Starting phenix.real_space_refine on Fri Feb 6 16:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dsm_47147/02_2026/9dsm_47147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dsm_47147/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dsm_47147/02_2026/9dsm_47147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dsm_47147/02_2026/9dsm_47147.map" model { file = "/net/cci-nas-00/data/ceres_data/9dsm_47147/02_2026/9dsm_47147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dsm_47147/02_2026/9dsm_47147.cif" } 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-2.0-5952/lib/python3.9/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: 3.53, 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.51 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: 5.06 Time building geometry restraints manager: 2.92 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.520 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 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 covalent geometry : bond 0.00172 (26720) covalent geometry : angle 0.44396 (35616) hydrogen bonds : bond 0.24078 ( 2896) hydrogen bonds : angle 6.67902 ( 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 : 0.034 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: 0.2305 time to fit residues: 2.3930 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 : 0.038 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.087192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.081814 restraints weight = 9353.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.082896 restraints weight = 6794.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.083693 restraints weight = 5097.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.084250 restraints weight = 3923.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.084676 restraints weight = 3144.865| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 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 M 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 covalent geometry : bond 0.00459 (26720) covalent geometry : angle 0.95100 (35616) hydrogen bonds : bond 0.06425 ( 2896) hydrogen bonds : angle 4.65226 ( 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 : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2343 time to fit residues: 3.6259 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 : 0.021 ------------------------------------------------------------------------------- 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: 3.9990 chunk 228 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 221 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 232 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.092070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.087021 restraints weight = 8933.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.088026 restraints weight = 6445.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.088995 restraints weight = 4882.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.089566 restraints weight = 3679.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.090021 restraints weight = 2875.410| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4661 moved from start: 1.8748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26720 Z= 0.232 Angle : 0.950 9.293 35616 Z= 0.531 Chirality : 0.052 0.236 3840 Planarity : 0.006 0.041 4736 Dihedral : 4.969 12.582 3584 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % 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: 2.71 (0.14), residues: 3104 helix: 1.88 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -5.59 (0.00), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 67 TYR 0.025 0.003 TYR X 79 PHE 0.007 0.002 PHE L 9 HIS 0.000 0.000 HIS X 102 Details of bonding type rmsd covalent geometry : bond 0.00492 (26720) covalent geometry : angle 0.95039 (35616) hydrogen bonds : bond 0.06478 ( 2896) hydrogen bonds : angle 4.66546 ( 8688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6014 Ramachandran restraints generated. 3007 Oldfield, 0 Emsley, 3007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6014 Ramachandran restraints generated. 3007 Oldfield, 0 Emsley, 3007 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: 0 poor density : 13 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1400 time to fit residues: 1.9201 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 : 0.035 ------------------------------------------------------------------------------- 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: 2.9990 chunk 266 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 198 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 286 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.102586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.095589 restraints weight = 6108.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.096612 restraints weight = 4757.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.097305 restraints weight = 3875.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.098080 restraints weight = 3289.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.098425 restraints weight = 2757.540| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 1.9243 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= 0.163 Angle : 0.771 6.320 35616 Z= 0.440 Chirality : 0.047 0.222 3840 Planarity : 0.005 0.040 4736 Dihedral : 4.912 18.450 3584 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.83 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: 3.16 (0.14), residues: 3104 helix: 2.20 (0.09), residues: 3008 sheet: None (None), residues: 0 loop : -1.54 (0.42), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 67 TYR 0.020 0.002 TYR F 79 PHE 0.008 0.002 PHE L 9 HIS 0.002 0.001 HIS b 102 Details of bonding type rmsd covalent geometry : bond 0.00293 (26720) covalent geometry : angle 0.77148 (35616) hydrogen bonds : bond 0.05525 ( 2896) hydrogen bonds : angle 4.65080 ( 8688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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 : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1843 time to fit residues: 2.3070 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.104175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.096573 restraints weight = 6341.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.097214 restraints weight = 5089.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.097970 restraints weight = 4345.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.098523 restraints weight = 3873.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.098808 restraints weight = 3411.537| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4832 moved from start: 1.9405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 26720 Z= 0.155 Angle : 0.754 7.285 35616 Z= 0.417 Chirality : 0.043 0.214 3840 Planarity : 0.003 0.012 4736 Dihedral : 4.859 19.014 3584 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 1.03 % Allowed : 0.00 % Favored : 98.97 % Rotamer: Outliers : 1.09 % Allowed : 2.17 % 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: 3.56 (0.14), residues: 3104 helix: 2.41 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -5.59 (0.00), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 64 TYR 0.020 0.002 TYR K 79 PHE 0.007 0.002 PHE C 9 HIS 0.003 0.002 HIS V 102 Details of bonding type rmsd covalent geometry : bond 0.00302 (26720) covalent geometry : angle 0.75354 (35616) hydrogen bonds : bond 0.05155 ( 2896) hydrogen bonds : angle 4.29982 ( 8688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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: 1 poor density : 9 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.0644 time to fit residues: 0.7329 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 : 0.032 ------------------------------------------------------------------------------- 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: 0.0980 chunk 246 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 262 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.086535 restraints weight = 8682.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.087732 restraints weight = 6147.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.088643 restraints weight = 4553.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.089272 restraints weight = 3489.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.089826 restraints weight = 2775.277| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 moved from start: 1.9662 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= 0.149 Angle : 0.679 5.544 35616 Z= 0.397 Chirality : 0.040 0.182 3840 Planarity : 0.003 0.019 4736 Dihedral : 4.459 11.872 3584 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.87 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: 4.24 (0.14), residues: 3104 helix: 2.89 (0.09), residues: 3008 sheet: None (None), residues: 0 loop : -1.62 (0.51), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG W 64 TYR 0.016 0.002 TYR K 79 PHE 0.004 0.001 PHE b 9 HIS 0.000 0.000 HIS J 102 Details of bonding type rmsd covalent geometry : bond 0.00266 (26720) covalent geometry : angle 0.67910 (35616) hydrogen bonds : bond 0.04942 ( 2896) hydrogen bonds : angle 4.26476 ( 8688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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: 0 poor density : 13 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1060 time to fit residues: 1.4739 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 221 optimal weight: 0.4980 chunk 41 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 242 optimal weight: 0.6980 chunk 228 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 276 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.096061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.090152 restraints weight = 8499.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.091207 restraints weight = 6245.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.091999 restraints weight = 4738.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.092663 restraints weight = 3727.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.093177 restraints weight = 2968.188| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4513 moved from start: 1.9833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26720 Z= 0.145 Angle : 0.702 6.782 35616 Z= 0.399 Chirality : 0.035 0.148 3840 Planarity : 0.003 0.016 4736 Dihedral : 4.234 13.522 3584 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.91 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: 4.46 (0.14), residues: 3104 helix: 3.16 (0.09), residues: 2848 sheet: None (None), residues: 0 loop : -0.26 (0.22), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 67 TYR 0.016 0.002 TYR Z 79 PHE 0.001 0.000 PHE T 92 HIS 0.000 0.000 HIS Z 102 Details of bonding type rmsd covalent geometry : bond 0.00275 (26720) covalent geometry : angle 0.70175 (35616) hydrogen bonds : bond 0.04725 ( 2896) hydrogen bonds : angle 3.99356 ( 8688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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 : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8858 (tppt) cc_final: 0.8584 (mttt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1235 time to fit residues: 1.5766 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 : 0.034 ------------------------------------------------------------------------------- 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: 6.9990 chunk 180 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 95 optimal weight: 0.0670 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.100704 restraints weight = 6143.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.101483 restraints weight = 5097.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.102324 restraints weight = 4429.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.102689 restraints weight = 3861.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.102795 restraints weight = 3563.453| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 1.9799 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= 0.145 Angle : 0.679 5.929 35616 Z= 0.392 Chirality : 0.038 0.155 3840 Planarity : 0.003 0.013 4736 Dihedral : 4.218 13.547 3584 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.73 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: 4.77 (0.14), residues: 3104 helix: 3.19 (0.09), residues: 2976 sheet: None (None), residues: 0 loop : 0.85 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 67 TYR 0.010 0.002 TYR D 97 PHE 0.003 0.001 PHE T 92 HIS 0.000 0.000 HIS J 102 Details of bonding type rmsd covalent geometry : bond 0.00280 (26720) covalent geometry : angle 0.67871 (35616) hydrogen bonds : bond 0.04594 ( 2896) hydrogen bonds : angle 4.17958 ( 8688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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 : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1315 time to fit residues: 1.5402 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 41 optimal weight: 0.0270 chunk 191 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.097025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.091303 restraints weight = 8546.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.092412 restraints weight = 6016.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.093210 restraints weight = 4485.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.093865 restraints weight = 3494.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.094355 restraints weight = 2781.524| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5133 moved from start: 2.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 26720 Z= 0.139 Angle : 0.641 5.687 35616 Z= 0.374 Chirality : 0.037 0.142 3840 Planarity : 0.003 0.013 4736 Dihedral : 4.192 13.296 3584 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.55 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: 4.98 (0.14), residues: 3104 helix: 3.34 (0.09), residues: 2976 sheet: None (None), residues: 0 loop : 0.38 (0.36), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 67 TYR 0.009 0.001 TYR f 97 PHE 0.004 0.001 PHE S 9 HIS 0.000 0.000 HIS Z 102 Details of bonding type rmsd covalent geometry : bond 0.00241 (26720) covalent geometry : angle 0.64072 (35616) hydrogen bonds : bond 0.04627 ( 2896) hydrogen bonds : angle 4.07946 ( 8688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 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 : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1238 time to fit residues: 1.4345 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 178 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.105874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.096458 restraints weight = 9305.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.096916 restraints weight = 8143.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.097131 restraints weight = 7275.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.097326 restraints weight = 6717.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.097430 restraints weight = 6309.497| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4713 moved from start: 1.9959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26720 Z= 0.155 Angle : 0.761 6.974 35616 Z= 0.429 Chirality : 0.039 0.151 3840 Planarity : 0.003 0.016 4736 Dihedral : 4.239 13.569 3584 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.10 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: 5.11 (0.14), residues: 3104 helix: 3.39 (0.09), residues: 2976 sheet: None (None), residues: 0 loop : 1.35 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 67 TYR 0.010 0.001 TYR B 97 PHE 0.005 0.001 PHE D 92 HIS 0.001 0.000 HIS Z 102 Details of bonding type rmsd covalent geometry : bond 0.00306 (26720) covalent geometry : angle 0.76059 (35616) hydrogen bonds : bond 0.04536 ( 2896) hydrogen bonds : angle 4.21349 ( 8688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 92 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: W 33 MET cc_start: 0.6759 (ppp) cc_final: 0.5398 (ttt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0956 time to fit residues: 2.6174 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 : 0.021 ------------------------------------------------------------------------------- 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: 7.9990 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 77 optimal weight: 0.0030 chunk 272 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.112375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.106904 restraints weight = 7603.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.107732 restraints weight = 6041.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.108307 restraints weight = 4917.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.108776 restraints weight = 4069.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.109043 restraints weight = 3465.593| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4562 moved from start: 2.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26720 Z= 0.258 Angle : 1.062 10.573 35616 Z= 0.575 Chirality : 0.057 0.328 3840 Planarity : 0.007 0.063 4736 Dihedral : 5.056 15.405 3584 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.71 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: 2.69 (0.14), residues: 3104 helix: 1.88 (0.09), residues: 3040 sheet: None (None), residues: 0 loop : -2.03 (0.45), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 94 TYR 0.023 0.006 TYR K 79 PHE 0.010 0.003 PHE a 92 HIS 0.001 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00555 (26720) covalent geometry : angle 1.06191 (35616) hydrogen bonds : bond 0.06500 ( 2896) hydrogen bonds : angle 4.96136 ( 8688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.01 seconds wall clock time: 27 minutes 20.50 seconds (1640.50 seconds total)