Starting phenix.real_space_refine on Sun Jul 5 08:54:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dsm_47147/07_2026/9dsm_47147.map" } resolution = 4.55 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= -0.000 sd= 1.000 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 64 5.16 5 C 16128 2.51 5 N 4704 2.21 5 O 5632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'TRANS': 98} Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'TRANS': 98} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'TRANS': 98} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'TRANS': 98} Restraints were copied for chains: E, I, M, Q, U, Y, c, F, J, N, R, V, Z, d, G, K, O, S, W, a, e, H, L, P, T, X, b, f Time building chain proxies: 3.34, per 1000 atoms: 0.13 Number of scatterers: 26528 At special positions: 0 Unit cell: (103.824, 103.824, 303.232, 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 64 16.00 O 5632 8.00 N 4704 7.00 C 16128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 763.1 milliseconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6208 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 99.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 105 removed outlier: 3.573A pdb=" N ARG B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 105 removed outlier: 3.666A pdb=" N LYS C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 105 removed outlier: 3.573A pdb=" N ARG F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS G 87 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS G 101 " --> pdb=" O TYR G 97 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 104 " --> pdb=" O THR I 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 105 removed outlier: 3.573A pdb=" N ARG J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 105 removed outlier: 3.664A pdb=" N LYS K 87 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS K 101 " --> pdb=" O TYR K 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS K 102 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN L 68 " --> pdb=" O ARG L 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS M 101 " --> pdb=" O TYR M 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 104 " --> pdb=" O THR M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 105 removed outlier: 3.573A pdb=" N ARG N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS O 87 " --> pdb=" O VAL O 83 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 89 " --> pdb=" O SER O 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS O 101 " --> pdb=" O TYR O 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN O 103 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP P 45 " --> pdb=" O ASN P 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU P 46 " --> pdb=" O GLU P 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA P 80 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN P 103 " --> pdb=" O ASP P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS Q 101 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 105 removed outlier: 3.572A pdb=" N ARG R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS S 87 " --> pdb=" O VAL S 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS S 101 " --> pdb=" O TYR S 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS S 102 " --> pdb=" O GLU S 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP T 45 " --> pdb=" O ASN T 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN T 68 " --> pdb=" O ARG T 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA T 80 " --> pdb=" O GLU T 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN T 103 " --> pdb=" O ASP T 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 105 removed outlier: 3.504A pdb=" N LYS U 81 " --> pdb=" O THR U 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS U 101 " --> pdb=" O TYR U 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS U 104 " --> pdb=" O THR U 100 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 105 removed outlier: 3.572A pdb=" N ARG V 24 " --> pdb=" O GLU V 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS W 87 " --> pdb=" O VAL W 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU W 89 " --> pdb=" O SER W 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS W 101 " --> pdb=" O TYR W 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS W 102 " --> pdb=" O GLU W 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN W 103 " --> pdb=" O ASP W 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP X 45 " --> pdb=" O ASN X 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU X 46 " --> pdb=" O GLU X 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN X 68 " --> pdb=" O ARG X 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA X 80 " --> pdb=" O GLU X 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN X 103 " --> pdb=" O ASP X 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS Y 81 " --> pdb=" O THR Y 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS Y 101 " --> pdb=" O TYR Y 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS Y 104 " --> pdb=" O THR Y 100 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 105 removed outlier: 3.572A pdb=" N ARG Z 24 " --> pdb=" O GLU Z 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS a 87 " --> pdb=" O VAL a 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU a 89 " --> pdb=" O SER a 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS a 101 " --> pdb=" O TYR a 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS a 102 " --> pdb=" O GLU a 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN a 103 " --> pdb=" O ASP a 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP b 45 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU b 46 " --> pdb=" O GLU b 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN b 68 " --> pdb=" O ARG b 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA b 80 " --> pdb=" O GLU b 76 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN b 103 " --> pdb=" O ASP b 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 105 removed outlier: 3.503A pdb=" N LYS c 81 " --> pdb=" O THR c 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS c 101 " --> pdb=" O TYR c 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS c 104 " --> pdb=" O THR c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 105 removed outlier: 3.573A pdb=" N ARG d 24 " --> pdb=" O GLU d 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 105 removed outlier: 3.665A pdb=" N LYS e 87 " --> pdb=" O VAL e 83 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU e 89 " --> pdb=" O SER e 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 101 " --> pdb=" O TYR e 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS e 102 " --> pdb=" O GLU e 98 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN e 103 " --> pdb=" O ASP e 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 105 removed outlier: 3.814A pdb=" N ASP f 45 " --> pdb=" O ASN f 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN f 68 " --> pdb=" O ARG f 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN f 103 " --> pdb=" O ASP f 99 " (cutoff:3.500A) 2896 hydrogen bonds defined for protein. 8688 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: 4.45 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9376 1.34 - 1.46: 2384 1.46 - 1.58: 14864 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 26720 Sorted by residual: bond pdb=" CB ARG W 67 " pdb=" CG ARG W 67 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CB ARG G 67 " pdb=" CG ARG G 67 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.47e-01 bond pdb=" CB ARG S 67 " pdb=" CG ARG S 67 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.36e-01 bond pdb=" CB ARG K 67 " pdb=" CG ARG K 67 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.36e-01 bond pdb=" CB ARG C 67 " pdb=" CG ARG C 67 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.31e-01 ... (remaining 26715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 34979 1.30 - 2.60: 509 2.60 - 3.90: 80 3.90 - 5.20: 24 5.20 - 6.50: 24 Bond angle restraints: 35616 Sorted by residual: angle pdb=" CA ARG G 67 " pdb=" CB ARG G 67 " pdb=" CG ARG G 67 " ideal model delta sigma weight residual 114.10 119.94 -5.84 2.00e+00 2.50e-01 8.52e+00 angle pdb=" CA ARG K 67 " pdb=" CB ARG K 67 " pdb=" CG ARG K 67 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.47e+00 angle pdb=" CA ARG a 67 " pdb=" CB ARG a 67 " pdb=" CG ARG a 67 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.46e+00 angle pdb=" CA ARG C 67 " pdb=" CB ARG C 67 " pdb=" CG ARG C 67 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.46e+00 angle pdb=" CA ARG O 67 " pdb=" CB ARG O 67 " pdb=" CG ARG O 67 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.46e+00 ... (remaining 35611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15080 17.95 - 35.90: 1521 35.90 - 53.85: 247 53.85 - 71.79: 280 71.79 - 89.74: 24 Dihedral angle restraints: 17152 sinusoidal: 7680 harmonic: 9472 Sorted by residual: dihedral pdb=" CB GLU f 21 " pdb=" CG GLU f 21 " pdb=" CD GLU f 21 " pdb=" OE1 GLU f 21 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU X 21 " pdb=" CG GLU X 21 " pdb=" CD GLU X 21 " pdb=" OE1 GLU X 21 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU b 21 " pdb=" CG GLU b 21 " pdb=" CD GLU b 21 " pdb=" OE1 GLU b 21 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 17149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 2296 0.021 - 0.043: 1084 0.043 - 0.064: 340 0.064 - 0.085: 104 0.085 - 0.106: 16 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CG LEU N 72 " pdb=" CB LEU N 72 " pdb=" CD1 LEU N 72 " pdb=" CD2 LEU N 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 2.83e-01 chirality pdb=" CG LEU d 72 " pdb=" CB LEU d 72 " pdb=" CD1 LEU d 72 " pdb=" CD2 LEU d 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.49 -0.10 2.00e-01 2.50e+01 2.69e-01 chirality pdb=" CG LEU F 72 " pdb=" CB LEU F 72 " pdb=" CD1 LEU F 72 " pdb=" CD2 LEU F 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.49 -0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 3837 not shown) Planarity restraints: 4736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 23 " 0.085 9.50e-02 1.11e+02 3.83e-02 9.19e-01 pdb=" NE ARG A 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 23 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 23 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 23 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG c 23 " 0.085 9.50e-02 1.11e+02 3.82e-02 9.17e-01 pdb=" NE ARG c 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG c 23 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG c 23 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG c 23 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 23 " 0.085 9.50e-02 1.11e+02 3.82e-02 9.12e-01 pdb=" NE ARG U 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG U 23 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG U 23 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG U 23 " 0.004 2.00e-02 2.50e+03 ... (remaining 4733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3921 2.75 - 3.29: 29977 3.29 - 3.83: 46681 3.83 - 4.36: 54854 4.36 - 4.90: 86181 Nonbonded interactions: 221614 Sorted by model distance: nonbonded pdb=" O LYS e 81 " pdb=" OG SER e 85 " model vdw 2.217 3.040 nonbonded pdb=" O LYS a 81 " pdb=" OG SER a 85 " model vdw 2.217 3.040 nonbonded pdb=" O LYS K 81 " pdb=" OG SER K 85 " model vdw 2.217 3.040 nonbonded pdb=" O LYS S 81 " pdb=" OG SER S 85 " model vdw 2.218 3.040 nonbonded pdb=" O LYS W 81 " pdb=" OG SER W 85 " model vdw 2.218 3.040 ... (remaining 221609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 : 0.002 0.028 26720 Z= 0.086 Angle : 0.444 6.498 35616 Z= 0.250 Chirality : 0.028 0.106 3840 Planarity : 0.002 0.038 4736 Dihedral : 16.882 89.742 10944 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.14), residues: 3104 helix: 1.86 (0.09), residues: 3048 sheet: None (None), residues: 0 loop : 5.61 (0.77), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 24 TYR 0.012 0.001 TYR f 105 PHE 0.014 0.001 PHE H 92 HIS 0.002 0.000 HIS P 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.09 (26720) covalent geometry : angle 0.44396 / 0.25 (35616) hydrogen bonds : bond 0.24078 / 15.96 ( 2896) hydrogen bonds : angle 6.67902 / 4.85 ( 8688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.6598 (tptp) cc_final: 0.6244 (mttm) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.2013 time to fit residues: 2.1049 Evaluate side-chains 7 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.086849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.081473 restraints weight = 9764.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.082476 restraints weight = 7075.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.083253 restraints weight = 5312.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.083852 restraints weight = 4100.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.084310 restraints weight = 3243.387| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 1.7706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 26720 Z= 0.230 Angle : 0.951 8.392 35616 Z= 0.522 Chirality : 0.051 0.268 3840 Planarity : 0.005 0.020 4736 Dihedral : 4.499 10.642 3584 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.13), residues: 3104 helix: 2.21 (0.08), residues: 3008 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 64 TYR 0.014 0.003 TYR b 15 PHE 0.004 0.002 PHE B 92 HIS 0.002 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (26720) covalent geometry : angle 0.95100 / 0.52 (35616) hydrogen bonds : bond 0.06425 / 4.27 ( 2896) hydrogen bonds : angle 4.65226 / 3.38 ( 8688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1729 time to fit residues: 2.6973 Evaluate side-chains 6 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 78 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 221 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 126 optimal weight: 30.0000 chunk 232 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.106126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.099728 restraints weight = 6270.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.100706 restraints weight = 4886.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.101418 restraints weight = 3812.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.102182 restraints weight = 3146.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.102548 restraints weight = 2574.026| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4858 moved from start: 1.8928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 26720 Z= 0.225 Angle : 0.864 6.482 35616 Z= 0.490 Chirality : 0.049 0.251 3840 Planarity : 0.013 0.141 4736 Dihedral : 5.292 20.792 3584 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 1.09 % Allowed : 5.43 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.81 (0.14), residues: 3104 helix: 2.62 (0.09), residues: 3008 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG f 67 TYR 0.018 0.002 TYR S 79 PHE 0.007 0.002 PHE X 9 HIS 0.002 0.001 HIS P 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.22 (26720) covalent geometry : angle 0.86368 / 0.49 (35616) hydrogen bonds : bond 0.06263 / 4.13 ( 2896) hydrogen bonds : angle 4.60491 / 3.34 ( 8688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: Y 70 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6892 (ttp80) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.1285 time to fit residues: 1.8995 Evaluate side-chains 6 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 23 optimal weight: 0.0000 chunk 266 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 284 optimal weight: 0.6980 chunk 198 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 176 optimal weight: 0.0870 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 286 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.100977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.094294 restraints weight = 8864.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.095257 restraints weight = 6930.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.096037 restraints weight = 5613.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.096614 restraints weight = 4624.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.097177 restraints weight = 3921.348| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4482 moved from start: 1.9641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 26720 Z= 0.180 Angle : 0.757 6.419 35616 Z= 0.442 Chirality : 0.044 0.196 3840 Planarity : 0.006 0.059 4736 Dihedral : 4.989 22.425 3584 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.14), residues: 3104 helix: 2.48 (0.09), residues: 3072 sheet: None (None), residues: 0 loop : -5.59 (0.00), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 64 TYR 0.015 0.001 TYR f 79 PHE 0.006 0.001 PHE C 9 HIS 0.003 0.002 HIS f 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.18 (26720) covalent geometry : angle 0.75658 / 0.44 (35616) hydrogen bonds : bond 0.06417 / 4.20 ( 2896) hydrogen bonds : angle 4.51680 / 3.26 ( 8688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.023 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7154 (mtt90) cc_final: 0.6765 (mtt180) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0775 time to fit residues: 1.0031 Evaluate side-chains 6 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 276 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 69 optimal weight: 0.0270 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.105816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.098989 restraints weight = 6611.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.100069 restraints weight = 5118.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.100825 restraints weight = 4111.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.101300 restraints weight = 3412.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.101906 restraints weight = 2978.632| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4620 moved from start: 1.9856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 26720 Z= 0.151 Angle : 0.741 7.671 35616 Z= 0.413 Chirality : 0.040 0.181 3840 Planarity : 0.004 0.037 4736 Dihedral : 4.368 14.641 3584 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.03 % Allowed : 1.03 % Favored : 97.94 % Rotamer: Outliers : 1.09 % Allowed : 3.26 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.32 (0.14), residues: 3104 helix: 2.90 (0.09), residues: 2976 sheet: None (None), residues: 0 loop : 0.94 (0.45), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 67 TYR 0.018 0.002 TYR H 79 PHE 0.004 0.001 PHE L 9 HIS 0.001 0.001 HIS Q 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (26720) covalent geometry : angle 0.74081 / 0.41 (35616) hydrogen bonds : bond 0.05656 / 3.71 ( 2896) hydrogen bonds : angle 4.12033 / 2.98 ( 8688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.045 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.1116 time to fit residues: 1.5533 Evaluate side-chains 5 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 41 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.108213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.100577 restraints weight = 6594.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.101448 restraints weight = 5602.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.102154 restraints weight = 4837.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.102683 restraints weight = 4242.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.102975 restraints weight = 3792.232| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 moved from start: 1.9947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 26720 Z= 0.148 Angle : 0.750 8.195 35616 Z= 0.429 Chirality : 0.038 0.175 3840 Planarity : 0.003 0.025 4736 Dihedral : 4.560 24.707 3584 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.74 (0.13), residues: 3104 helix: 3.15 (0.09), residues: 2976 sheet: None (None), residues: 0 loop : 1.32 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 67 TYR 0.015 0.002 TYR D 79 PHE 0.002 0.001 PHE L 92 HIS 0.001 0.001 HIS J 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (26720) covalent geometry : angle 0.75043 / 0.43 (35616) hydrogen bonds : bond 0.05341 / 3.50 ( 2896) hydrogen bonds : angle 4.25937 / 3.06 ( 8688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.060 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0959 time to fit residues: 1.2632 Evaluate side-chains 5 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 221 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 242 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.111029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.102875 restraints weight = 6536.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.103730 restraints weight = 5565.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.104247 restraints weight = 4816.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.104929 restraints weight = 4324.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.105221 restraints weight = 3879.153| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4640 moved from start: 2.0241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 26720 Z= 0.144 Angle : 0.725 8.242 35616 Z= 0.412 Chirality : 0.037 0.154 3840 Planarity : 0.004 0.023 4736 Dihedral : 4.831 29.175 3584 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 5.20 (0.13), residues: 3104 helix: 3.46 (0.08), residues: 2976 sheet: None (None), residues: 0 loop : 1.11 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 67 TYR 0.012 0.002 TYR X 105 PHE 0.004 0.001 PHE D 9 HIS 0.001 0.001 HIS Z 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (26720) covalent geometry : angle 0.72547 / 0.41 (35616) hydrogen bonds : bond 0.05335 / 3.51 ( 2896) hydrogen bonds : angle 4.00942 / 2.88 ( 8688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 98 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8564 (mt-10) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1322 time to fit residues: 1.5542 Evaluate side-chains 7 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 60 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 14 optimal weight: 0.0370 chunk 39 optimal weight: 8.9990 chunk 95 optimal weight: 0.0970 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.103163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.096316 restraints weight = 8377.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.097599 restraints weight = 6111.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.098553 restraints weight = 4610.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.099226 restraints weight = 3602.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.099837 restraints weight = 2928.059| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 2.0471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 26720 Z= 0.149 Angle : 0.674 7.954 35616 Z= 0.401 Chirality : 0.039 0.184 3840 Planarity : 0.004 0.025 4736 Dihedral : 4.945 31.701 3584 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: 5.03 (0.13), residues: 3104 helix: 3.33 (0.08), residues: 2976 sheet: None (None), residues: 0 loop : 1.52 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 67 TYR 0.010 0.002 TYR C 105 PHE 0.002 0.000 PHE b 92 HIS 0.001 0.000 HIS Z 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (26720) covalent geometry : angle 0.67375 / 0.40 (35616) hydrogen bonds : bond 0.05264 / 3.47 ( 2896) hydrogen bonds : angle 4.18542 / 2.99 ( 8688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1404 time to fit residues: 2.0729 Evaluate side-chains 6 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 chunk 191 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.099803 restraints weight = 6818.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.100542 restraints weight = 5336.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.101281 restraints weight = 4515.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.101752 restraints weight = 3857.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.102239 restraints weight = 3461.852| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4429 moved from start: 2.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26720 Z= 0.181 Angle : 0.813 8.232 35616 Z= 0.476 Chirality : 0.043 0.188 3840 Planarity : 0.004 0.028 4736 Dihedral : 5.046 29.415 3584 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.56 (0.14), residues: 3104 helix: 2.97 (0.09), residues: 3072 sheet: None (None), residues: 0 loop : 2.29 (0.00), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG F 67 TYR 0.028 0.004 TYR H 79 PHE 0.005 0.001 PHE X 92 HIS 0.001 0.001 HIS Z 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (26720) covalent geometry : angle 0.81330 / 0.48 (35616) hydrogen bonds : bond 0.05492 / 3.63 ( 2896) hydrogen bonds : angle 4.40886 / 3.15 ( 8688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.6648 (mtt180) cc_final: 0.6070 (ppt170) REVERT: A 89 LEU cc_start: 0.6101 (tt) cc_final: 0.5801 (mt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1354 time to fit residues: 1.4475 Evaluate side-chains 7 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 178 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 186 optimal weight: 0.0470 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 183 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.115580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.106528 restraints weight = 6072.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.106944 restraints weight = 5289.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.107472 restraints weight = 4833.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.107564 restraints weight = 4473.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.108038 restraints weight = 4371.261| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4428 moved from start: 2.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26720 Z= 0.164 Angle : 0.793 8.261 35616 Z= 0.454 Chirality : 0.040 0.189 3840 Planarity : 0.004 0.025 4736 Dihedral : 4.951 28.079 3584 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.84 (0.14), residues: 3104 helix: 3.22 (0.09), residues: 3040 sheet: None (None), residues: 0 loop : -1.19 (0.55), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 67 TYR 0.023 0.003 TYR T 79 PHE 0.001 0.000 PHE b 92 HIS 0.001 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (26720) covalent geometry : angle 0.79305 / 0.45 (35616) hydrogen bonds : bond 0.05229 / 3.45 ( 2896) hydrogen bonds : angle 4.37561 / 3.13 ( 8688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.023 Fit side-chains REVERT: A 70 ARG cc_start: 0.6569 (mtt180) cc_final: 0.6182 (ppt170) REVERT: A 89 LEU cc_start: 0.6328 (tt) cc_final: 0.6016 (mm) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1437 time to fit residues: 1.3667 Evaluate side-chains 8 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.109601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.102932 restraints weight = 6836.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.103889 restraints weight = 5519.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.104476 restraints weight = 4531.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.105228 restraints weight = 3850.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.105615 restraints weight = 3266.175| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 2.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 26720 Z= 0.150 Angle : 0.744 8.970 35616 Z= 0.431 Chirality : 0.040 0.199 3840 Planarity : 0.004 0.018 4736 Dihedral : 5.038 29.978 3584 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.16 (0.14), residues: 3104 helix: 3.46 (0.09), residues: 3040 sheet: None (None), residues: 0 loop : -3.32 (0.29), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG O 67 TYR 0.016 0.003 TYR P 79 PHE 0.002 0.000 PHE V 92 HIS 0.000 0.000 HIS f 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (26720) covalent geometry : angle 0.74382 / 0.43 (35616) hydrogen bonds : bond 0.05054 / 3.34 ( 2896) hydrogen bonds : angle 4.38491 / 3.13 ( 8688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.66 seconds wall clock time: 45 minutes 34.15 seconds (2734.15 seconds total)