51 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8670 (ttp-170) REVERT: K 52 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8265 (mt-10) REVERT: K 81 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8411 (tm-30) REVERT: K 82 ILE cc_start: 0.9498 (mt) cc_final: 0.8890 (mt) REVERT: K 85 ASP cc_start: 0.8883 (m-30) cc_final: 0.8478 (p0) REVERT: K 98 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: K 106 MET cc_start: 0.8464 (ttm) cc_final: 0.8258 (ttt) REVERT: K 111 ASP cc_start: 0.8591 (p0) cc_final: 0.8155 (p0) REVERT: K 123 GLU cc_start: 0.8294 (mp0) cc_final: 0.8080 (mp0) REVERT: L 60 ARG cc_start: 0.8919 (ptp-110) cc_final: 0.8638 (mpp80) REVERT: L 92 GLN cc_start: 0.9035 (tt0) cc_final: 0.8675 (tt0) REVERT: L 98 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: L 111 ASP cc_start: 0.8488 (p0) cc_final: 0.8017 (p0) REVERT: M 51 ARG cc_start: 0.8976 (ttp-110) cc_final: 0.8267 (ttp-170) REVERT: M 52 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8150 (mp0) REVERT: M 70 PHE cc_start: 0.8956 (t80) cc_final: 0.8369 (t80) REVERT: M 78 ARG cc_start: 0.9319 (tpp80) cc_final: 0.9057 (tpp80) REVERT: N 4 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7944 (mp10) REVERT: N 70 PHE cc_start: 0.8423 (t80) cc_final: 0.6765 (t80) REVERT: N 74 ASP cc_start: 0.8928 (p0) cc_final: 0.8622 (p0) REVERT: N 76 ASP cc_start: 0.8680 (t0) cc_final: 0.8100 (t0) REVERT: N 98 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.6577 (m-10) REVERT: O 70 PHE cc_start: 0.8329 (t80) cc_final: 0.5852 (t80) REVERT: O 76 ASP cc_start: 0.9159 (t0) cc_final: 0.8531 (t0) REVERT: O 81 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8574 (pp30) REVERT: O 82 ILE cc_start: 0.9491 (mt) cc_final: 0.9251 (mt) REVERT: P 35 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.9029 (p0) REVERT: P 70 PHE cc_start: 0.8709 (t80) cc_final: 0.8239 (t80) REVERT: P 76 ASP cc_start: 0.8963 (t0) cc_final: 0.8663 (t0) REVERT: P 85 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8315 (p0) REVERT: P 87 GLU cc_start: 0.8727 (mt-10) cc_final: 0.7393 (mt-10) REVERT: P 92 GLN cc_start: 0.9013 (tt0) cc_final: 0.8735 (tt0) REVERT: P 98 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: P 119 GLU cc_start: 0.8693 (pm20) cc_final: 0.8475 (pm20) REVERT: P 126 MET cc_start: 0.8277 (mmm) cc_final: 0.7646 (mmt) REVERT: Q 24 ILE cc_start: 0.9116 (pt) cc_final: 0.8773 (tp) REVERT: Q 51 ARG cc_start: 0.8955 (ttp-110) cc_final: 0.8156 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7806 (mp0) REVERT: Q 70 PHE cc_start: 0.9189 (t80) cc_final: 0.8838 (t80) REVERT: R 70 PHE cc_start: 0.8426 (t80) cc_final: 0.5898 (t80) REVERT: R 74 ASP cc_start: 0.9015 (p0) cc_final: 0.8774 (p0) REVERT: R 76 ASP cc_start: 0.8784 (t0) cc_final: 0.7995 (t0) REVERT: R 98 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.6699 (m-10) REVERT: S 31 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7607 (ttt90) REVERT: S 51 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8633 (ttp-170) REVERT: S 78 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8588 (tpp80) REVERT: S 81 GLN cc_start: 0.8997 (tm-30) cc_final: 0.7764 (tm-30) REVERT: S 82 ILE cc_start: 0.9510 (mt) cc_final: 0.8927 (mm) REVERT: S 85 ASP cc_start: 0.8861 (m-30) cc_final: 0.8464 (p0) REVERT: T 31 ARG cc_start: 0.9089 (ptm-80) cc_final: 0.8376 (ptm-80) REVERT: T 76 ASP cc_start: 0.8986 (t0) cc_final: 0.8689 (t0) REVERT: T 85 ASP cc_start: 0.8940 (m-30) cc_final: 0.8698 (p0) REVERT: U 5 ASN cc_start: 0.9054 (t0) cc_final: 0.8800 (t0) REVERT: U 24 ILE cc_start: 0.8983 (pt) cc_final: 0.8573 (tp) REVERT: U 27 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8614 (tp) REVERT: U 31 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8756 (mmm-85) REVERT: U 51 ARG cc_start: 0.9010 (ttp-110) cc_final: 0.8200 (ttp-170) REVERT: U 52 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7711 (mt-10) REVERT: U 82 ILE cc_start: 0.9513 (mt) cc_final: 0.9119 (mm) REVERT: U 87 GLU cc_start: 0.8872 (pm20) cc_final: 0.8426 (pm20) REVERT: U 98 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: U 124 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.8796 (tt) REVERT: V 70 PHE cc_start: 0.8308 (t80) cc_final: 0.5751 (t80) REVERT: V 76 ASP cc_start: 0.8541 (t0) cc_final: 0.7285 (t0) REVERT: V 98 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6857 (m-10) REVERT: W 7 LYS cc_start: 0.9433 (mtmt) cc_final: 0.9086 (mtmm) REVERT: W 51 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8692 (ttp-170) REVERT: W 52 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8282 (mt-10) REVERT: W 81 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8411 (tm-30) REVERT: W 82 ILE cc_start: 0.9492 (mt) cc_final: 0.8889 (mt) REVERT: W 85 ASP cc_start: 0.8892 (m-30) cc_final: 0.8478 (p0) REVERT: W 111 ASP cc_start: 0.8585 (p0) cc_final: 0.8160 (p0) REVERT: W 123 GLU cc_start: 0.8297 (mp0) cc_final: 0.8080 (mp0) REVERT: X 60 ARG cc_start: 0.8922 (ptp-110) cc_final: 0.8634 (mpp80) REVERT: X 92 GLN cc_start: 0.9046 (tt0) cc_final: 0.8690 (tt0) REVERT: X 98 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.6883 (m-10) REVERT: X 111 ASP cc_start: 0.8484 (p0) cc_final: 0.8012 (p0) outliers start: 248 outliers final: 154 residues processed: 996 average time/residue: 0.1690 time to fit residues: 263.1553 Evaluate side-chains 975 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 798 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 14 ASP Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 46 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN B 102 GLN C 20 GLN A 20 GLN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 102 GLN I 92 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN N 102 GLN O 20 GLN P 20 GLN R 92 GLN R 102 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN T 102 GLN U 92 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045696 restraints weight = 109110.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047259 restraints weight = 59094.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048360 restraints weight = 36935.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049160 restraints weight = 24965.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049742 restraints weight = 17956.006| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23688 Z= 0.200 Angle : 0.826 11.298 31968 Z= 0.408 Chirality : 0.051 0.261 3576 Planarity : 0.004 0.040 4248 Dihedral : 5.861 24.007 3264 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 11.03 % Allowed : 23.15 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.13), residues: 3024 helix: -1.49 (0.21), residues: 480 sheet: -1.60 (0.13), residues: 1224 loop : -3.59 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 51 TYR 0.014 0.001 TYR H 122 PHE 0.024 0.002 PHE F 91 TRP 0.011 0.002 TRP L 50 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00434 (23688) covalent geometry : angle 0.82579 (31968) hydrogen bonds : bond 0.03352 ( 816) hydrogen bonds : angle 5.90104 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 847 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8680 (tp) REVERT: D 51 ARG cc_start: 0.9012 (ttp-110) cc_final: 0.8466 (ttp-170) REVERT: D 52 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8069 (mp0) REVERT: D 70 PHE cc_start: 0.9008 (t80) cc_final: 0.8388 (t80) REVERT: D 76 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: B 4 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7951 (mp10) REVERT: B 8 ASP cc_start: 0.8873 (m-30) cc_final: 0.8588 (m-30) REVERT: B 74 ASP cc_start: 0.8925 (p0) cc_final: 0.8639 (p0) REVERT: B 76 ASP cc_start: 0.8590 (t0) cc_final: 0.7403 (t0) REVERT: B 98 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: B 123 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8584 (mt-10) REVERT: C 20 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: C 31 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.7661 (ttt90) REVERT: C 81 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8550 (pp30) REVERT: C 82 ILE cc_start: 0.9441 (mt) cc_final: 0.9234 (mt) REVERT: C 133 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9207 (p) REVERT: A 35 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9084 (p0) REVERT: A 70 PHE cc_start: 0.8731 (t80) cc_final: 0.7459 (t80) REVERT: A 76 ASP cc_start: 0.8988 (t0) cc_final: 0.8382 (t0) REVERT: A 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8388 (p0) REVERT: A 87 GLU cc_start: 0.8763 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 92 GLN cc_start: 0.8991 (tt0) cc_final: 0.8665 (tt0) REVERT: A 98 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: E 13 LEU cc_start: 0.9418 (pp) cc_final: 0.9202 (pp) REVERT: E 51 ARG cc_start: 0.8956 (ttp-170) cc_final: 0.8215 (ttp-170) REVERT: E 52 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7700 (mp0) REVERT: E 70 PHE cc_start: 0.9139 (t80) cc_final: 0.8818 (t80) REVERT: F 4 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7862 (mp10) REVERT: F 70 PHE cc_start: 0.8387 (t80) cc_final: 0.5866 (t80) REVERT: F 74 ASP cc_start: 0.9001 (p0) cc_final: 0.8768 (p0) REVERT: F 76 ASP cc_start: 0.8789 (t0) cc_final: 0.7868 (t0) REVERT: F 98 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.6311 (m-10) REVERT: G 31 ARG cc_start: 0.8212 (ttt90) cc_final: 0.7663 (ttt90) REVERT: G 51 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8649 (ttp-170) REVERT: G 81 GLN cc_start: 0.9038 (tm-30) cc_final: 0.7722 (tm-30) REVERT: G 82 ILE cc_start: 0.9503 (mt) cc_final: 0.9131 (mt) REVERT: G 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8361 (p0) REVERT: G 87 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7534 (mt-10) REVERT: G 111 ASP cc_start: 0.8244 (p0) cc_final: 0.7693 (p0) REVERT: H 31 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8281 (ptm-80) REVERT: H 76 ASP cc_start: 0.9020 (t0) cc_final: 0.8794 (t0) REVERT: H 85 ASP cc_start: 0.8983 (m-30) cc_final: 0.8446 (p0) REVERT: H 87 GLU cc_start: 0.8796 (mt-10) cc_final: 0.7905 (mt-10) REVERT: I 5 ASN cc_start: 0.8742 (t0) cc_final: 0.8438 (t0) REVERT: I 51 ARG cc_start: 0.9018 (ttp-170) cc_final: 0.8447 (ttp-170) REVERT: I 52 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7722 (mt-10) REVERT: I 85 ASP cc_start: 0.8892 (m-30) cc_final: 0.8575 (m-30) REVERT: J 4 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8422 (mm-40) REVERT: J 70 PHE cc_start: 0.8286 (t80) cc_final: 0.5799 (t80) REVERT: J 76 ASP cc_start: 0.8580 (t0) cc_final: 0.7271 (t0) REVERT: J 98 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: K 7 LYS cc_start: 0.9401 (mtmt) cc_final: 0.9071 (mtmm) REVERT: K 31 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8302 (mtp85) REVERT: K 81 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8050 (tm-30) REVERT: K 82 ILE cc_start: 0.9464 (mt) cc_final: 0.8170 (mt) REVERT: K 85 ASP cc_start: 0.8873 (m-30) cc_final: 0.7913 (p0) REVERT: K 87 GLU cc_start: 0.8850 (mt-10) cc_final: 0.7922 (mp0) REVERT: K 98 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: K 111 ASP cc_start: 0.8653 (p0) cc_final: 0.8144 (p0) REVERT: K 123 GLU cc_start: 0.8357 (mp0) cc_final: 0.8140 (mp0) REVERT: L 35 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.9078 (p0) REVERT: L 92 GLN cc_start: 0.8990 (tt0) cc_final: 0.8694 (tt0) REVERT: L 98 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: L 111 ASP cc_start: 0.8463 (p0) cc_final: 0.7714 (p0) REVERT: M 27 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8684 (tp) REVERT: M 51 ARG cc_start: 0.9005 (ttp-110) cc_final: 0.8463 (ttp-170) REVERT: M 52 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8072 (mp0) REVERT: M 70 PHE cc_start: 0.9002 (t80) cc_final: 0.8537 (t80) REVERT: M 76 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8966 (m-30) REVERT: N 4 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7930 (mp10) REVERT: N 8 ASP cc_start: 0.8875 (m-30) cc_final: 0.8599 (m-30) REVERT: N 74 ASP cc_start: 0.8924 (p0) cc_final: 0.8584 (p0) REVERT: N 76 ASP cc_start: 0.8725 (t0) cc_final: 0.7812 (t0) REVERT: N 98 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.6394 (m-10) REVERT: O 20 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: O 31 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.7673 (ttt90) REVERT: O 70 PHE cc_start: 0.8243 (t80) cc_final: 0.5907 (t80) REVERT: O 76 ASP cc_start: 0.9218 (t0) cc_final: 0.8827 (t0) REVERT: O 81 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8576 (pp30) REVERT: O 133 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.9206 (p) REVERT: P 35 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9053 (p0) REVERT: P 70 PHE cc_start: 0.8733 (t80) cc_final: 0.8408 (t80) REVERT: P 85 ASP cc_start: 0.8951 (m-30) cc_final: 0.8394 (p0) REVERT: P 87 GLU cc_start: 0.8777 (mt-10) cc_final: 0.7549 (mt-10) REVERT: P 92 GLN cc_start: 0.9000 (tt0) cc_final: 0.8672 (tt0) REVERT: P 98 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: Q 13 LEU cc_start: 0.9418 (pp) cc_final: 0.9203 (pp) REVERT: Q 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8233 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7685 (mp0) REVERT: Q 70 PHE cc_start: 0.9140 (t80) cc_final: 0.8824 (t80) REVERT: R 4 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7867 (mp10) REVERT: R 70 PHE cc_start: 0.8393 (t80) cc_final: 0.5909 (t80) REVERT: R 74 ASP cc_start: 0.8998 (p0) cc_final: 0.8744 (p0) REVERT: R 76 ASP cc_start: 0.8786 (t0) cc_final: 0.7885 (t0) REVERT: R 98 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: S 31 ARG cc_start: 0.8204 (ttt90) cc_final: 0.7666 (ttt90) REVERT: S 51 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8640 (ttp-170) REVERT: S 81 GLN cc_start: 0.9031 (tm-30) cc_final: 0.7725 (tm-30) REVERT: S 82 ILE cc_start: 0.9506 (mt) cc_final: 0.9140 (mt) REVERT: S 85 ASP cc_start: 0.8885 (m-30) cc_final: 0.8366 (p0) REVERT: S 87 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7538 (mt-10) REVERT: S 111 ASP cc_start: 0.8248 (p0) cc_final: 0.7706 (p0) REVERT: T 31 ARG cc_start: 0.9187 (ptm-80) cc_final: 0.8308 (ptm-80) REVERT: T 76 ASP cc_start: 0.9044 (t0) cc_final: 0.8777 (t0) REVERT: U 5 ASN cc_start: 0.9094 (t0) cc_final: 0.8018 (t0) REVERT: U 7 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9097 (mtmm) REVERT: U 51 ARG cc_start: 0.9014 (ttp-170) cc_final: 0.8444 (ttp-170) REVERT: U 52 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7743 (mt-10) REVERT: U 85 ASP cc_start: 0.8880 (m-30) cc_final: 0.8564 (m-30) REVERT: U 98 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: V 70 PHE cc_start: 0.8299 (t80) cc_final: 0.5785 (t80) REVERT: V 76 ASP cc_start: 0.8587 (t0) cc_final: 0.7324 (t0) REVERT: V 98 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6654 (m-10) REVERT: W 7 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9072 (mtmm) REVERT: W 81 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8057 (tm-30) REVERT: W 82 ILE cc_start: 0.9455 (mt) cc_final: 0.8166 (mt) REVERT: W 85 ASP cc_start: 0.8896 (m-30) cc_final: 0.7916 (p0) REVERT: W 87 GLU cc_start: 0.8832 (mt-10) cc_final: 0.7921 (mp0) REVERT: W 111 ASP cc_start: 0.8661 (p0) cc_final: 0.8166 (p0) REVERT: W 123 GLU cc_start: 0.8347 (mp0) cc_final: 0.8147 (mp0) REVERT: X 31 ARG cc_start: 0.9179 (ptm-80) cc_final: 0.8695 (ptm-80) REVERT: X 35 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9085 (p0) REVERT: X 71 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8294 (mtmm) REVERT: X 92 GLN cc_start: 0.8993 (tt0) cc_final: 0.8718 (tt0) REVERT: X 98 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.6658 (m-10) REVERT: X 111 ASP cc_start: 0.8460 (p0) cc_final: 0.7639 (p0) outliers start: 262 outliers final: 152 residues processed: 984 average time/residue: 0.1649 time to fit residues: 255.0218 Evaluate side-chains 931 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 752 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 235 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN C 102 GLN A 20 GLN F 102 GLN G 20 GLN H 20 GLN I 92 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN O 20 GLN O 102 GLN P 20 GLN S 20 GLN T 20 GLN U 92 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047311 restraints weight = 107347.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048969 restraints weight = 57043.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050125 restraints weight = 35080.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050951 restraints weight = 23519.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051547 restraints weight = 16725.293| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23688 Z= 0.150 Angle : 0.841 10.638 31968 Z= 0.411 Chirality : 0.052 0.227 3576 Planarity : 0.004 0.041 4248 Dihedral : 5.658 24.059 3264 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 9.68 % Allowed : 25.55 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.13), residues: 3024 helix: -1.04 (0.22), residues: 456 sheet: -1.46 (0.13), residues: 1224 loop : -3.51 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 78 TYR 0.015 0.001 TYR L 122 PHE 0.029 0.002 PHE R 91 TRP 0.004 0.001 TRP X 50 HIS 0.002 0.001 HIS S 116 Details of bonding type rmsd covalent geometry : bond 0.00336 (23688) covalent geometry : angle 0.84092 (31968) hydrogen bonds : bond 0.03146 ( 816) hydrogen bonds : angle 5.62988 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 851 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8704 (tp) REVERT: D 31 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8806 (mmm-85) REVERT: D 51 ARG cc_start: 0.9037 (ttp-110) cc_final: 0.8458 (ttp-170) REVERT: D 52 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8122 (mp0) REVERT: D 60 ARG cc_start: 0.9086 (ptp-110) cc_final: 0.8649 (ptp90) REVERT: D 70 PHE cc_start: 0.8961 (t80) cc_final: 0.8529 (t80) REVERT: D 87 GLU cc_start: 0.8849 (pm20) cc_final: 0.8194 (pp20) REVERT: B 4 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8192 (mp10) REVERT: B 8 ASP cc_start: 0.8840 (m-30) cc_final: 0.8578 (m-30) REVERT: B 74 ASP cc_start: 0.8827 (p0) cc_final: 0.8532 (p0) REVERT: B 76 ASP cc_start: 0.8468 (t0) cc_final: 0.7280 (t0) REVERT: B 98 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.5701 (m-10) REVERT: C 31 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.6353 (ttt90) REVERT: C 51 ARG cc_start: 0.8911 (ttp-110) cc_final: 0.8558 (ttp-110) REVERT: C 82 ILE cc_start: 0.9425 (mt) cc_final: 0.9115 (mt) REVERT: A 20 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7117 (pp30) REVERT: A 35 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9067 (p0) REVERT: A 70 PHE cc_start: 0.8709 (t80) cc_final: 0.7296 (t80) REVERT: A 76 ASP cc_start: 0.8870 (t0) cc_final: 0.8230 (t0) REVERT: A 85 ASP cc_start: 0.8893 (m-30) cc_final: 0.8359 (p0) REVERT: A 92 GLN cc_start: 0.8955 (tt0) cc_final: 0.8718 (tt0) REVERT: A 98 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: A 111 ASP cc_start: 0.8401 (p0) cc_final: 0.5706 (p0) REVERT: A 122 TYR cc_start: 0.8221 (p90) cc_final: 0.7586 (p90) REVERT: E 51 ARG cc_start: 0.8915 (ttp-170) cc_final: 0.8326 (ttp-170) REVERT: E 52 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7760 (mp0) REVERT: E 60 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8690 (ptp90) REVERT: E 70 PHE cc_start: 0.9006 (t80) cc_final: 0.8777 (t80) REVERT: F 4 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7909 (mp10) REVERT: F 52 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8216 (mt-10) REVERT: F 70 PHE cc_start: 0.8302 (t80) cc_final: 0.5776 (t80) REVERT: F 76 ASP cc_start: 0.8692 (t0) cc_final: 0.7969 (t0) REVERT: F 98 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6183 (m-10) REVERT: F 117 ASN cc_start: 0.9452 (p0) cc_final: 0.9172 (p0) REVERT: G 31 ARG cc_start: 0.8177 (ttt90) cc_final: 0.7619 (ttt90) REVERT: G 51 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8522 (ttp-110) REVERT: G 81 GLN cc_start: 0.9008 (tm-30) cc_final: 0.7619 (tm-30) REVERT: G 82 ILE cc_start: 0.9504 (mt) cc_final: 0.9022 (mt) REVERT: G 85 ASP cc_start: 0.8796 (m-30) cc_final: 0.8282 (p0) REVERT: G 87 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7567 (mt-10) REVERT: G 111 ASP cc_start: 0.8237 (p0) cc_final: 0.7075 (p0) REVERT: H 20 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7268 (pp30) REVERT: H 31 ARG cc_start: 0.9178 (ptm-80) cc_final: 0.8466 (ptm-80) REVERT: H 76 ASP cc_start: 0.8985 (t0) cc_final: 0.8733 (t0) REVERT: H 85 ASP cc_start: 0.8912 (m-30) cc_final: 0.8456 (p0) REVERT: I 5 ASN cc_start: 0.8782 (t0) cc_final: 0.8400 (t0) REVERT: I 31 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8726 (mtp85) REVERT: I 51 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8571 (ttp-170) REVERT: I 52 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7816 (mt-10) REVERT: J 4 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8113 (mp10) REVERT: J 70 PHE cc_start: 0.8163 (t80) cc_final: 0.5614 (t80) REVERT: J 76 ASP cc_start: 0.8584 (t0) cc_final: 0.7330 (t0) REVERT: J 98 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.6488 (m-10) REVERT: K 7 LYS cc_start: 0.9384 (mtmt) cc_final: 0.9110 (mtmm) REVERT: K 81 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8231 (tm-30) REVERT: K 82 ILE cc_start: 0.9473 (mt) cc_final: 0.8176 (mt) REVERT: K 85 ASP cc_start: 0.8776 (m-30) cc_final: 0.7882 (p0) REVERT: K 87 GLU cc_start: 0.8823 (mt-10) cc_final: 0.7982 (mp0) REVERT: K 111 ASP cc_start: 0.8617 (p0) cc_final: 0.8095 (p0) REVERT: K 123 GLU cc_start: 0.8363 (mp0) cc_final: 0.8122 (mp0) REVERT: L 35 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.9036 (p0) REVERT: L 71 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8302 (mtmm) REVERT: L 98 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: L 111 ASP cc_start: 0.8417 (p0) cc_final: 0.7735 (p0) REVERT: M 27 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8707 (tt) REVERT: M 31 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8800 (mmm-85) REVERT: M 51 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8452 (ttp-170) REVERT: M 52 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8124 (mp0) REVERT: M 60 ARG cc_start: 0.9086 (ptp-110) cc_final: 0.8637 (ptp90) REVERT: M 70 PHE cc_start: 0.8922 (t80) cc_final: 0.8682 (t80) REVERT: M 77 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9209 (tp30) REVERT: N 4 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8162 (mp10) REVERT: N 74 ASP cc_start: 0.8779 (p0) cc_final: 0.8485 (p0) REVERT: N 76 ASP cc_start: 0.8583 (t0) cc_final: 0.7567 (t0) REVERT: N 98 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.5727 (m-10) REVERT: O 31 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.6369 (ttt90) REVERT: O 51 ARG cc_start: 0.8930 (ttp-110) cc_final: 0.8570 (ttp-110) REVERT: P 20 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7104 (pp30) REVERT: P 35 ASN cc_start: 0.9301 (OUTLIER) cc_final: 0.9069 (p0) REVERT: P 70 PHE cc_start: 0.8706 (t80) cc_final: 0.8491 (t80) REVERT: P 85 ASP cc_start: 0.8894 (m-30) cc_final: 0.8338 (p0) REVERT: P 92 GLN cc_start: 0.8956 (tt0) cc_final: 0.8725 (tt0) REVERT: P 98 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: Q 51 ARG cc_start: 0.8924 (ttp-170) cc_final: 0.8330 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7754 (mp0) REVERT: Q 60 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8673 (ptp90) REVERT: Q 70 PHE cc_start: 0.9012 (t80) cc_final: 0.8763 (t80) REVERT: R 4 GLN cc_start: 0.8583 (mm-40) cc_final: 0.7916 (mp10) REVERT: R 52 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8230 (mt-10) REVERT: R 70 PHE cc_start: 0.8301 (t80) cc_final: 0.5810 (t80) REVERT: R 76 ASP cc_start: 0.8685 (t0) cc_final: 0.7978 (t0) REVERT: R 98 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6112 (m-10) REVERT: R 117 ASN cc_start: 0.9454 (p0) cc_final: 0.9175 (p0) REVERT: S 31 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7563 (ttt90) REVERT: S 81 GLN cc_start: 0.9001 (tm-30) cc_final: 0.7623 (tm-30) REVERT: S 82 ILE cc_start: 0.9501 (mt) cc_final: 0.9025 (mt) REVERT: S 85 ASP cc_start: 0.8801 (m-30) cc_final: 0.8292 (p0) REVERT: S 87 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7564 (mt-10) REVERT: S 111 ASP cc_start: 0.8244 (p0) cc_final: 0.7065 (p0) REVERT: T 20 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: T 31 ARG cc_start: 0.9186 (ptm-80) cc_final: 0.8469 (ptm-80) REVERT: T 71 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8071 (mtmm) REVERT: T 76 ASP cc_start: 0.8990 (t0) cc_final: 0.8724 (t0) REVERT: U 5 ASN cc_start: 0.9115 (t0) cc_final: 0.8084 (t0) REVERT: U 7 LYS cc_start: 0.9393 (mtmt) cc_final: 0.9060 (mtmm) REVERT: U 51 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8574 (ttp-170) REVERT: U 52 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7810 (mt-10) REVERT: V 70 PHE cc_start: 0.8200 (t80) cc_final: 0.5761 (t80) REVERT: V 76 ASP cc_start: 0.8547 (t0) cc_final: 0.7191 (t0) REVERT: V 98 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: W 7 LYS cc_start: 0.9384 (mtmt) cc_final: 0.9107 (mtmm) REVERT: W 81 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8242 (tm-30) REVERT: W 82 ILE cc_start: 0.9463 (mt) cc_final: 0.8181 (mt) REVERT: W 85 ASP cc_start: 0.8803 (m-30) cc_final: 0.7891 (p0) REVERT: W 87 GLU cc_start: 0.8823 (mt-10) cc_final: 0.7965 (mp0) REVERT: W 111 ASP cc_start: 0.8641 (p0) cc_final: 0.7895 (p0) REVERT: W 123 GLU cc_start: 0.8347 (mp0) cc_final: 0.7862 (mp0) REVERT: X 31 ARG cc_start: 0.9205 (ptm-80) cc_final: 0.8721 (ptm-80) REVERT: X 35 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.9073 (p0) REVERT: X 71 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8226 (mtmm) REVERT: X 98 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: X 111 ASP cc_start: 0.8444 (p0) cc_final: 0.7770 (p0) outliers start: 230 outliers final: 156 residues processed: 972 average time/residue: 0.1668 time to fit residues: 254.3295 Evaluate side-chains 939 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 763 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU 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 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 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 35 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 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 124 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 156 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 266 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 259 optimal weight: 0.0980 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN A 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN M 20 GLN M 92 GLN O 20 GLN P 20 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 102 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046447 restraints weight = 109104.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048077 restraints weight = 57956.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049214 restraints weight = 35840.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050031 restraints weight = 24165.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050654 restraints weight = 17351.795| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.6141 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= 0.182 Angle : 0.852 12.736 31968 Z= 0.416 Chirality : 0.051 0.238 3576 Planarity : 0.004 0.045 4248 Dihedral : 5.602 25.851 3264 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 10.82 % Allowed : 27.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.14), residues: 3024 helix: -0.95 (0.22), residues: 480 sheet: -1.35 (0.13), residues: 1224 loop : -3.37 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 78 TYR 0.014 0.001 TYR T 122 PHE 0.023 0.002 PHE R 91 TRP 0.009 0.001 TRP F 50 HIS 0.002 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00405 (23688) covalent geometry : angle 0.85167 (31968) hydrogen bonds : bond 0.03133 ( 816) hydrogen bonds : angle 5.48645 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 791 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8671 (tp) REVERT: D 51 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8486 (ttp-170) REVERT: D 52 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8090 (mp0) REVERT: D 60 ARG cc_start: 0.9107 (ptp-110) cc_final: 0.8809 (ptp90) REVERT: D 70 PHE cc_start: 0.8930 (t80) cc_final: 0.8639 (t80) REVERT: D 77 GLU cc_start: 0.9456 (tm-30) cc_final: 0.9196 (tp30) REVERT: D 87 GLU cc_start: 0.8788 (pm20) cc_final: 0.8275 (pp20) REVERT: B 8 ASP cc_start: 0.8841 (m-30) cc_final: 0.8578 (m-30) REVERT: B 74 ASP cc_start: 0.8858 (p0) cc_final: 0.8568 (p0) REVERT: B 76 ASP cc_start: 0.8507 (t0) cc_final: 0.7369 (t0) REVERT: B 98 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.5752 (m-10) REVERT: C 20 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 31 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7749 (ttm-80) REVERT: C 51 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8727 (ttp-110) REVERT: A 20 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7192 (pp30) REVERT: A 35 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.9108 (p0) REVERT: A 76 ASP cc_start: 0.8918 (t0) cc_final: 0.8057 (t0) REVERT: A 85 ASP cc_start: 0.8920 (m-30) cc_final: 0.8448 (p0) REVERT: A 92 GLN cc_start: 0.9006 (tt0) cc_final: 0.8691 (tt0) REVERT: A 98 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: E 51 ARG cc_start: 0.8939 (ttp-170) cc_final: 0.8357 (ttp-170) REVERT: E 52 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7715 (mp0) REVERT: E 60 ARG cc_start: 0.9102 (ptp-110) cc_final: 0.8836 (ptp90) REVERT: E 70 PHE cc_start: 0.9024 (t80) cc_final: 0.8819 (t80) REVERT: E 71 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7951 (mtmm) REVERT: F 4 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7944 (mp10) REVERT: F 70 PHE cc_start: 0.8373 (t80) cc_final: 0.5692 (t80) REVERT: F 74 ASP cc_start: 0.8948 (p0) cc_final: 0.8692 (p0) REVERT: F 76 ASP cc_start: 0.8698 (t0) cc_final: 0.7935 (t0) REVERT: F 92 GLN cc_start: 0.8945 (tt0) cc_final: 0.8504 (tt0) REVERT: F 98 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: G 31 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7529 (ttt90) REVERT: G 51 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8531 (ttp-110) REVERT: G 81 GLN cc_start: 0.8971 (tm-30) cc_final: 0.7930 (tm-30) REVERT: G 82 ILE cc_start: 0.9494 (mt) cc_final: 0.8945 (mt) REVERT: G 85 ASP cc_start: 0.8778 (m-30) cc_final: 0.8316 (p0) REVERT: G 87 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7414 (mt-10) REVERT: G 123 GLU cc_start: 0.8234 (mp0) cc_final: 0.7876 (mp0) REVERT: H 20 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7329 (pp30) REVERT: H 31 ARG cc_start: 0.9178 (ptm-80) cc_final: 0.8499 (ptm-80) REVERT: H 71 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8086 (mtmm) REVERT: H 76 ASP cc_start: 0.8968 (t0) cc_final: 0.8763 (t0) REVERT: H 85 ASP cc_start: 0.8940 (m-30) cc_final: 0.8480 (p0) REVERT: I 5 ASN cc_start: 0.8819 (t0) cc_final: 0.8524 (t0) REVERT: I 51 ARG cc_start: 0.9010 (ttp-170) cc_final: 0.8370 (ttp-170) REVERT: I 52 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7221 (mp0) REVERT: I 60 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8782 (ptp90) REVERT: J 70 PHE cc_start: 0.8305 (t80) cc_final: 0.5643 (t80) REVERT: J 74 ASP cc_start: 0.8923 (p0) cc_final: 0.8660 (p0) REVERT: J 76 ASP cc_start: 0.8607 (t0) cc_final: 0.7269 (t0) REVERT: J 98 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: K 7 LYS cc_start: 0.9427 (mtmt) cc_final: 0.9165 (mtmm) REVERT: K 81 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8266 (tm-30) REVERT: K 82 ILE cc_start: 0.9467 (mt) cc_final: 0.8121 (mt) REVERT: K 85 ASP cc_start: 0.8791 (m-30) cc_final: 0.7880 (p0) REVERT: K 87 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7946 (mp0) REVERT: K 111 ASP cc_start: 0.8687 (p0) cc_final: 0.8067 (p0) REVERT: K 123 GLU cc_start: 0.8343 (mp0) cc_final: 0.8104 (mp0) REVERT: L 35 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.9166 (p0) REVERT: L 71 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8321 (mtmm) REVERT: M 27 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8656 (tt) REVERT: M 51 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8485 (ttp-170) REVERT: M 52 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8089 (mp0) REVERT: M 60 ARG cc_start: 0.9104 (ptp-110) cc_final: 0.8797 (ptp90) REVERT: M 70 PHE cc_start: 0.8998 (t80) cc_final: 0.8698 (t80) REVERT: M 77 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9119 (tm-30) REVERT: M 91 PHE cc_start: 0.8425 (m-10) cc_final: 0.8070 (m-10) REVERT: N 8 ASP cc_start: 0.8849 (m-30) cc_final: 0.8593 (m-30) REVERT: N 70 PHE cc_start: 0.8582 (t80) cc_final: 0.8287 (t80) REVERT: N 74 ASP cc_start: 0.8864 (p0) cc_final: 0.8596 (p0) REVERT: N 98 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.5736 (m-10) REVERT: O 31 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: O 51 ARG cc_start: 0.8936 (ttp-110) cc_final: 0.8736 (ttp-110) REVERT: O 76 ASP cc_start: 0.8878 (t0) cc_final: 0.8601 (t0) REVERT: O 81 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8439 (pp30) REVERT: O 111 ASP cc_start: 0.8733 (p0) cc_final: 0.8510 (p0) REVERT: O 123 GLU cc_start: 0.8325 (mp0) cc_final: 0.8099 (mp0) REVERT: P 20 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7172 (pp30) REVERT: P 35 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9079 (p0) REVERT: P 85 ASP cc_start: 0.8917 (m-30) cc_final: 0.8385 (p0) REVERT: P 92 GLN cc_start: 0.9000 (tt0) cc_final: 0.8696 (tt0) REVERT: P 98 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: Q 51 ARG cc_start: 0.8944 (ttp-170) cc_final: 0.8351 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7707 (mp0) REVERT: Q 60 ARG cc_start: 0.9097 (ptp-110) cc_final: 0.8826 (ptp90) REVERT: Q 70 PHE cc_start: 0.9021 (t80) cc_final: 0.8819 (t80) REVERT: Q 71 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7944 (mtmm) REVERT: R 4 GLN cc_start: 0.8656 (mm-40) cc_final: 0.7954 (mp10) REVERT: R 70 PHE cc_start: 0.8421 (t80) cc_final: 0.5757 (t80) REVERT: R 74 ASP cc_start: 0.8945 (p0) cc_final: 0.8686 (p0) REVERT: R 76 ASP cc_start: 0.8693 (t0) cc_final: 0.7931 (t0) REVERT: R 98 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: S 31 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7549 (ttt90) REVERT: S 81 GLN cc_start: 0.8967 (tm-30) cc_final: 0.7930 (tm-30) REVERT: S 82 ILE cc_start: 0.9492 (mt) cc_final: 0.8941 (mt) REVERT: S 85 ASP cc_start: 0.8790 (m-30) cc_final: 0.8324 (p0) REVERT: S 87 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7424 (mt-10) REVERT: S 123 GLU cc_start: 0.8249 (mp0) cc_final: 0.7813 (mp0) REVERT: T 20 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7337 (pp30) REVERT: T 31 ARG cc_start: 0.9264 (ptm-80) cc_final: 0.8572 (ptm-80) REVERT: T 71 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8095 (mtmm) REVERT: T 76 ASP cc_start: 0.8962 (t0) cc_final: 0.8713 (t0) REVERT: T 98 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: U 5 ASN cc_start: 0.9110 (t0) cc_final: 0.8059 (t0) REVERT: U 7 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9063 (mtmm) REVERT: U 51 ARG cc_start: 0.9029 (ttp-170) cc_final: 0.8419 (ttp-170) REVERT: U 52 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7231 (mp0) REVERT: U 60 ARG cc_start: 0.9030 (ptp-110) cc_final: 0.8742 (ptp90) REVERT: V 70 PHE cc_start: 0.8344 (t80) cc_final: 0.5653 (t80) REVERT: V 74 ASP cc_start: 0.8928 (p0) cc_final: 0.8658 (p0) REVERT: V 76 ASP cc_start: 0.8614 (t0) cc_final: 0.7363 (t0) REVERT: V 98 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.6512 (m-10) REVERT: V 124 LEU cc_start: 0.9628 (tt) cc_final: 0.8847 (tt) REVERT: W 7 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9163 (mtmm) REVERT: W 81 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8272 (tm-30) REVERT: W 82 ILE cc_start: 0.9464 (mt) cc_final: 0.8125 (mt) REVERT: W 85 ASP cc_start: 0.8803 (m-30) cc_final: 0.7891 (p0) REVERT: W 87 GLU cc_start: 0.8814 (mt-10) cc_final: 0.7940 (mp0) REVERT: W 111 ASP cc_start: 0.8667 (p0) cc_final: 0.8048 (p0) REVERT: W 123 GLU cc_start: 0.8342 (mp0) cc_final: 0.8121 (mp0) REVERT: X 31 ARG cc_start: 0.9196 (ptm-80) cc_final: 0.8848 (ptm-80) REVERT: X 71 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8248 (mtmm) REVERT: X 76 ASP cc_start: 0.8638 (t0) cc_final: 0.7606 (t0) REVERT: X 98 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6430 (m-10) outliers start: 257 outliers final: 175 residues processed: 933 average time/residue: 0.1674 time to fit residues: 246.6262 Evaluate side-chains 952 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 755 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 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 20 GLN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN C 20 GLN A 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN L 20 GLN M 20 GLN O 20 GLN P 20 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.043901 restraints weight = 113463.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.045464 restraints weight = 59708.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046582 restraints weight = 36486.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.047286 restraints weight = 24324.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047883 restraints weight = 17972.095| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23688 Z= 0.277 Angle : 0.887 11.852 31968 Z= 0.443 Chirality : 0.052 0.257 3576 Planarity : 0.004 0.050 4248 Dihedral : 5.865 29.104 3264 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 11.28 % Allowed : 27.23 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.14), residues: 3024 helix: -0.96 (0.22), residues: 480 sheet: -1.28 (0.14), residues: 1224 loop : -3.27 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 31 TYR 0.014 0.001 TYR A 122 PHE 0.028 0.002 PHE V 91 TRP 0.013 0.002 TRP F 50 HIS 0.002 0.001 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00598 (23688) covalent geometry : angle 0.88680 (31968) hydrogen bonds : bond 0.03248 ( 816) hydrogen bonds : angle 5.68575 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 763 time to evaluate : 0.990 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 27 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8770 (tp) REVERT: D 31 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8675 (mmm-85) REVERT: D 51 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8392 (ttp-170) REVERT: D 52 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8009 (mp0) REVERT: D 70 PHE cc_start: 0.9045 (t80) cc_final: 0.8796 (t80) REVERT: D 87 GLU cc_start: 0.8817 (pm20) cc_final: 0.8318 (pp20) REVERT: B 8 ASP cc_start: 0.8886 (m-30) cc_final: 0.8619 (m-30) REVERT: B 74 ASP cc_start: 0.8993 (p0) cc_final: 0.8726 (p0) REVERT: B 76 ASP cc_start: 0.8593 (t0) cc_final: 0.7169 (t0) REVERT: B 98 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: C 35 ASN cc_start: 0.9215 (m-40) cc_final: 0.9006 (m-40) REVERT: A 14 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6989 (t70) REVERT: A 20 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7602 (pp30) REVERT: A 35 ASN cc_start: 0.9480 (OUTLIER) cc_final: 0.9189 (p0) REVERT: A 76 ASP cc_start: 0.8972 (t0) cc_final: 0.8207 (t0) REVERT: A 85 ASP cc_start: 0.9013 (m-30) cc_final: 0.8532 (p0) REVERT: A 92 GLN cc_start: 0.8993 (tt0) cc_final: 0.8628 (tt0) REVERT: A 98 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: A 119 GLU cc_start: 0.9133 (pm20) cc_final: 0.8917 (pm20) REVERT: E 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8429 (ttp-170) REVERT: E 52 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7917 (mt-10) REVERT: E 70 PHE cc_start: 0.9138 (t80) cc_final: 0.8928 (t80) REVERT: E 71 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8017 (mtmm) REVERT: E 92 GLN cc_start: 0.9042 (tt0) cc_final: 0.8831 (tt0) REVERT: F 70 PHE cc_start: 0.8642 (t80) cc_final: 0.6137 (t80) REVERT: F 74 ASP cc_start: 0.9047 (p0) cc_final: 0.8742 (p0) REVERT: F 76 ASP cc_start: 0.8875 (t0) cc_final: 0.7866 (t0) REVERT: F 92 GLN cc_start: 0.8973 (tt0) cc_final: 0.8492 (tt0) REVERT: F 98 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: G 31 ARG cc_start: 0.8133 (ttt90) cc_final: 0.7443 (ttt90) REVERT: G 51 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8531 (ttp-170) REVERT: G 81 GLN cc_start: 0.9044 (tm-30) cc_final: 0.7900 (tm-30) REVERT: G 82 ILE cc_start: 0.9471 (mt) cc_final: 0.8899 (mt) REVERT: G 85 ASP cc_start: 0.8926 (m-30) cc_final: 0.8316 (p0) REVERT: G 87 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7092 (mt-10) REVERT: H 20 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: H 31 ARG cc_start: 0.9266 (ptm-80) cc_final: 0.8511 (ptm-80) REVERT: H 71 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8103 (mtmm) REVERT: H 76 ASP cc_start: 0.8898 (t0) cc_final: 0.8062 (t0) REVERT: H 85 ASP cc_start: 0.9043 (m-30) cc_final: 0.8604 (p0) REVERT: H 119 GLU cc_start: 0.9111 (pm20) cc_final: 0.8865 (pm20) REVERT: I 5 ASN cc_start: 0.8851 (t0) cc_final: 0.8576 (t0) REVERT: I 51 ARG cc_start: 0.9000 (ttp-170) cc_final: 0.8451 (ttp-170) REVERT: I 52 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7146 (mp0) REVERT: J 4 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7964 (mp10) REVERT: J 8 ASP cc_start: 0.8897 (m-30) cc_final: 0.8658 (m-30) REVERT: J 31 ARG cc_start: 0.8441 (ttt90) cc_final: 0.7873 (ttt90) REVERT: J 60 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: J 70 PHE cc_start: 0.8529 (t80) cc_final: 0.5759 (t80) REVERT: J 74 ASP cc_start: 0.9025 (p0) cc_final: 0.8613 (p0) REVERT: J 75 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8737 (p) REVERT: J 76 ASP cc_start: 0.8719 (t0) cc_final: 0.7265 (t0) REVERT: J 98 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: K 7 LYS cc_start: 0.9454 (mtmt) cc_final: 0.9179 (mtmm) REVERT: K 31 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8377 (mmm160) REVERT: K 81 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8413 (tm-30) REVERT: K 82 ILE cc_start: 0.9460 (mt) cc_final: 0.8153 (mt) REVERT: K 85 ASP cc_start: 0.8853 (m-30) cc_final: 0.7827 (p0) REVERT: K 87 GLU cc_start: 0.8851 (mt-10) cc_final: 0.7711 (mp0) REVERT: K 111 ASP cc_start: 0.8758 (p0) cc_final: 0.8242 (p0) REVERT: K 123 GLU cc_start: 0.8393 (mp0) cc_final: 0.8149 (mp0) REVERT: L 35 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9205 (p0) REVERT: L 71 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8021 (mtmm) REVERT: M 27 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8762 (tp) REVERT: M 31 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8633 (mmm-85) REVERT: M 51 ARG cc_start: 0.8978 (ttp-170) cc_final: 0.8394 (ttp-170) REVERT: M 52 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8015 (mp0) REVERT: M 70 PHE cc_start: 0.9078 (t80) cc_final: 0.8838 (t80) REVERT: N 8 ASP cc_start: 0.8882 (m-30) cc_final: 0.8625 (m-30) REVERT: N 74 ASP cc_start: 0.8967 (p0) cc_final: 0.8655 (p0) REVERT: N 76 ASP cc_start: 0.8752 (t0) cc_final: 0.7579 (t0) REVERT: N 98 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: N 111 ASP cc_start: 0.8740 (p0) cc_final: 0.8539 (p0) REVERT: O 35 ASN cc_start: 0.9209 (m-40) cc_final: 0.9004 (m-40) REVERT: O 76 ASP cc_start: 0.9026 (t0) cc_final: 0.8740 (t0) REVERT: O 81 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8509 (pp30) REVERT: P 14 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6994 (t70) REVERT: P 20 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7588 (pp30) REVERT: P 35 ASN cc_start: 0.9474 (OUTLIER) cc_final: 0.9194 (p0) REVERT: P 85 ASP cc_start: 0.9009 (m-30) cc_final: 0.8441 (p0) REVERT: P 92 GLN cc_start: 0.9013 (tt0) cc_final: 0.8644 (tt0) REVERT: P 98 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: P 119 GLU cc_start: 0.9104 (pm20) cc_final: 0.8897 (pm20) REVERT: Q 51 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8433 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7916 (mt-10) REVERT: Q 70 PHE cc_start: 0.9128 (t80) cc_final: 0.8919 (t80) REVERT: Q 71 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8017 (mtmm) REVERT: Q 92 GLN cc_start: 0.9041 (tt0) cc_final: 0.8828 (tt0) REVERT: R 70 PHE cc_start: 0.8660 (t80) cc_final: 0.6115 (t80) REVERT: R 74 ASP cc_start: 0.9039 (p0) cc_final: 0.8730 (p0) REVERT: R 76 ASP cc_start: 0.8846 (t0) cc_final: 0.7856 (t0) REVERT: R 98 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: S 31 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7477 (ttt90) REVERT: S 81 GLN cc_start: 0.9045 (tm-30) cc_final: 0.7909 (tm-30) REVERT: S 82 ILE cc_start: 0.9473 (mt) cc_final: 0.8911 (mt) REVERT: S 85 ASP cc_start: 0.8919 (m-30) cc_final: 0.8325 (p0) REVERT: S 87 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7090 (mt-10) REVERT: T 20 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7457 (pp30) REVERT: T 31 ARG cc_start: 0.9301 (ptm-80) cc_final: 0.8566 (ptm-80) REVERT: T 71 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8109 (mtmm) REVERT: T 76 ASP cc_start: 0.8885 (t0) cc_final: 0.8672 (t0) REVERT: T 98 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: T 119 GLU cc_start: 0.9117 (pm20) cc_final: 0.8871 (pm20) REVERT: U 5 ASN cc_start: 0.9106 (t0) cc_final: 0.8306 (t0) REVERT: U 7 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9010 (mtmm) REVERT: U 51 ARG cc_start: 0.9002 (ttp-170) cc_final: 0.8516 (ttp-170) REVERT: U 52 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7137 (mp0) REVERT: V 8 ASP cc_start: 0.8900 (m-30) cc_final: 0.8637 (m-30) REVERT: V 60 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7895 (mtp85) REVERT: V 70 PHE cc_start: 0.8575 (t80) cc_final: 0.5910 (t80) REVERT: V 74 ASP cc_start: 0.9032 (p0) cc_final: 0.8620 (p0) REVERT: V 76 ASP cc_start: 0.8711 (t0) cc_final: 0.7594 (t0) REVERT: V 98 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: W 7 LYS cc_start: 0.9457 (mtmt) cc_final: 0.9181 (mtmm) REVERT: W 81 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8413 (tm-30) REVERT: W 82 ILE cc_start: 0.9447 (mt) cc_final: 0.8246 (mt) REVERT: W 85 ASP cc_start: 0.8868 (m-30) cc_final: 0.7838 (p0) REVERT: W 87 GLU cc_start: 0.8826 (mt-10) cc_final: 0.7693 (mp0) REVERT: W 111 ASP cc_start: 0.8781 (p0) cc_final: 0.8290 (p0) REVERT: W 123 GLU cc_start: 0.8407 (mp0) cc_final: 0.8192 (mp0) REVERT: X 71 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8159 (mtmm) REVERT: X 76 ASP cc_start: 0.8688 (t0) cc_final: 0.7529 (t0) REVERT: X 98 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: X 126 MET cc_start: 0.8852 (mpp) cc_final: 0.8649 (mpp) outliers start: 268 outliers final: 194 residues processed: 918 average time/residue: 0.1589 time to fit residues: 232.1998 Evaluate side-chains 942 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 722 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 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 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 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 30 THR 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 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 39 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain 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 75 THR 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 108 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 20 GLN 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 100 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 32 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 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 126 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 87 GLU 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 39 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 106 MET Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 ASN Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 225 optimal weight: 0.9980 chunk 289 optimal weight: 0.6980 chunk 234 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 278 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN A 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN O 20 GLN P 20 GLN S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046985 restraints weight = 108111.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048656 restraints weight = 57202.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049811 restraints weight = 34838.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050602 restraints weight = 23192.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051222 restraints weight = 16845.485| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23688 Z= 0.161 Angle : 0.893 13.666 31968 Z= 0.434 Chirality : 0.052 0.340 3576 Planarity : 0.004 0.044 4248 Dihedral : 5.622 29.051 3264 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 9.64 % Allowed : 29.04 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.14), residues: 3024 helix: -0.60 (0.23), residues: 480 sheet: -1.25 (0.14), residues: 1224 loop : -3.08 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 31 TYR 0.017 0.001 TYR L 122 PHE 0.023 0.002 PHE V 91 TRP 0.005 0.001 TRP F 50 HIS 0.001 0.000 HIS W 116 Details of bonding type rmsd covalent geometry : bond 0.00368 (23688) covalent geometry : angle 0.89273 (31968) hydrogen bonds : bond 0.03011 ( 816) hydrogen bonds : angle 5.48264 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 831 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8620 (tp) REVERT: D 31 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: D 51 ARG cc_start: 0.8958 (ttp-170) cc_final: 0.8482 (ttp-170) REVERT: D 52 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7977 (mp0) REVERT: D 70 PHE cc_start: 0.8911 (t80) cc_final: 0.8649 (t80) REVERT: D 87 GLU cc_start: 0.8652 (pm20) cc_final: 0.8158 (pp20) REVERT: B 4 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8106 (mp10) REVERT: B 8 ASP cc_start: 0.8843 (m-30) cc_final: 0.8591 (m-30) REVERT: B 74 ASP cc_start: 0.8921 (p0) cc_final: 0.8678 (p0) REVERT: B 76 ASP cc_start: 0.8424 (t0) cc_final: 0.6955 (t0) REVERT: B 98 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6108 (m-10) REVERT: C 51 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8657 (ttp-110) REVERT: A 20 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: A 35 ASN cc_start: 0.9433 (OUTLIER) cc_final: 0.9178 (p0) REVERT: A 76 ASP cc_start: 0.8839 (t0) cc_final: 0.7987 (t0) REVERT: A 85 ASP cc_start: 0.8956 (m-30) cc_final: 0.8498 (p0) REVERT: A 98 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: A 119 GLU cc_start: 0.9090 (pm20) cc_final: 0.8835 (pm20) REVERT: E 51 ARG cc_start: 0.8925 (ttp-170) cc_final: 0.8344 (ttp-170) REVERT: E 52 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7694 (mp0) REVERT: E 71 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7888 (mtmm) REVERT: F 4 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7934 (mp10) REVERT: F 74 ASP cc_start: 0.8927 (p0) cc_final: 0.8641 (p0) REVERT: F 76 ASP cc_start: 0.8779 (t0) cc_final: 0.8208 (t0) REVERT: F 92 GLN cc_start: 0.8996 (tt0) cc_final: 0.8507 (tt0) REVERT: F 98 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: G 51 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8617 (ttp-110) REVERT: G 81 GLN cc_start: 0.9083 (tm-30) cc_final: 0.7998 (tm-30) REVERT: G 82 ILE cc_start: 0.9503 (mt) cc_final: 0.8297 (mt) REVERT: G 85 ASP cc_start: 0.8759 (m-30) cc_final: 0.8021 (p0) REVERT: G 87 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7702 (mp0) REVERT: H 20 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7214 (pp30) REVERT: H 31 ARG cc_start: 0.9236 (ptm-80) cc_final: 0.8756 (ptm-80) REVERT: H 71 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8158 (mtmm) REVERT: H 85 ASP cc_start: 0.8976 (m-30) cc_final: 0.8394 (p0) REVERT: H 87 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7865 (mt-10) REVERT: H 119 GLU cc_start: 0.9037 (pm20) cc_final: 0.8833 (pm20) REVERT: I 5 ASN cc_start: 0.8830 (t0) cc_final: 0.8549 (t0) REVERT: I 51 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8529 (ttp-170) REVERT: I 52 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7221 (mp0) REVERT: I 100 ILE cc_start: 0.8648 (pp) cc_final: 0.8198 (tp) REVERT: J 4 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7876 (mp10) REVERT: J 8 ASP cc_start: 0.8867 (m-30) cc_final: 0.8630 (m-30) REVERT: J 31 ARG cc_start: 0.8362 (ttt90) cc_final: 0.8110 (ttt90) REVERT: J 60 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: J 70 PHE cc_start: 0.8446 (t80) cc_final: 0.6186 (t80) REVERT: J 74 ASP cc_start: 0.8907 (p0) cc_final: 0.8536 (p0) REVERT: J 76 ASP cc_start: 0.8619 (t0) cc_final: 0.7446 (t0) REVERT: J 98 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: K 81 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8370 (tm-30) REVERT: K 82 ILE cc_start: 0.9456 (mt) cc_final: 0.8195 (mt) REVERT: K 85 ASP cc_start: 0.8799 (m-30) cc_final: 0.7843 (p0) REVERT: K 87 GLU cc_start: 0.8814 (mt-10) cc_final: 0.7945 (mp0) REVERT: K 123 GLU cc_start: 0.8323 (mp0) cc_final: 0.7968 (mp0) REVERT: L 35 ASN cc_start: 0.9394 (OUTLIER) cc_final: 0.9155 (p0) REVERT: L 71 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8118 (mtmm) REVERT: M 27 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8599 (tp) REVERT: M 31 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: M 51 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8491 (ttp-170) REVERT: M 52 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7972 (mp0) REVERT: M 70 PHE cc_start: 0.8948 (t80) cc_final: 0.8726 (t80) REVERT: M 77 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9192 (tp30) REVERT: M 78 ARG cc_start: 0.9262 (tpt-90) cc_final: 0.8836 (tpp80) REVERT: N 4 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8093 (mp10) REVERT: N 8 ASP cc_start: 0.8840 (m-30) cc_final: 0.8591 (m-30) REVERT: N 74 ASP cc_start: 0.8874 (p0) cc_final: 0.8570 (p0) REVERT: N 76 ASP cc_start: 0.8626 (t0) cc_final: 0.7412 (t0) REVERT: N 98 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6121 (m-10) REVERT: N 111 ASP cc_start: 0.8818 (p0) cc_final: 0.8223 (p0) REVERT: O 51 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8667 (ttp-110) REVERT: O 78 ARG cc_start: 0.9280 (tpt170) cc_final: 0.9040 (tpt-90) REVERT: P 20 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7248 (pp30) REVERT: P 35 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9162 (p0) REVERT: P 85 ASP cc_start: 0.8981 (m-30) cc_final: 0.8437 (p0) REVERT: P 98 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: P 119 GLU cc_start: 0.9073 (pm20) cc_final: 0.8809 (pm20) REVERT: Q 51 ARG cc_start: 0.8949 (ttp-170) cc_final: 0.8492 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7731 (mp0) REVERT: Q 71 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7877 (mtmm) REVERT: R 4 GLN cc_start: 0.8476 (mm-40) cc_final: 0.7942 (mp10) REVERT: R 74 ASP cc_start: 0.8930 (p0) cc_final: 0.8642 (p0) REVERT: R 76 ASP cc_start: 0.8784 (t0) cc_final: 0.8202 (t0) REVERT: R 98 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.6422 (m-10) REVERT: S 81 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8139 (tm-30) REVERT: S 82 ILE cc_start: 0.9499 (mt) cc_final: 0.8707 (mt) REVERT: S 85 ASP cc_start: 0.8760 (m-30) cc_final: 0.8425 (p0) REVERT: S 87 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7468 (mt-10) REVERT: T 20 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7221 (pp30) REVERT: T 31 ARG cc_start: 0.9272 (ptm-80) cc_final: 0.8769 (ptm-80) REVERT: T 71 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8081 (mtmm) REVERT: T 98 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7090 (m-10) REVERT: T 111 ASP cc_start: 0.8270 (p0) cc_final: 0.6983 (p0) REVERT: T 122 TYR cc_start: 0.8153 (p90) cc_final: 0.7550 (p90) REVERT: U 5 ASN cc_start: 0.9037 (t0) cc_final: 0.8274 (t0) REVERT: U 7 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9084 (mtmm) REVERT: U 51 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8524 (ttp-170) REVERT: U 52 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7249 (mp0) REVERT: V 8 ASP cc_start: 0.8856 (m-30) cc_final: 0.8651 (m-30) REVERT: V 60 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7965 (mtp85) REVERT: V 70 PHE cc_start: 0.8512 (t80) cc_final: 0.6149 (t80) REVERT: V 74 ASP cc_start: 0.8863 (p0) cc_final: 0.8528 (p0) REVERT: V 76 ASP cc_start: 0.8715 (t0) cc_final: 0.7607 (t0) REVERT: V 98 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: W 31 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8175 (mmm160) REVERT: W 81 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8283 (tm-30) REVERT: W 82 ILE cc_start: 0.9459 (mt) cc_final: 0.8215 (mt) REVERT: W 85 ASP cc_start: 0.8813 (m-30) cc_final: 0.7855 (p0) REVERT: W 87 GLU cc_start: 0.8819 (mt-10) cc_final: 0.7949 (mp0) REVERT: W 123 GLU cc_start: 0.8350 (mp0) cc_final: 0.8010 (mp0) REVERT: X 71 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8110 (mtmm) REVERT: X 76 ASP cc_start: 0.8656 (t0) cc_final: 0.7590 (t0) REVERT: X 98 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6270 (m-10) outliers start: 229 outliers final: 161 residues processed: 960 average time/residue: 0.1608 time to fit residues: 244.9862 Evaluate side-chains 956 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 773 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 98 PHE 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 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain 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 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 39 VAL 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 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 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 126 MET Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 7 LYS Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain S residue 39 VAL 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 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.0470 chunk 181 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN F 102 GLN G 20 GLN ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 20 GLN O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN V 92 GLN W 20 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.046557 restraints weight = 109958.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.048190 restraints weight = 57762.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049325 restraints weight = 35516.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050072 restraints weight = 23853.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050711 restraints weight = 17519.849| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23688 Z= 0.180 Angle : 0.924 12.744 31968 Z= 0.451 Chirality : 0.052 0.262 3576 Planarity : 0.004 0.040 4248 Dihedral : 5.625 26.662 3264 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 8.71 % Allowed : 31.06 % Favored : 60.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.14), residues: 3024 helix: -0.57 (0.22), residues: 480 sheet: -1.26 (0.14), residues: 1224 loop : -2.99 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 31 TYR 0.013 0.001 TYR A 122 PHE 0.030 0.002 PHE F 91 TRP 0.007 0.001 TRP R 50 HIS 0.002 0.001 HIS G 116 Details of bonding type rmsd covalent geometry : bond 0.00413 (23688) covalent geometry : angle 0.92366 (31968) hydrogen bonds : bond 0.03078 ( 816) hydrogen bonds : angle 5.52061 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 797 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8679 (tp) REVERT: D 51 ARG cc_start: 0.8950 (ttp-170) cc_final: 0.8473 (ttp-170) REVERT: D 52 GLU cc_start: 0.8649 (mt-10) cc_final: 0.7964 (mp0) REVERT: D 70 PHE cc_start: 0.8896 (t80) cc_final: 0.8617 (t80) REVERT: D 87 GLU cc_start: 0.8668 (pm20) cc_final: 0.8275 (pp20) REVERT: B 4 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8117 (mp10) REVERT: B 8 ASP cc_start: 0.8838 (m-30) cc_final: 0.8584 (m-30) REVERT: B 74 ASP cc_start: 0.8918 (p0) cc_final: 0.8659 (p0) REVERT: B 76 ASP cc_start: 0.8447 (t0) cc_final: 0.7019 (t0) REVERT: B 98 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: B 123 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8344 (mp0) REVERT: C 51 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8656 (ttp-110) REVERT: A 35 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9185 (p0) REVERT: A 76 ASP cc_start: 0.8867 (t0) cc_final: 0.8015 (t0) REVERT: A 85 ASP cc_start: 0.8958 (m-30) cc_final: 0.8541 (p0) REVERT: A 119 GLU cc_start: 0.9087 (pm20) cc_final: 0.8821 (pm20) REVERT: E 31 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8646 (mmm-85) REVERT: E 51 ARG cc_start: 0.8933 (ttp-170) cc_final: 0.8507 (ttp-170) REVERT: E 52 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7760 (mt-10) REVERT: E 71 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7935 (mtmm) REVERT: F 4 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7928 (mp10) REVERT: F 74 ASP cc_start: 0.8949 (p0) cc_final: 0.8655 (p0) REVERT: F 76 ASP cc_start: 0.8704 (t0) cc_final: 0.8160 (t0) REVERT: F 92 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: F 98 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.6410 (m-10) REVERT: G 31 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.7404 (ttt90) REVERT: G 51 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8603 (ttp-110) REVERT: G 71 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8549 (mtmm) REVERT: G 81 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8195 (tm-30) REVERT: G 82 ILE cc_start: 0.9493 (mt) cc_final: 0.8763 (mt) REVERT: G 85 ASP cc_start: 0.8775 (m-30) cc_final: 0.8423 (p0) REVERT: G 87 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7569 (mt-10) REVERT: H 20 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7096 (pp30) REVERT: H 31 ARG cc_start: 0.9243 (ptm-80) cc_final: 0.8743 (ptm-80) REVERT: H 71 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8223 (mtmm) REVERT: H 85 ASP cc_start: 0.8984 (m-30) cc_final: 0.8461 (p0) REVERT: H 87 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7822 (mt-10) REVERT: I 5 ASN cc_start: 0.8831 (t0) cc_final: 0.8515 (t0) REVERT: I 51 ARG cc_start: 0.8956 (ttp-170) cc_final: 0.8547 (ttp-170) REVERT: I 52 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7193 (mp0) REVERT: I 111 ASP cc_start: 0.8105 (p0) cc_final: 0.7840 (p0) REVERT: J 4 GLN cc_start: 0.8549 (mm-40) cc_final: 0.7913 (mp10) REVERT: J 8 ASP cc_start: 0.8861 (m-30) cc_final: 0.8623 (m-30) REVERT: J 60 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8018 (mtp85) REVERT: J 70 PHE cc_start: 0.8474 (t80) cc_final: 0.6243 (t80) REVERT: J 74 ASP cc_start: 0.8869 (p0) cc_final: 0.8528 (p0) REVERT: J 76 ASP cc_start: 0.8699 (t0) cc_final: 0.7511 (t0) REVERT: J 98 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7041 (m-10) REVERT: J 112 TYR cc_start: 0.9100 (m-80) cc_final: 0.8888 (m-10) REVERT: K 31 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8109 (mtp85) REVERT: K 81 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8295 (tm-30) REVERT: K 82 ILE cc_start: 0.9426 (mt) cc_final: 0.8096 (mt) REVERT: K 85 ASP cc_start: 0.8815 (m-30) cc_final: 0.7851 (p0) REVERT: K 87 GLU cc_start: 0.8811 (mt-10) cc_final: 0.7867 (mp0) REVERT: K 111 ASP cc_start: 0.8710 (p0) cc_final: 0.8062 (p0) REVERT: K 123 GLU cc_start: 0.8481 (mp0) cc_final: 0.7929 (mp0) REVERT: L 71 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8194 (mtmm) REVERT: M 27 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8606 (tp) REVERT: M 51 ARG cc_start: 0.8961 (ttp-170) cc_final: 0.8475 (ttp-170) REVERT: M 52 GLU cc_start: 0.8640 (mt-10) cc_final: 0.7955 (mp0) REVERT: M 70 PHE cc_start: 0.8943 (t80) cc_final: 0.8698 (t80) REVERT: M 77 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9150 (tp30) REVERT: M 91 PHE cc_start: 0.8866 (m-80) cc_final: 0.8618 (m-10) REVERT: N 4 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8106 (mp10) REVERT: N 8 ASP cc_start: 0.8840 (m-30) cc_final: 0.8582 (m-30) REVERT: N 74 ASP cc_start: 0.8929 (p0) cc_final: 0.8616 (p0) REVERT: N 76 ASP cc_start: 0.8619 (t0) cc_final: 0.7208 (t0) REVERT: N 98 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.6085 (m-10) REVERT: O 51 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8663 (ttp-110) REVERT: O 78 ARG cc_start: 0.9287 (tpt170) cc_final: 0.9065 (tpt-90) REVERT: P 20 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7179 (pp30) REVERT: P 35 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9193 (p0) REVERT: P 85 ASP cc_start: 0.8980 (m-30) cc_final: 0.8441 (p0) REVERT: P 119 GLU cc_start: 0.9085 (pm20) cc_final: 0.8828 (pm20) REVERT: Q 31 ARG cc_start: 0.8967 (tpp80) cc_final: 0.8637 (mmm-85) REVERT: Q 51 ARG cc_start: 0.8945 (ttp-170) cc_final: 0.8510 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7742 (mt-10) REVERT: Q 71 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7925 (mtmm) REVERT: R 4 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7932 (mp10) REVERT: R 74 ASP cc_start: 0.8955 (p0) cc_final: 0.8663 (p0) REVERT: R 76 ASP cc_start: 0.8717 (t0) cc_final: 0.8152 (t0) REVERT: R 92 GLN cc_start: 0.9023 (tt0) cc_final: 0.8758 (tt0) REVERT: R 98 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: S 31 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.7415 (ttt90) REVERT: S 71 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8445 (mtmm) REVERT: S 81 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8203 (tm-30) REVERT: S 82 ILE cc_start: 0.9495 (mt) cc_final: 0.8769 (mt) REVERT: S 85 ASP cc_start: 0.8781 (m-30) cc_final: 0.8435 (p0) REVERT: S 87 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7564 (mt-10) REVERT: S 123 GLU cc_start: 0.8308 (mp0) cc_final: 0.7967 (mp0) REVERT: T 20 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7045 (pp30) REVERT: T 31 ARG cc_start: 0.9286 (ptm-80) cc_final: 0.8817 (ptm-80) REVERT: T 71 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8097 (mtmm) REVERT: T 98 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: U 5 ASN cc_start: 0.9068 (t0) cc_final: 0.8312 (t0) REVERT: U 7 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9045 (mtmm) REVERT: U 51 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8550 (ttp-170) REVERT: U 52 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7246 (mp0) REVERT: U 111 ASP cc_start: 0.8133 (p0) cc_final: 0.7891 (p0) REVERT: V 8 ASP cc_start: 0.8867 (m-30) cc_final: 0.8663 (m-30) REVERT: V 60 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8020 (mtp85) REVERT: V 70 PHE cc_start: 0.8524 (t80) cc_final: 0.6172 (t80) REVERT: V 74 ASP cc_start: 0.8878 (p0) cc_final: 0.8526 (p0) REVERT: V 76 ASP cc_start: 0.8683 (t0) cc_final: 0.7500 (t0) REVERT: V 98 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6135 (m-10) REVERT: W 31 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8100 (mmm160) REVERT: W 81 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8229 (tm-30) REVERT: W 82 ILE cc_start: 0.9444 (mt) cc_final: 0.8192 (mt) REVERT: W 85 ASP cc_start: 0.8823 (m-30) cc_final: 0.7853 (p0) REVERT: W 87 GLU cc_start: 0.8752 (mt-10) cc_final: 0.7851 (mp0) REVERT: W 111 ASP cc_start: 0.8727 (p0) cc_final: 0.8218 (p0) REVERT: W 123 GLU cc_start: 0.8470 (mp0) cc_final: 0.8025 (mp0) REVERT: X 71 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8141 (mtmm) REVERT: X 76 ASP cc_start: 0.8670 (t0) cc_final: 0.7629 (t0) REVERT: X 98 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6303 (m-10) outliers start: 207 outliers final: 171 residues processed: 922 average time/residue: 0.1606 time to fit residues: 235.0079 Evaluate side-chains 945 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 755 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 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 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 11 ILE Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 20 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain 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 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 39 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 20 GLN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain 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 60 ARG Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 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 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 32 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 146 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN F 92 GLN G 20 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN K 20 GLN M 20 GLN O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 20 GLN X 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045155 restraints weight = 111645.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.046755 restraints weight = 58845.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047881 restraints weight = 35762.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048666 restraints weight = 23859.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049204 restraints weight = 17166.730| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23688 Z= 0.233 Angle : 0.946 16.317 31968 Z= 0.466 Chirality : 0.052 0.352 3576 Planarity : 0.004 0.042 4248 Dihedral : 5.777 29.258 3264 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 8.67 % Allowed : 30.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.14), residues: 3024 helix: -0.51 (0.23), residues: 456 sheet: -1.16 (0.14), residues: 1200 loop : -3.06 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 31 TYR 0.024 0.001 TYR J 122 PHE 0.031 0.002 PHE F 91 TRP 0.011 0.001 TRP R 50 HIS 0.002 0.001 HIS G 116 Details of bonding type rmsd covalent geometry : bond 0.00530 (23688) covalent geometry : angle 0.94621 (31968) hydrogen bonds : bond 0.03267 ( 816) hydrogen bonds : angle 5.67913 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 755 time to evaluate : 0.906 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: D 27 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8687 (tt) REVERT: D 51 ARG cc_start: 0.8999 (ttp-170) cc_final: 0.8404 (ttp-170) REVERT: D 52 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7993 (mp0) REVERT: D 70 PHE cc_start: 0.8942 (t80) cc_final: 0.8711 (t80) REVERT: D 87 GLU cc_start: 0.8722 (pm20) cc_final: 0.8277 (pp20) REVERT: B 8 ASP cc_start: 0.8844 (m-30) cc_final: 0.8598 (m-30) REVERT: B 74 ASP cc_start: 0.8954 (p0) cc_final: 0.8696 (p0) REVERT: B 76 ASP cc_start: 0.8511 (t0) cc_final: 0.7049 (t0) REVERT: B 98 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: B 123 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8366 (mp0) REVERT: C 31 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8140 (ttm-80) REVERT: C 51 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8655 (ttp-110) REVERT: C 85 ASP cc_start: 0.8752 (m-30) cc_final: 0.8180 (m-30) REVERT: A 35 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9211 (p0) REVERT: A 76 ASP cc_start: 0.8941 (t0) cc_final: 0.8243 (t0) REVERT: A 85 ASP cc_start: 0.8999 (m-30) cc_final: 0.8447 (p0) REVERT: A 119 GLU cc_start: 0.9123 (pm20) cc_final: 0.8846 (pm20) REVERT: E 7 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8798 (mtmm) REVERT: E 51 ARG cc_start: 0.8955 (ttp-170) cc_final: 0.8527 (ttp-170) REVERT: E 52 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8050 (mt-10) REVERT: E 71 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8132 (mtmm) REVERT: F 74 ASP cc_start: 0.8972 (p0) cc_final: 0.8639 (p0) REVERT: F 76 ASP cc_start: 0.8712 (t0) cc_final: 0.8035 (t0) REVERT: F 92 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: F 98 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.6314 (m-10) REVERT: G 31 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.7408 (ttt90) REVERT: G 51 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8600 (ttp-110) REVERT: G 81 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 82 ILE cc_start: 0.9482 (mt) cc_final: 0.8779 (mt) REVERT: G 85 ASP cc_start: 0.8831 (m-30) cc_final: 0.8455 (p0) REVERT: G 87 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7083 (mt-10) REVERT: G 123 GLU cc_start: 0.8568 (mp0) cc_final: 0.7936 (mp0) REVERT: H 31 ARG cc_start: 0.9296 (ptm-80) cc_final: 0.8640 (ptm-80) REVERT: H 71 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8231 (mtmm) REVERT: H 85 ASP cc_start: 0.9038 (m-30) cc_final: 0.8480 (p0) REVERT: H 87 GLU cc_start: 0.8786 (mt-10) cc_final: 0.7974 (mt-10) REVERT: I 5 ASN cc_start: 0.8850 (t0) cc_final: 0.8505 (t0) REVERT: I 51 ARG cc_start: 0.8951 (ttp-170) cc_final: 0.8525 (ttp-170) REVERT: I 52 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7137 (mp0) REVERT: J 4 GLN cc_start: 0.8603 (mm-40) cc_final: 0.7912 (mp10) REVERT: J 8 ASP cc_start: 0.8926 (m-30) cc_final: 0.8691 (m-30) REVERT: J 60 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: J 70 PHE cc_start: 0.8533 (t80) cc_final: 0.6138 (t80) REVERT: J 74 ASP cc_start: 0.8919 (p0) cc_final: 0.8528 (p0) REVERT: J 76 ASP cc_start: 0.8750 (t0) cc_final: 0.7512 (t0) REVERT: J 98 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: K 31 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8198 (mmm160) REVERT: K 81 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8289 (tm-30) REVERT: K 82 ILE cc_start: 0.9407 (mt) cc_final: 0.8084 (mt) REVERT: K 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.7887 (p0) REVERT: K 87 GLU cc_start: 0.8853 (mt-10) cc_final: 0.7873 (mp0) REVERT: K 111 ASP cc_start: 0.8730 (p0) cc_final: 0.8075 (p0) REVERT: K 123 GLU cc_start: 0.8522 (mp0) cc_final: 0.7960 (mp0) REVERT: L 71 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8267 (mtmm) REVERT: M 27 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8708 (tp) REVERT: M 51 ARG cc_start: 0.9004 (ttp-170) cc_final: 0.8415 (ttp-170) REVERT: M 52 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7988 (mp0) REVERT: M 70 PHE cc_start: 0.8971 (t80) cc_final: 0.8762 (t80) REVERT: M 77 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9133 (tp30) REVERT: M 91 PHE cc_start: 0.8908 (m-80) cc_final: 0.8692 (m-10) REVERT: N 8 ASP cc_start: 0.8857 (m-30) cc_final: 0.8603 (m-30) REVERT: N 74 ASP cc_start: 0.8966 (p0) cc_final: 0.8654 (p0) REVERT: N 76 ASP cc_start: 0.8680 (t0) cc_final: 0.7262 (t0) REVERT: N 98 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: N 111 ASP cc_start: 0.8787 (p0) cc_final: 0.8582 (p0) REVERT: O 51 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8643 (ttp-110) REVERT: O 85 ASP cc_start: 0.8803 (m-30) cc_final: 0.8240 (m-30) REVERT: O 111 ASP cc_start: 0.8663 (p0) cc_final: 0.8427 (p0) REVERT: P 35 ASN cc_start: 0.9432 (OUTLIER) cc_final: 0.9209 (p0) REVERT: P 85 ASP cc_start: 0.9030 (m-30) cc_final: 0.8481 (p0) REVERT: P 119 GLU cc_start: 0.9112 (pm20) cc_final: 0.8856 (pm20) REVERT: Q 7 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8790 (mtmm) REVERT: Q 51 ARG cc_start: 0.8985 (ttp-170) cc_final: 0.8395 (ttp-170) REVERT: Q 52 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7715 (mt-10) REVERT: Q 71 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8085 (mtmm) REVERT: R 70 PHE cc_start: 0.8611 (t80) cc_final: 0.5930 (t80) REVERT: R 74 ASP cc_start: 0.8990 (p0) cc_final: 0.8703 (p0) REVERT: R 76 ASP cc_start: 0.8743 (t0) cc_final: 0.7876 (t0) REVERT: R 92 GLN cc_start: 0.9098 (tt0) cc_final: 0.8691 (tt0) REVERT: R 98 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: S 31 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.7466 (ttt90) REVERT: S 81 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8040 (tm-30) REVERT: S 82 ILE cc_start: 0.9485 (mt) cc_final: 0.8791 (mt) REVERT: S 85 ASP cc_start: 0.8830 (m-30) cc_final: 0.8466 (p0) REVERT: S 87 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7090 (mt-10) REVERT: S 123 GLU cc_start: 0.8250 (mp0) cc_final: 0.7872 (mp0) REVERT: T 31 ARG cc_start: 0.9307 (ptm-80) cc_final: 0.8777 (ptm-80) REVERT: T 71 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8191 (mtmm) REVERT: T 98 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: U 5 ASN cc_start: 0.9067 (t0) cc_final: 0.8425 (t0) REVERT: U 7 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9098 (mtmm) REVERT: U 51 ARG cc_start: 0.8989 (ttp-170) cc_final: 0.8563 (ttp-170) REVERT: U 52 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7197 (mp0) REVERT: V 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8702 (m-30) REVERT: V 60 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: V 70 PHE cc_start: 0.8531 (t80) cc_final: 0.5695 (t80) REVERT: V 74 ASP cc_start: 0.8915 (p0) cc_final: 0.8525 (p0) REVERT: V 76 ASP cc_start: 0.8770 (t0) cc_final: 0.7627 (t0) REVERT: V 98 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.6345 (m-10) REVERT: W 81 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8306 (tm-30) REVERT: W 82 ILE cc_start: 0.9408 (mt) cc_final: 0.8124 (mt) REVERT: W 85 ASP cc_start: 0.8861 (m-30) cc_final: 0.7835 (p0) REVERT: W 87 GLU cc_start: 0.8768 (mt-10) cc_final: 0.7835 (mp0) REVERT: W 111 ASP cc_start: 0.8888 (p0) cc_final: 0.8326 (p0) REVERT: W 123 GLU cc_start: 0.8541 (mp0) cc_final: 0.7979 (mp0) REVERT: X 71 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8121 (mtmm) REVERT: X 76 ASP cc_start: 0.8715 (t0) cc_final: 0.7681 (t0) REVERT: X 98 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: X 126 MET cc_start: 0.8890 (mpp) cc_final: 0.8593 (mpp) outliers start: 206 outliers final: 172 residues processed: 882 average time/residue: 0.1615 time to fit residues: 226.1207 Evaluate side-chains 924 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 736 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 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 69 VAL Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 9 LEU 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 107 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 11 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 ILE 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 126 MET Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 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 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain 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 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 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 100 ILE Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN K 20 GLN M 20 GLN O 20 GLN ** O 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN ** S 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 GLN W 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046463 restraints weight = 109215.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048049 restraints weight = 57547.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049208 restraints weight = 35540.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050018 restraints weight = 23743.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050549 restraints weight = 17014.764| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23688 Z= 0.187 Angle : 0.960 15.620 31968 Z= 0.467 Chirality : 0.053 0.331 3576 Planarity : 0.004 0.043 4248 Dihedral : 5.829 30.623 3264 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 8.38 % Allowed : 31.48 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.14), residues: 3024 helix: -0.53 (0.23), residues: 456 sheet: -1.34 (0.14), residues: 1224 loop : -2.94 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 78 TYR 0.015 0.001 TYR P 122 PHE 0.033 0.002 PHE K 91 TRP 0.006 0.001 TRP R 50 HIS 0.002 0.001 HIS W 116 Details of bonding type rmsd covalent geometry : bond 0.00441 (23688) covalent geometry : angle 0.96020 (31968) hydrogen bonds : bond 0.03274 ( 816) hydrogen bonds : angle 5.74394 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.92 seconds wall clock time: 83 minutes 1.95 seconds (4981.95 seconds total)