Starting phenix.real_space_refine on Thu Feb 5 09:23:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7a_63933/02_2026/9u7a_63933.map" } resolution = 2.82 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= 0.015 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 72 5.16 5 C 10368 2.51 5 N 2952 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16512 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y Time building chain proxies: 1.47, per 1000 atoms: 0.09 Number of scatterers: 16512 At special positions: 0 Unit cell: (101.438, 102.195, 142.316, 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 72 16.00 O 3120 8.00 N 2952 7.00 C 10368 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: 1.48 Conformation dependent library (CDL) restraints added in 650.0 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.535A pdb=" N LEU E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.594A pdb=" N ARG E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.535A pdb=" N LEU F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 32 through 37 Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.594A pdb=" N ARG G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 32 through 37 Processing helix chain 'J' and resid 41 through 52 removed outlier: 3.535A pdb=" N LEU J 45 " --> pdb=" O SER J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 32 through 37 Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 32 through 37 Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.535A pdb=" N LEU L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU M 45 " --> pdb=" O SER M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG M 78 " --> pdb=" O ASP M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU N 45 " --> pdb=" O SER N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU P 45 " --> pdb=" O SER P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG Q 78 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 32 through 37 Processing helix chain 'R' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG R 78 " --> pdb=" O ASP R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU S 45 " --> pdb=" O SER S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 70 Processing helix chain 'S' and resid 72 through 86 removed outlier: 3.594A pdb=" N ARG S 78 " --> pdb=" O ASP S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.535A pdb=" N LEU T 45 " --> pdb=" O SER T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 70 Processing helix chain 'T' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG T 78 " --> pdb=" O ASP T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 70 Processing helix chain 'U' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG U 78 " --> pdb=" O ASP U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 13 Processing helix chain 'V' and resid 16 through 27 Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG V 78 " --> pdb=" O ASP V 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'W' and resid 16 through 27 Processing helix chain 'W' and resid 32 through 37 Processing helix chain 'W' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 70 Processing helix chain 'W' and resid 72 through 86 removed outlier: 3.594A pdb=" N ARG W 78 " --> pdb=" O ASP W 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 13 Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 32 through 37 Processing helix chain 'X' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU X 45 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 70 Processing helix chain 'X' and resid 72 through 86 removed outlier: 3.596A pdb=" N ARG X 78 " --> pdb=" O ASP X 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 13 Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 32 through 37 Processing helix chain 'Y' and resid 41 through 52 removed outlier: 3.536A pdb=" N LEU Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 70 Processing helix chain 'Y' and resid 72 through 86 removed outlier: 3.595A pdb=" N ARG Y 78 " --> pdb=" O ASP Y 74 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3436 1.33 - 1.45: 3332 1.45 - 1.57: 9816 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16704 Sorted by residual: bond pdb=" N VAL I 31 " pdb=" CA VAL I 31 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N VAL M 31 " pdb=" CA VAL M 31 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.79e+00 bond pdb=" N VAL Y 31 " pdb=" CA VAL Y 31 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.75e+00 bond pdb=" N VAL Q 31 " pdb=" CA VAL Q 31 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.70e+00 bond pdb=" N VAL G 31 " pdb=" CA VAL G 31 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.61e+00 ... (remaining 16699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 12220 1.08 - 2.15: 7138 2.15 - 3.23: 2552 3.23 - 4.31: 399 4.31 - 5.38: 107 Bond angle restraints: 22416 Sorted by residual: angle pdb=" N ALA H 86 " pdb=" CA ALA H 86 " pdb=" C ALA H 86 " ideal model delta sigma weight residual 112.97 108.40 4.57 1.06e+00 8.90e-01 1.86e+01 angle pdb=" N ALA P 86 " pdb=" CA ALA P 86 " pdb=" C ALA P 86 " ideal model delta sigma weight residual 112.97 108.41 4.56 1.06e+00 8.90e-01 1.85e+01 angle pdb=" N ALA N 86 " pdb=" CA ALA N 86 " pdb=" C ALA N 86 " ideal model delta sigma weight residual 112.97 108.41 4.56 1.06e+00 8.90e-01 1.85e+01 angle pdb=" N ALA L 86 " pdb=" CA ALA L 86 " pdb=" C ALA L 86 " ideal model delta sigma weight residual 112.97 108.42 4.55 1.06e+00 8.90e-01 1.85e+01 angle pdb=" N ALA T 86 " pdb=" CA ALA T 86 " pdb=" C ALA T 86 " ideal model delta sigma weight residual 112.97 108.42 4.55 1.06e+00 8.90e-01 1.84e+01 ... (remaining 22411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 8521 15.45 - 30.90: 983 30.90 - 46.35: 528 46.35 - 61.80: 240 61.80 - 77.25: 96 Dihedral angle restraints: 10368 sinusoidal: 4368 harmonic: 6000 Sorted by residual: dihedral pdb=" CD ARG F 64 " pdb=" NE ARG F 64 " pdb=" CZ ARG F 64 " pdb=" NH1 ARG F 64 " ideal model delta sinusoidal sigma weight residual 0.00 76.55 -76.55 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CD ARG O 64 " pdb=" NE ARG O 64 " pdb=" CZ ARG O 64 " pdb=" NH1 ARG O 64 " ideal model delta sinusoidal sigma weight residual 0.00 76.52 -76.52 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CD ARG K 64 " pdb=" NE ARG K 64 " pdb=" CZ ARG K 64 " pdb=" NH1 ARG K 64 " ideal model delta sinusoidal sigma weight residual 0.00 76.51 -76.51 1 1.00e+01 1.00e-02 7.36e+01 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1145 0.046 - 0.091: 488 0.091 - 0.137: 806 0.137 - 0.183: 129 0.183 - 0.228: 72 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB VAL K 6 " pdb=" CA VAL K 6 " pdb=" CG1 VAL K 6 " pdb=" CG2 VAL K 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL D 6 " pdb=" CA VAL D 6 " pdb=" CG1 VAL D 6 " pdb=" CG2 VAL D 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL M 6 " pdb=" CA VAL M 6 " pdb=" CG1 VAL M 6 " pdb=" CG2 VAL M 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2637 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 64 " 1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG I 64 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG I 64 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 64 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG I 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 64 " 1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG X 64 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG X 64 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG X 64 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG X 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 64 " -1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG P 64 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG P 64 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG P 64 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG P 64 " -0.019 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 7744 3.01 - 3.48: 16575 3.48 - 3.95: 27663 3.95 - 4.43: 32339 4.43 - 4.90: 49751 Nonbonded interactions: 134072 Sorted by model distance: nonbonded pdb=" N SER S 17 " pdb=" OG SER S 17 " model vdw 2.536 2.496 nonbonded pdb=" N SER J 17 " pdb=" OG SER J 17 " model vdw 2.536 2.496 nonbonded pdb=" N SER K 17 " pdb=" OG SER K 17 " model vdw 2.536 2.496 nonbonded pdb=" N SER R 17 " pdb=" OG SER R 17 " model vdw 2.536 2.496 nonbonded pdb=" N SER N 17 " pdb=" OG SER N 17 " model vdw 2.536 2.496 ... (remaining 134067 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0262 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 : 0.012 0.038 16704 Z= 0.880 Angle : 1.429 5.384 22416 Z= 1.131 Chirality : 0.086 0.228 2640 Planarity : 0.074 0.474 2880 Dihedral : 19.883 77.248 6432 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 12.82 % Allowed : 10.26 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.15), residues: 2040 helix: -1.56 (0.10), residues: 1728 sheet: None (None), residues: 0 loop : -1.97 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 64 PHE 0.006 0.002 PHE O 4 HIS 0.003 0.002 HIS N 9 Details of bonding type rmsd covalent geometry : bond 0.01164 (16704) covalent geometry : angle 1.42891 (22416) hydrogen bonds : bond 0.26454 ( 1008) hydrogen bonds : angle 6.20591 ( 3024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 119 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 HIS cc_start: 0.0037 (OUTLIER) cc_final: -0.0895 (t-170) REVERT: B 75 LEU cc_start: 0.0487 (OUTLIER) cc_final: 0.0254 (mt) REVERT: B 77 ARG cc_start: -0.0341 (OUTLIER) cc_final: -0.0903 (mmt90) REVERT: C 77 ARG cc_start: -0.1163 (OUTLIER) cc_final: -0.1877 (mmt90) REVERT: C 83 GLU cc_start: 0.0410 (OUTLIER) cc_final: -0.0589 (mm-30) REVERT: D 75 LEU cc_start: 0.0765 (OUTLIER) cc_final: 0.0410 (mt) REVERT: D 77 ARG cc_start: -0.1192 (OUTLIER) cc_final: -0.1957 (mmt180) REVERT: E 77 ARG cc_start: -0.1919 (OUTLIER) cc_final: -0.2254 (mpt-90) REVERT: F 61 GLU cc_start: -0.0495 (OUTLIER) cc_final: -0.1094 (mt-10) REVERT: F 77 ARG cc_start: -0.1121 (OUTLIER) cc_final: -0.1595 (mmt180) REVERT: G 83 GLU cc_start: 0.1706 (OUTLIER) cc_final: 0.0781 (mm-30) REVERT: H 59 HIS cc_start: -0.2025 (OUTLIER) cc_final: -0.2406 (t-170) REVERT: H 77 ARG cc_start: -0.0900 (OUTLIER) cc_final: -0.2983 (tpt170) REVERT: I 59 HIS cc_start: -0.1017 (OUTLIER) cc_final: -0.2560 (t-170) REVERT: I 77 ARG cc_start: -0.1269 (OUTLIER) cc_final: -0.1501 (mmt90) REVERT: J 75 LEU cc_start: 0.1193 (OUTLIER) cc_final: 0.0106 (mt) REVERT: J 77 ARG cc_start: -0.0598 (OUTLIER) cc_final: -0.0966 (mmt90) REVERT: K 77 ARG cc_start: -0.0778 (OUTLIER) cc_final: -0.1722 (mmt180) REVERT: K 83 GLU cc_start: -0.0801 (OUTLIER) cc_final: -0.1070 (mm-30) REVERT: L 59 HIS cc_start: 0.0132 (OUTLIER) cc_final: -0.0516 (t-170) REVERT: L 61 GLU cc_start: 0.0695 (OUTLIER) cc_final: 0.0007 (mm-30) REVERT: L 75 LEU cc_start: 0.1866 (OUTLIER) cc_final: 0.0825 (mt) REVERT: L 77 ARG cc_start: -0.1843 (OUTLIER) cc_final: -0.2752 (mmt180) REVERT: M 77 ARG cc_start: -0.1883 (OUTLIER) cc_final: -0.2352 (mmt90) REVERT: N 61 GLU cc_start: 0.0053 (OUTLIER) cc_final: -0.1181 (pp20) REVERT: O 6 VAL cc_start: 0.1584 (OUTLIER) cc_final: 0.1376 (p) REVERT: O 61 GLU cc_start: 0.1160 (OUTLIER) cc_final: 0.0765 (mt-10) REVERT: O 77 ARG cc_start: -0.1782 (OUTLIER) cc_final: -0.2819 (mmt180) REVERT: O 83 GLU cc_start: 0.1038 (OUTLIER) cc_final: 0.0494 (mm-30) REVERT: P 77 ARG cc_start: -0.1702 (OUTLIER) cc_final: -0.2521 (tpp80) REVERT: P 83 GLU cc_start: -0.1612 (OUTLIER) cc_final: -0.1874 (mm-30) REVERT: Q 6 VAL cc_start: 0.1227 (OUTLIER) cc_final: 0.0582 (p) REVERT: R 77 ARG cc_start: -0.1755 (OUTLIER) cc_final: -0.2462 (mmt90) REVERT: T 75 LEU cc_start: 0.0530 (OUTLIER) cc_final: 0.0223 (mt) REVERT: T 77 ARG cc_start: -0.1173 (OUTLIER) cc_final: -0.3064 (tpt170) REVERT: U 59 HIS cc_start: 0.0215 (OUTLIER) cc_final: -0.1837 (m170) REVERT: U 77 ARG cc_start: -0.1357 (OUTLIER) cc_final: -0.1683 (mpt-90) REVERT: V 75 LEU cc_start: 0.0862 (OUTLIER) cc_final: 0.0301 (mt) REVERT: W 59 HIS cc_start: -0.0633 (OUTLIER) cc_final: -0.2102 (m170) REVERT: X 59 HIS cc_start: 0.0081 (OUTLIER) cc_final: -0.0222 (m170) REVERT: X 77 ARG cc_start: -0.1430 (OUTLIER) cc_final: -0.3133 (tpt170) REVERT: Y 59 HIS cc_start: 0.0425 (OUTLIER) cc_final: 0.0094 (t-170) REVERT: Y 77 ARG cc_start: -0.1280 (OUTLIER) cc_final: -0.3270 (mmt-90) outliers start: 240 outliers final: 42 residues processed: 345 average time/residue: 0.6667 time to fit residues: 253.4542 Evaluate side-chains 182 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 97 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 59 HIS Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 59 HIS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain M residue 77 ARG Chi-restraints excluded: chain N residue 59 HIS Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain S residue 44 ASP Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain T residue 44 ASP Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 83 GLU Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain V residue 44 ASP Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain W residue 59 HIS Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 59 HIS Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain Y residue 59 HIS Chi-restraints excluded: chain Y residue 77 ARG Chi-restraints excluded: chain Y residue 83 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS C 52 GLN F 59 HIS H 59 HIS K 52 GLN L 59 HIS M 52 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 HIS O 59 HIS R 52 GLN V 59 HIS ** W 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 HIS X 59 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.324209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.305855 restraints weight = 28177.361| |-----------------------------------------------------------------------------| r_work (start): 0.5199 rms_B_bonded: 2.96 r_work: 0.5111 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.5111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0716 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16704 Z= 0.141 Angle : 0.609 13.066 22416 Z= 0.299 Chirality : 0.042 0.423 2640 Planarity : 0.005 0.053 2880 Dihedral : 8.840 56.896 2490 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.19 % Allowed : 17.79 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2040 helix: 0.65 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.18 (0.19), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 71 PHE 0.013 0.002 PHE L 4 HIS 0.007 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00280 (16704) covalent geometry : angle 0.60884 (22416) hydrogen bonds : bond 0.02820 ( 1008) hydrogen bonds : angle 3.72341 ( 3024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.625 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: C 1 MET cc_start: 0.1109 (pp-130) cc_final: -0.1025 (ttm) REVERT: C 30 ARG cc_start: -0.0511 (OUTLIER) cc_final: -0.1896 (tpm170) REVERT: D 44 ASP cc_start: 0.1565 (m-30) cc_final: 0.0804 (m-30) REVERT: E 1 MET cc_start: 0.1584 (mmt) cc_final: 0.1307 (ppp) REVERT: F 75 LEU cc_start: -0.0050 (OUTLIER) cc_final: -0.1544 (tp) REVERT: G 1 MET cc_start: -0.0622 (pp-130) cc_final: -0.1354 (ptm) REVERT: I 30 ARG cc_start: -0.0996 (OUTLIER) cc_final: -0.1732 (tpp-160) REVERT: J 1 MET cc_start: -0.2161 (ttm) cc_final: -0.2723 (mmp) REVERT: J 7 LEU cc_start: 0.1218 (tp) cc_final: 0.0375 (pp) REVERT: K 1 MET cc_start: 0.1776 (pp-130) cc_final: -0.1177 (ppp) REVERT: M 30 ARG cc_start: -0.0941 (OUTLIER) cc_final: -0.2471 (mmt180) REVERT: N 30 ARG cc_start: -0.0239 (OUTLIER) cc_final: -0.1141 (ttm170) REVERT: O 30 ARG cc_start: -0.0024 (OUTLIER) cc_final: -0.1381 (tpp-160) REVERT: Q 30 ARG cc_start: -0.0365 (OUTLIER) cc_final: -0.1179 (tpp-160) REVERT: R 1 MET cc_start: -0.2278 (ppp) cc_final: -0.3021 (ppp) REVERT: S 30 ARG cc_start: -0.0812 (OUTLIER) cc_final: -0.1903 (tpm170) REVERT: T 30 ARG cc_start: -0.0509 (OUTLIER) cc_final: -0.0761 (ttm110) REVERT: U 30 ARG cc_start: -0.0095 (OUTLIER) cc_final: -0.1497 (tpp-160) REVERT: W 30 ARG cc_start: 0.0362 (OUTLIER) cc_final: -0.0222 (ttm110) REVERT: X 75 LEU cc_start: -0.0577 (OUTLIER) cc_final: -0.1802 (tp) REVERT: Y 30 ARG cc_start: -0.0262 (OUTLIER) cc_final: -0.1739 (mmm160) outliers start: 41 outliers final: 10 residues processed: 134 average time/residue: 0.7704 time to fit residues: 113.0682 Evaluate side-chains 109 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS H 73 HIS J 73 HIS K 73 HIS L 73 HIS ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 GLN T 73 HIS ** W 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5646 r_free = 0.5646 target = 0.387005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.368614 restraints weight = 33619.657| |-----------------------------------------------------------------------------| r_work (start): 0.5283 rms_B_bonded: 0.86 r_work: 0.5249 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.5205 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.5205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1090 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16704 Z= 0.140 Angle : 0.651 11.147 22416 Z= 0.304 Chirality : 0.039 0.280 2640 Planarity : 0.005 0.066 2880 Dihedral : 3.527 11.362 2256 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.58 % Allowed : 18.54 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2040 helix: 1.27 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -0.90 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 30 PHE 0.012 0.002 PHE Q 25 HIS 0.007 0.001 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00287 (16704) covalent geometry : angle 0.65059 (22416) hydrogen bonds : bond 0.03163 ( 1008) hydrogen bonds : angle 3.53559 ( 3024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 102 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: -0.0318 (OUTLIER) cc_final: -0.1984 (mmtt) REVERT: D 44 ASP cc_start: 0.2212 (m-30) cc_final: 0.1423 (m-30) REVERT: E 1 MET cc_start: 0.2099 (mmt) cc_final: 0.1462 (ppp) REVERT: E 30 ARG cc_start: 0.0277 (OUTLIER) cc_final: -0.2761 (mmm160) REVERT: F 75 LEU cc_start: -0.0710 (OUTLIER) cc_final: -0.0929 (mt) REVERT: G 1 MET cc_start: 0.0482 (pp-130) cc_final: -0.1393 (ptm) REVERT: G 37 GLU cc_start: -0.0700 (OUTLIER) cc_final: -0.0928 (tt0) REVERT: K 44 ASP cc_start: 0.2289 (OUTLIER) cc_final: 0.1704 (m-30) REVERT: L 1 MET cc_start: 0.2018 (tmm) cc_final: 0.1521 (ppp) REVERT: N 7 LEU cc_start: 0.1226 (tp) cc_final: 0.0645 (pp) REVERT: O 35 LYS cc_start: -0.0987 (OUTLIER) cc_final: -0.2976 (mmtt) REVERT: O 37 GLU cc_start: -0.1674 (OUTLIER) cc_final: -0.3301 (pt0) REVERT: P 1 MET cc_start: -0.0779 (tmt) cc_final: -0.2451 (mmp) REVERT: R 1 MET cc_start: -0.2576 (ppp) cc_final: -0.3254 (ppp) REVERT: R 7 LEU cc_start: 0.1775 (tp) cc_final: 0.0888 (pp) outliers start: 67 outliers final: 14 residues processed: 160 average time/residue: 0.7094 time to fit residues: 124.9809 Evaluate side-chains 109 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain X residue 31 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.321663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.303474 restraints weight = 28475.430| |-----------------------------------------------------------------------------| r_work (start): 0.5183 rms_B_bonded: 3.02 r_work: 0.5098 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1196 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16704 Z= 0.109 Angle : 0.576 10.740 22416 Z= 0.267 Chirality : 0.036 0.186 2640 Planarity : 0.003 0.031 2880 Dihedral : 3.522 12.616 2256 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.88 % Allowed : 20.03 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2040 helix: 1.50 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.18 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 30 PHE 0.012 0.001 PHE Q 4 HIS 0.006 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00229 (16704) covalent geometry : angle 0.57592 (22416) hydrogen bonds : bond 0.02574 ( 1008) hydrogen bonds : angle 3.22694 ( 3024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 85 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: B 35 LYS cc_start: -0.0757 (OUTLIER) cc_final: -0.2288 (mmtt) REVERT: C 1 MET cc_start: 0.2569 (pp-130) cc_final: -0.0560 (ppp) REVERT: C 7 LEU cc_start: 0.1463 (tp) cc_final: 0.0476 (pp) REVERT: C 30 ARG cc_start: 0.0208 (OUTLIER) cc_final: -0.1422 (tpp-160) REVERT: E 1 MET cc_start: 0.2122 (mmt) cc_final: 0.1548 (ppp) REVERT: E 30 ARG cc_start: 0.0348 (OUTLIER) cc_final: -0.2507 (mmm-85) REVERT: G 1 MET cc_start: 0.1012 (pp-130) cc_final: -0.0638 (ptm) REVERT: G 30 ARG cc_start: 0.1078 (OUTLIER) cc_final: -0.1176 (mmm-85) REVERT: G 37 GLU cc_start: -0.0664 (OUTLIER) cc_final: -0.1061 (tt0) REVERT: K 7 LEU cc_start: 0.1375 (tp) cc_final: 0.0770 (pp) REVERT: L 1 MET cc_start: 0.2510 (tmm) cc_final: 0.1951 (ppp) REVERT: M 1 MET cc_start: 0.0309 (OUTLIER) cc_final: -0.0221 (ppp) REVERT: N 30 ARG cc_start: 0.0480 (OUTLIER) cc_final: -0.1554 (mmm-85) REVERT: N 35 LYS cc_start: -0.1298 (OUTLIER) cc_final: -0.3458 (mttt) REVERT: O 30 ARG cc_start: 0.0724 (OUTLIER) cc_final: -0.1570 (mmm160) REVERT: O 35 LYS cc_start: -0.1285 (OUTLIER) cc_final: -0.2877 (mmtt) REVERT: Q 1 MET cc_start: 0.0726 (mmm) cc_final: -0.0221 (ppp) REVERT: Q 56 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.2220 (tp30) REVERT: R 1 MET cc_start: -0.1726 (ppp) cc_final: -0.2421 (ppp) REVERT: S 35 LYS cc_start: -0.0085 (OUTLIER) cc_final: -0.0699 (mptt) REVERT: W 30 ARG cc_start: 0.1118 (OUTLIER) cc_final: -0.1045 (tpp-160) REVERT: Y 7 LEU cc_start: 0.1452 (tp) cc_final: 0.0488 (pp) REVERT: Y 30 ARG cc_start: 0.0475 (OUTLIER) cc_final: -0.1550 (tpm170) outliers start: 54 outliers final: 11 residues processed: 131 average time/residue: 0.6797 time to fit residues: 98.6063 Evaluate side-chains 100 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.318667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.303592 restraints weight = 31088.164| |-----------------------------------------------------------------------------| r_work (start): 0.5218 rms_B_bonded: 2.76 r_work: 0.5141 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.5141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1319 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16704 Z= 0.103 Angle : 0.568 10.913 22416 Z= 0.263 Chirality : 0.036 0.140 2640 Planarity : 0.003 0.033 2880 Dihedral : 3.459 11.066 2256 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.15 % Allowed : 20.35 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.19), residues: 2040 helix: 1.70 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.33 (0.19), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 71 PHE 0.010 0.001 PHE P 25 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00224 (16704) covalent geometry : angle 0.56783 (22416) hydrogen bonds : bond 0.02621 ( 1008) hydrogen bonds : angle 3.13561 ( 3024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 80 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.2808 (tmm) cc_final: -0.0299 (ppp) REVERT: B 28 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.1974 (mt) REVERT: B 35 LYS cc_start: -0.0745 (OUTLIER) cc_final: -0.2269 (mmtt) REVERT: C 30 ARG cc_start: 0.0265 (OUTLIER) cc_final: -0.1475 (tpm170) REVERT: E 1 MET cc_start: 0.2120 (mmt) cc_final: 0.1501 (ppp) REVERT: E 30 ARG cc_start: 0.0333 (OUTLIER) cc_final: -0.2594 (tpm170) REVERT: G 1 MET cc_start: 0.0446 (pp-130) cc_final: 0.0140 (ppp) REVERT: G 30 ARG cc_start: 0.1258 (OUTLIER) cc_final: -0.0938 (mmm-85) REVERT: G 37 GLU cc_start: -0.0528 (OUTLIER) cc_final: -0.0913 (tt0) REVERT: J 7 LEU cc_start: 0.3658 (OUTLIER) cc_final: 0.2285 (mm) REVERT: L 1 MET cc_start: 0.2928 (tmm) cc_final: 0.2423 (ppp) REVERT: L 65 GLU cc_start: -0.0464 (OUTLIER) cc_final: -0.0917 (tm-30) REVERT: M 1 MET cc_start: 0.1124 (mmt) cc_final: 0.0670 (ppp) REVERT: M 30 ARG cc_start: 0.0309 (OUTLIER) cc_final: -0.1353 (tpp-160) REVERT: N 35 LYS cc_start: -0.1295 (OUTLIER) cc_final: -0.3585 (mttt) REVERT: O 30 ARG cc_start: 0.0888 (OUTLIER) cc_final: -0.1166 (tpm170) REVERT: O 37 GLU cc_start: -0.1463 (OUTLIER) cc_final: -0.3407 (pt0) REVERT: Q 56 GLU cc_start: 0.2752 (OUTLIER) cc_final: 0.2304 (mm-30) REVERT: R 1 MET cc_start: -0.2074 (ppp) cc_final: -0.2666 (ppp) REVERT: S 35 LYS cc_start: 0.0042 (OUTLIER) cc_final: -0.0652 (mptt) REVERT: U 1 MET cc_start: 0.0953 (mmp) cc_final: 0.0714 (ppp) REVERT: U 30 ARG cc_start: 0.1380 (OUTLIER) cc_final: -0.1047 (mmp-170) REVERT: W 30 ARG cc_start: 0.1356 (OUTLIER) cc_final: -0.1087 (tpm170) REVERT: Y 30 ARG cc_start: 0.0763 (OUTLIER) cc_final: -0.1409 (mmm-85) outliers start: 59 outliers final: 13 residues processed: 133 average time/residue: 0.5998 time to fit residues: 89.4506 Evaluate side-chains 102 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain W residue 44 ASP Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 181 optimal weight: 0.0020 chunk 159 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS G 52 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.316702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.301757 restraints weight = 30941.045| |-----------------------------------------------------------------------------| r_work (start): 0.5187 rms_B_bonded: 2.74 r_work: 0.5113 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.5113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1339 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16704 Z= 0.093 Angle : 0.522 8.901 22416 Z= 0.243 Chirality : 0.034 0.149 2640 Planarity : 0.003 0.032 2880 Dihedral : 3.363 12.638 2256 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.72 % Allowed : 20.78 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.18), residues: 2040 helix: 1.96 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.39 (0.19), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 71 PHE 0.008 0.001 PHE S 25 HIS 0.004 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00204 (16704) covalent geometry : angle 0.52218 (22416) hydrogen bonds : bond 0.02394 ( 1008) hydrogen bonds : angle 3.01661 ( 3024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 73 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3115 (tmm) cc_final: -0.0246 (ppp) REVERT: B 35 LYS cc_start: -0.0860 (OUTLIER) cc_final: -0.2240 (mmtt) REVERT: C 1 MET cc_start: 0.2767 (tmm) cc_final: 0.0191 (ppp) REVERT: C 30 ARG cc_start: 0.0221 (OUTLIER) cc_final: -0.1465 (mmm160) REVERT: E 1 MET cc_start: 0.2050 (mmt) cc_final: 0.1492 (ppp) REVERT: E 30 ARG cc_start: 0.0348 (OUTLIER) cc_final: -0.0117 (tpp80) REVERT: F 37 GLU cc_start: -0.0482 (OUTLIER) cc_final: -0.1166 (mt-10) REVERT: G 1 MET cc_start: 0.0349 (pp-130) cc_final: 0.0086 (ppp) REVERT: G 30 ARG cc_start: 0.1396 (OUTLIER) cc_final: -0.0637 (tpm170) REVERT: G 37 GLU cc_start: -0.0702 (OUTLIER) cc_final: -0.1037 (tt0) REVERT: J 7 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.2304 (mm) REVERT: K 1 MET cc_start: 0.1877 (pp-130) cc_final: -0.1192 (ppp) REVERT: L 65 GLU cc_start: -0.0280 (OUTLIER) cc_final: -0.0764 (tm-30) REVERT: M 1 MET cc_start: 0.1260 (mmt) cc_final: 0.0221 (ptm) REVERT: M 30 ARG cc_start: 0.0155 (OUTLIER) cc_final: -0.1653 (mmp-170) REVERT: N 30 ARG cc_start: 0.0527 (OUTLIER) cc_final: -0.1461 (mmm-85) REVERT: N 35 LYS cc_start: -0.1555 (OUTLIER) cc_final: -0.3815 (mttt) REVERT: O 30 ARG cc_start: 0.1094 (OUTLIER) cc_final: -0.1079 (mmp-170) REVERT: O 35 LYS cc_start: -0.1462 (OUTLIER) cc_final: -0.1911 (mtpp) REVERT: O 37 GLU cc_start: -0.1373 (OUTLIER) cc_final: -0.3288 (pt0) REVERT: Q 56 GLU cc_start: 0.2956 (OUTLIER) cc_final: 0.2670 (tp30) REVERT: R 1 MET cc_start: -0.1817 (ppp) cc_final: -0.2074 (ppp) REVERT: S 35 LYS cc_start: 0.0160 (OUTLIER) cc_final: -0.0500 (mptt) REVERT: T 1 MET cc_start: 0.1725 (pp-130) cc_final: 0.0145 (ppp) REVERT: U 1 MET cc_start: 0.1801 (mmp) cc_final: 0.1442 (ppp) REVERT: U 30 ARG cc_start: 0.1310 (OUTLIER) cc_final: -0.1125 (tpm170) REVERT: W 30 ARG cc_start: 0.1332 (OUTLIER) cc_final: 0.1056 (tpp80) REVERT: Y 30 ARG cc_start: 0.0649 (OUTLIER) cc_final: -0.1100 (tpm170) outliers start: 51 outliers final: 11 residues processed: 121 average time/residue: 0.6380 time to fit residues: 86.0411 Evaluate side-chains 96 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 chunk 168 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.316444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.301532 restraints weight = 30697.972| |-----------------------------------------------------------------------------| r_work (start): 0.5184 rms_B_bonded: 2.71 r_work: 0.5108 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.5108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1468 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16704 Z= 0.100 Angle : 0.546 12.355 22416 Z= 0.252 Chirality : 0.034 0.113 2640 Planarity : 0.003 0.033 2880 Dihedral : 3.448 11.172 2256 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.99 % Allowed : 20.73 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.18), residues: 2040 helix: 2.03 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.46 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 71 PHE 0.010 0.001 PHE B 82 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00222 (16704) covalent geometry : angle 0.54638 (22416) hydrogen bonds : bond 0.02480 ( 1008) hydrogen bonds : angle 3.07050 ( 3024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 70 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: -0.0855 (OUTLIER) cc_final: -0.2360 (mmtt) REVERT: C 30 ARG cc_start: 0.0375 (OUTLIER) cc_final: -0.1455 (mmp-170) REVERT: D 28 LEU cc_start: 0.3288 (OUTLIER) cc_final: 0.2947 (tt) REVERT: E 30 ARG cc_start: 0.0478 (OUTLIER) cc_final: -0.2169 (mmp80) REVERT: F 37 GLU cc_start: -0.0484 (OUTLIER) cc_final: -0.1294 (mt-10) REVERT: G 1 MET cc_start: 0.0886 (pp-130) cc_final: 0.0284 (ppp) REVERT: G 30 ARG cc_start: 0.1572 (OUTLIER) cc_final: -0.0602 (tpm170) REVERT: G 37 GLU cc_start: -0.0609 (OUTLIER) cc_final: -0.0980 (tt0) REVERT: J 7 LEU cc_start: 0.3884 (OUTLIER) cc_final: 0.2424 (mm) REVERT: J 28 LEU cc_start: 0.3397 (OUTLIER) cc_final: 0.3157 (mt) REVERT: L 1 MET cc_start: 0.2675 (tmm) cc_final: 0.2061 (tpp) REVERT: L 65 GLU cc_start: -0.0394 (OUTLIER) cc_final: -0.0876 (tm-30) REVERT: M 1 MET cc_start: 0.1782 (mmt) cc_final: 0.0930 (ttm) REVERT: M 30 ARG cc_start: 0.0343 (OUTLIER) cc_final: -0.1476 (mmp-170) REVERT: N 1 MET cc_start: 0.0336 (tmm) cc_final: -0.1126 (pp-130) REVERT: N 30 ARG cc_start: 0.0757 (OUTLIER) cc_final: -0.1027 (tpm170) REVERT: N 35 LYS cc_start: -0.1482 (OUTLIER) cc_final: -0.4022 (mttt) REVERT: O 30 ARG cc_start: 0.1240 (OUTLIER) cc_final: -0.0815 (mmm160) REVERT: O 37 GLU cc_start: -0.1118 (OUTLIER) cc_final: -0.3240 (pt0) REVERT: Q 1 MET cc_start: 0.2318 (tmm) cc_final: 0.1533 (tpp) REVERT: Q 56 GLU cc_start: 0.3119 (OUTLIER) cc_final: 0.2798 (tp30) REVERT: S 35 LYS cc_start: 0.0144 (OUTLIER) cc_final: -0.1487 (mptt) REVERT: U 1 MET cc_start: 0.2225 (mmp) cc_final: 0.1964 (ppp) REVERT: U 30 ARG cc_start: 0.1544 (OUTLIER) cc_final: -0.0700 (mmp-170) REVERT: W 30 ARG cc_start: 0.1551 (OUTLIER) cc_final: -0.1263 (mmp-170) REVERT: Y 1 MET cc_start: -0.0412 (mmt) cc_final: -0.1222 (mmt) REVERT: Y 30 ARG cc_start: 0.0789 (OUTLIER) cc_final: -0.0847 (mmp-170) outliers start: 56 outliers final: 11 residues processed: 123 average time/residue: 0.6687 time to fit residues: 91.0009 Evaluate side-chains 98 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 159 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5319 r_free = 0.5319 target = 0.318834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.300604 restraints weight = 28052.983| |-----------------------------------------------------------------------------| r_work (start): 0.5178 rms_B_bonded: 3.09 r_work: 0.5082 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.5082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1474 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16704 Z= 0.089 Angle : 0.522 11.826 22416 Z= 0.240 Chirality : 0.034 0.134 2640 Planarity : 0.003 0.033 2880 Dihedral : 3.385 10.468 2256 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.40 % Allowed : 21.26 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.18), residues: 2040 helix: 2.18 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 71 PHE 0.011 0.001 PHE S 4 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00194 (16704) covalent geometry : angle 0.52169 (22416) hydrogen bonds : bond 0.02323 ( 1008) hydrogen bonds : angle 3.03673 ( 3024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 69 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: -0.0941 (OUTLIER) cc_final: -0.2273 (mmtt) REVERT: C 1 MET cc_start: 0.3434 (tmm) cc_final: 0.1964 (ppp) REVERT: C 26 LEU cc_start: 0.5393 (pp) cc_final: 0.4992 (mt) REVERT: D 28 LEU cc_start: 0.2974 (OUTLIER) cc_final: 0.2660 (tt) REVERT: E 28 LEU cc_start: 0.1447 (OUTLIER) cc_final: 0.1188 (tt) REVERT: E 30 ARG cc_start: 0.0288 (OUTLIER) cc_final: -0.2184 (mmp80) REVERT: G 1 MET cc_start: 0.1408 (pp-130) cc_final: 0.0828 (ppp) REVERT: G 30 ARG cc_start: 0.1748 (OUTLIER) cc_final: -0.0525 (tpm170) REVERT: J 7 LEU cc_start: 0.3704 (OUTLIER) cc_final: 0.2260 (mm) REVERT: K 1 MET cc_start: 0.2436 (OUTLIER) cc_final: 0.1856 (ppp) REVERT: L 1 MET cc_start: 0.3022 (tmm) cc_final: 0.1347 (ppp) REVERT: L 65 GLU cc_start: -0.0481 (OUTLIER) cc_final: -0.0882 (tm-30) REVERT: M 1 MET cc_start: 0.1871 (mmt) cc_final: 0.1004 (ttm) REVERT: M 30 ARG cc_start: 0.0077 (OUTLIER) cc_final: -0.1480 (mmp-170) REVERT: N 1 MET cc_start: 0.0826 (tmm) cc_final: -0.0898 (pp-130) REVERT: N 30 ARG cc_start: 0.0600 (OUTLIER) cc_final: -0.1017 (tpm170) REVERT: N 35 LYS cc_start: -0.1799 (OUTLIER) cc_final: -0.4064 (mttt) REVERT: O 37 GLU cc_start: -0.1247 (OUTLIER) cc_final: -0.3243 (pt0) REVERT: Q 7 LEU cc_start: 0.2084 (OUTLIER) cc_final: 0.1363 (mt) REVERT: Q 56 GLU cc_start: 0.3008 (OUTLIER) cc_final: 0.2703 (tp30) REVERT: Q 71 ARG cc_start: 0.3833 (ttm170) cc_final: 0.2277 (tmt170) REVERT: R 1 MET cc_start: 0.1060 (tmm) cc_final: -0.0778 (ttp) REVERT: S 35 LYS cc_start: -0.0614 (OUTLIER) cc_final: -0.1473 (mptt) REVERT: U 30 ARG cc_start: 0.1661 (OUTLIER) cc_final: -0.0580 (mmp-170) REVERT: W 30 ARG cc_start: 0.1528 (OUTLIER) cc_final: -0.0784 (tpm170) REVERT: Y 1 MET cc_start: -0.0023 (mmt) cc_final: -0.0819 (mmt) REVERT: Y 30 ARG cc_start: 0.0691 (OUTLIER) cc_final: -0.1151 (mmp-170) outliers start: 45 outliers final: 13 residues processed: 111 average time/residue: 0.6773 time to fit residues: 83.3742 Evaluate side-chains 97 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 59 HIS Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Y residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 164 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.320337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.302666 restraints weight = 28147.088| |-----------------------------------------------------------------------------| r_work (start): 0.5197 rms_B_bonded: 3.07 r_work: 0.5099 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.5099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1583 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16704 Z= 0.099 Angle : 0.559 13.218 22416 Z= 0.256 Chirality : 0.035 0.118 2640 Planarity : 0.003 0.034 2880 Dihedral : 3.493 11.848 2256 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.03 % Allowed : 21.74 % Favored : 76.23 % 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 are not related in a simple way. whole: 2.41 (0.18), residues: 2040 helix: 2.17 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 71 PHE 0.012 0.002 PHE O 4 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00218 (16704) covalent geometry : angle 0.55903 (22416) hydrogen bonds : bond 0.02492 ( 1008) hydrogen bonds : angle 3.07661 ( 3024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3266 (tmm) cc_final: -0.1365 (pp-130) REVERT: B 35 LYS cc_start: -0.0851 (OUTLIER) cc_final: -0.2306 (mmtt) REVERT: C 26 LEU cc_start: 0.5509 (pp) cc_final: 0.5065 (mt) REVERT: D 28 LEU cc_start: 0.2887 (OUTLIER) cc_final: 0.2659 (tt) REVERT: E 28 LEU cc_start: 0.1841 (OUTLIER) cc_final: 0.1497 (tt) REVERT: E 30 ARG cc_start: 0.0268 (OUTLIER) cc_final: -0.2391 (mmp80) REVERT: G 1 MET cc_start: 0.1606 (pp-130) cc_final: -0.0583 (ttm) REVERT: G 30 ARG cc_start: 0.1852 (OUTLIER) cc_final: -0.0253 (mmp-170) REVERT: J 7 LEU cc_start: 0.4016 (OUTLIER) cc_final: 0.2568 (mm) REVERT: L 1 MET cc_start: 0.2915 (tmm) cc_final: 0.1248 (ppp) REVERT: M 1 MET cc_start: 0.2046 (mmt) cc_final: 0.1375 (ttm) REVERT: M 30 ARG cc_start: 0.0491 (OUTLIER) cc_final: -0.0837 (mmp-170) REVERT: N 1 MET cc_start: 0.1255 (tmm) cc_final: -0.0648 (pp-130) REVERT: N 30 ARG cc_start: 0.0576 (OUTLIER) cc_final: -0.1024 (tpm170) REVERT: N 35 LYS cc_start: -0.1287 (OUTLIER) cc_final: -0.4023 (mttt) REVERT: O 37 GLU cc_start: -0.1312 (OUTLIER) cc_final: -0.3334 (pt0) REVERT: P 1 MET cc_start: -0.0965 (tmt) cc_final: -0.1879 (pp-130) REVERT: Q 71 ARG cc_start: 0.4189 (ttm170) cc_final: 0.2269 (tmt170) REVERT: S 35 LYS cc_start: -0.0523 (OUTLIER) cc_final: -0.1438 (mptt) REVERT: U 1 MET cc_start: 0.1664 (ppp) cc_final: 0.0071 (pp-130) REVERT: U 30 ARG cc_start: 0.1453 (OUTLIER) cc_final: -0.0580 (mmp-170) REVERT: W 30 ARG cc_start: 0.1803 (OUTLIER) cc_final: 0.0192 (mmp80) REVERT: Y 30 ARG cc_start: 0.0680 (OUTLIER) cc_final: -0.0780 (mmp-170) outliers start: 38 outliers final: 13 residues processed: 101 average time/residue: 0.6365 time to fit residues: 71.7652 Evaluate side-chains 93 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain Q residue 59 HIS Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain X residue 48 MET Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 77 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.0270 chunk 114 optimal weight: 4.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.322907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.305648 restraints weight = 28347.291| |-----------------------------------------------------------------------------| r_work (start): 0.5217 rms_B_bonded: 3.09 r_work: 0.5123 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.5123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1569 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16704 Z= 0.088 Angle : 0.545 14.313 22416 Z= 0.246 Chirality : 0.034 0.127 2640 Planarity : 0.003 0.034 2880 Dihedral : 3.407 10.962 2256 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.44 % Allowed : 22.44 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.18), residues: 2040 helix: 2.27 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 71 PHE 0.010 0.002 PHE S 4 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00195 (16704) covalent geometry : angle 0.54465 (22416) hydrogen bonds : bond 0.02286 ( 1008) hydrogen bonds : angle 3.06875 ( 3024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: -0.0737 (OUTLIER) cc_final: -0.2088 (mmtt) REVERT: C 1 MET cc_start: 0.3503 (tmm) cc_final: -0.1035 (ppp) REVERT: C 26 LEU cc_start: 0.5542 (pp) cc_final: 0.5112 (mt) REVERT: D 28 LEU cc_start: 0.2731 (OUTLIER) cc_final: 0.2457 (tt) REVERT: E 30 ARG cc_start: 0.0469 (OUTLIER) cc_final: -0.2326 (mmp-170) REVERT: G 30 ARG cc_start: 0.1948 (OUTLIER) cc_final: -0.0254 (tpp-160) REVERT: J 7 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.2671 (tt) REVERT: L 1 MET cc_start: 0.3010 (tmm) cc_final: 0.0880 (ppp) REVERT: M 1 MET cc_start: 0.2356 (mmt) cc_final: 0.1719 (ttt) REVERT: M 30 ARG cc_start: 0.0807 (OUTLIER) cc_final: -0.0640 (mmp-170) REVERT: N 1 MET cc_start: 0.1214 (tmm) cc_final: 0.0552 (tmm) REVERT: N 30 ARG cc_start: 0.0574 (OUTLIER) cc_final: -0.0976 (tpm170) REVERT: N 35 LYS cc_start: -0.1212 (OUTLIER) cc_final: -0.3981 (mttt) REVERT: O 35 LYS cc_start: -0.1482 (OUTLIER) cc_final: -0.3534 (mmtt) REVERT: O 37 GLU cc_start: -0.1296 (OUTLIER) cc_final: -0.3320 (pt0) REVERT: P 1 MET cc_start: -0.0727 (tmt) cc_final: -0.2035 (pp-130) REVERT: Q 71 ARG cc_start: 0.4119 (ttm170) cc_final: 0.2728 (tmt170) REVERT: R 1 MET cc_start: -0.0823 (tmt) cc_final: -0.1524 (mpt) REVERT: S 1 MET cc_start: -0.2109 (tpp) cc_final: -0.2803 (tmt) REVERT: S 35 LYS cc_start: -0.0232 (OUTLIER) cc_final: -0.1248 (mptt) REVERT: U 1 MET cc_start: 0.1394 (ppp) cc_final: -0.0168 (pp-130) REVERT: U 30 ARG cc_start: 0.1583 (OUTLIER) cc_final: -0.0420 (mmp-170) REVERT: W 30 ARG cc_start: 0.1936 (OUTLIER) cc_final: 0.0293 (mmp80) REVERT: Y 28 LEU cc_start: 0.2676 (OUTLIER) cc_final: 0.1933 (mt) REVERT: Y 30 ARG cc_start: 0.0724 (OUTLIER) cc_final: -0.0724 (mmp-170) outliers start: 27 outliers final: 8 residues processed: 93 average time/residue: 0.6246 time to fit residues: 64.7581 Evaluate side-chains 90 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain S residue 35 LYS Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain W residue 30 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 30 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 0.8980 chunk 165 optimal weight: 0.0020 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5355 r_free = 0.5355 target = 0.325771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5254 r_free = 0.5254 target = 0.308489 restraints weight = 28163.260| |-----------------------------------------------------------------------------| r_work (start): 0.5228 rms_B_bonded: 3.08 r_work: 0.5133 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.5133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1724 moved from start: 0.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16704 Z= 0.108 Angle : 0.606 14.851 22416 Z= 0.275 Chirality : 0.036 0.135 2640 Planarity : 0.003 0.048 2880 Dihedral : 3.670 13.937 2256 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.82 % Allowed : 22.17 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.18), residues: 2040 helix: 2.13 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 71 PHE 0.017 0.002 PHE K 4 HIS 0.005 0.000 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00238 (16704) covalent geometry : angle 0.60625 (22416) hydrogen bonds : bond 0.02709 ( 1008) hydrogen bonds : angle 3.23127 ( 3024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.42 seconds wall clock time: 85 minutes 13.18 seconds (5113.18 seconds total)