Starting phenix.real_space_refine on Tue Apr 29 21:32:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.map" model { file = "/net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hqe_0252/04_2025/6hqe_0252.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 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: 3 Type Number sf(0) Gaussians C 5668 2.51 5 N 1976 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, s, r, u, t, w, v, y, x, z Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9360 At special positions: 0 Unit cell: (91.08, 91.08, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1716 8.00 N 1976 7.00 C 5668 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG I 16 " --> pdb=" O ASP I 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG J 16 " --> pdb=" O ASP J 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 23 removed outlier: 3.590A pdb=" N ARG K 16 " --> pdb=" O ASP K 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG M 16 " --> pdb=" O ASP M 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG N 16 " --> pdb=" O ASP N 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG O 16 " --> pdb=" O ASP O 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG P 16 " --> pdb=" O ASP P 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG R 16 " --> pdb=" O ASP R 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 7 Processing helix chain 'T' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG T 16 " --> pdb=" O ASP T 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG U 16 " --> pdb=" O ASP U 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 7 Processing helix chain 'V' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG V 16 " --> pdb=" O ASP V 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG W 16 " --> pdb=" O ASP W 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 7 Processing helix chain 'X' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG X 16 " --> pdb=" O ASP X 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG Y 16 " --> pdb=" O ASP Y 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 7 Processing helix chain 'Z' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG Z 16 " --> pdb=" O ASP Z 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 7 Processing helix chain 'a' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 7 Processing helix chain 'b' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG b 16 " --> pdb=" O ASP b 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG c 16 " --> pdb=" O ASP c 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 7 Processing helix chain 'e' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG e 16 " --> pdb=" O ASP e 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 7 Processing helix chain 'f' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG f 16 " --> pdb=" O ASP f 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 7 Processing helix chain 'g' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG g 16 " --> pdb=" O ASP g 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 7 Processing helix chain 'h' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG h 16 " --> pdb=" O ASP h 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 Processing helix chain 'i' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG i 16 " --> pdb=" O ASP i 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 7 Processing helix chain 'j' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG j 16 " --> pdb=" O ASP j 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 7 Processing helix chain 'k' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG k 16 " --> pdb=" O ASP k 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 7 Processing helix chain 'l' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG l 16 " --> pdb=" O ASP l 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 7 Processing helix chain 'm' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG m 16 " --> pdb=" O ASP m 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 7 Processing helix chain 'n' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG n 16 " --> pdb=" O ASP n 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 7 Processing helix chain 'o' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG o 16 " --> pdb=" O ASP o 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG p 16 " --> pdb=" O ASP p 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 7 Processing helix chain 'q' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG q 16 " --> pdb=" O ASP q 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 7 Processing helix chain 'r' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG r 16 " --> pdb=" O ASP r 12 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 7 Processing helix chain 's' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 7 Processing helix chain 't' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG t 16 " --> pdb=" O ASP t 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 7 Processing helix chain 'u' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG u 16 " --> pdb=" O ASP u 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 7 Processing helix chain 'v' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG v 16 " --> pdb=" O ASP v 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 7 Processing helix chain 'w' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG w 16 " --> pdb=" O ASP w 12 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 7 Processing helix chain 'x' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG x 16 " --> pdb=" O ASP x 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 Processing helix chain 'y' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG y 16 " --> pdb=" O ASP y 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 7 Processing helix chain 'z' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG z 16 " --> pdb=" O ASP z 12 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1716 1.29 - 1.35: 1924 1.35 - 1.41: 0 1.41 - 1.48: 1602 1.48 - 1.54: 4170 Bond restraints: 9412 Sorted by residual: bond pdb=" CG LEU c 23 " pdb=" CD1 LEU c 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CG LEU e 23 " pdb=" CD1 LEU e 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU v 23 " pdb=" CD1 LEU v 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU r 23 " pdb=" CD1 LEU r 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CG LEU R 23 " pdb=" CD1 LEU R 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 ... (remaining 9407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11206 1.67 - 3.34: 1222 3.34 - 5.01: 156 5.01 - 6.68: 0 6.68 - 8.35: 52 Bond angle restraints: 12636 Sorted by residual: angle pdb=" CA LEU U 4 " pdb=" CB LEU U 4 " pdb=" CG LEU U 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.70e+00 angle pdb=" CA LEU E 4 " pdb=" CB LEU E 4 " pdb=" CG LEU E 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 angle pdb=" CA LEU L 4 " pdb=" CB LEU L 4 " pdb=" CG LEU L 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 angle pdb=" CA LEU p 4 " pdb=" CB LEU p 4 " pdb=" CG LEU p 4 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.68e+00 angle pdb=" CA LEU T 4 " pdb=" CB LEU T 4 " pdb=" CG LEU T 4 " ideal model delta sigma weight residual 116.30 124.63 -8.33 3.50e+00 8.16e-02 5.67e+00 ... (remaining 12631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.46: 4147 5.46 - 10.93: 1157 10.93 - 16.39: 572 16.39 - 21.86: 208 21.86 - 27.32: 156 Dihedral angle restraints: 6240 sinusoidal: 2704 harmonic: 3536 Sorted by residual: dihedral pdb=" CA ALA o 20 " pdb=" C ALA o 20 " pdb=" N ARG o 21 " pdb=" CA ARG o 21 " ideal model delta harmonic sigma weight residual 180.00 166.99 13.01 0 5.00e+00 4.00e-02 6.77e+00 dihedral pdb=" CA ALA z 20 " pdb=" C ALA z 20 " pdb=" N ARG z 21 " pdb=" CA ARG z 21 " ideal model delta harmonic sigma weight residual 180.00 166.99 13.01 0 5.00e+00 4.00e-02 6.77e+00 dihedral pdb=" CA ALA Q 20 " pdb=" C ALA Q 20 " pdb=" N ARG Q 21 " pdb=" CA ARG Q 21 " ideal model delta harmonic sigma weight residual 180.00 167.00 13.00 0 5.00e+00 4.00e-02 6.76e+00 ... (remaining 6237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 526 0.029 - 0.059: 491 0.059 - 0.088: 225 0.088 - 0.118: 110 0.118 - 0.147: 104 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA LEU Z 23 " pdb=" N LEU Z 23 " pdb=" C LEU Z 23 " pdb=" CB LEU Z 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA LEU m 23 " pdb=" N LEU m 23 " pdb=" C LEU m 23 " pdb=" CB LEU m 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA LEU g 23 " pdb=" N LEU g 23 " pdb=" C LEU g 23 " pdb=" CB LEU g 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1453 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP o 10 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO o 11 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO o 11 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO o 11 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 10 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO X 11 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO X 11 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO X 11 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP n 10 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO n 11 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO n 11 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO n 11 " 0.032 5.00e-02 4.00e+02 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2964 2.83 - 3.34: 9236 3.34 - 3.86: 16004 3.86 - 4.38: 18566 4.38 - 4.90: 27403 Nonbonded interactions: 74173 Sorted by model distance: nonbonded pdb=" OD2 ASP b 10 " pdb=" NE ARG d 16 " model vdw 2.307 3.120 nonbonded pdb=" OD2 ASP v 10 " pdb=" NE ARG x 16 " model vdw 2.338 3.120 nonbonded pdb=" OD2 ASP L 10 " pdb=" NE ARG N 16 " model vdw 2.350 3.120 nonbonded pdb=" NE ARG e 16 " pdb=" OD2 ASP g 10 " model vdw 2.372 3.120 nonbonded pdb=" NE ARG M 16 " pdb=" OD2 ASP O 10 " model vdw 2.394 3.120 ... (remaining 74168 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' selection = chain 'q' selection = chain 'p' selection = chain 's' selection = chain 'r' selection = chain 'u' selection = chain 't' selection = chain 'w' selection = chain 'v' selection = chain 'y' selection = chain 'x' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.009 0.039 9412 Z= 0.417 Angle : 1.254 8.355 12636 Z= 0.667 Chirality : 0.061 0.147 1456 Planarity : 0.011 0.058 1716 Dihedral : 9.670 27.320 3848 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.05 (0.13), residues: 1092 helix: -4.24 (0.08), residues: 988 sheet: None (None), residues: 0 loop : -4.94 (0.43), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG v 22 Details of bonding type rmsd hydrogen bonds : bond 0.22594 ( 468) hydrogen bonds : angle 8.93699 ( 1404) covalent geometry : bond 0.00929 ( 9412) covalent geometry : angle 1.25400 (12636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8373 (ttp-110) REVERT: E 10 ASP cc_start: 0.8970 (t0) cc_final: 0.8706 (t0) REVERT: F 6 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8415 (ttp-110) REVERT: G 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8943 (t0) REVERT: K 15 VAL cc_start: 0.9481 (t) cc_final: 0.9242 (p) REVERT: N 10 ASP cc_start: 0.9197 (t0) cc_final: 0.8935 (t0) REVERT: P 10 ASP cc_start: 0.8947 (t0) cc_final: 0.8717 (t0) REVERT: Q 6 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8416 (ttm110) REVERT: S 6 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8306 (ttm-80) REVERT: T 6 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8596 (ttm110) REVERT: Y 10 ASP cc_start: 0.9088 (t0) cc_final: 0.8808 (t0) REVERT: Z 6 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8509 (ttm-80) REVERT: b 10 ASP cc_start: 0.9091 (t0) cc_final: 0.8881 (t0) REVERT: c 15 VAL cc_start: 0.9502 (t) cc_final: 0.9168 (p) REVERT: c 19 VAL cc_start: 0.9375 (t) cc_final: 0.9107 (t) REVERT: c 22 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8137 (mmt-90) REVERT: d 10 ASP cc_start: 0.9044 (t0) cc_final: 0.8794 (t0) REVERT: f 10 ASP cc_start: 0.9147 (t0) cc_final: 0.8944 (t0) REVERT: g 10 ASP cc_start: 0.9048 (t0) cc_final: 0.8729 (t0) REVERT: i 10 ASP cc_start: 0.8748 (t0) cc_final: 0.8503 (t0) REVERT: k 10 ASP cc_start: 0.9057 (t0) cc_final: 0.8788 (t0) REVERT: l 5 GLU cc_start: 0.8968 (mp0) cc_final: 0.8660 (mp0) REVERT: l 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8872 (t0) REVERT: n 6 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8649 (ttp-110) REVERT: o 15 VAL cc_start: 0.9438 (t) cc_final: 0.9215 (p) REVERT: p 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8802 (t0) REVERT: q 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8909 (t0) REVERT: u 10 ASP cc_start: 0.9032 (t0) cc_final: 0.8695 (t0) REVERT: v 10 ASP cc_start: 0.9113 (t0) cc_final: 0.8682 (t0) REVERT: x 10 ASP cc_start: 0.9008 (t0) cc_final: 0.8775 (t0) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3405 time to fit residues: 227.0817 Evaluate side-chains 396 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080726 restraints weight = 19627.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.082924 restraints weight = 10501.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084412 restraints weight = 6330.216| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9412 Z= 0.170 Angle : 0.618 5.463 12636 Z= 0.331 Chirality : 0.042 0.125 1456 Planarity : 0.010 0.056 1716 Dihedral : 4.326 12.110 1404 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.26), residues: 1092 helix: -1.67 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.88 (0.69), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 6 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 468) hydrogen bonds : angle 7.38262 ( 1404) covalent geometry : bond 0.00386 ( 9412) covalent geometry : angle 0.61753 (12636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8452 (ttm110) REVERT: B 10 ASP cc_start: 0.9217 (t0) cc_final: 0.9006 (t0) REVERT: E 5 GLU cc_start: 0.9158 (mp0) cc_final: 0.8920 (mm-30) REVERT: E 10 ASP cc_start: 0.9116 (t0) cc_final: 0.8643 (t0) REVERT: F 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8870 (t0) REVERT: G 21 ARG cc_start: 0.9081 (mmm-85) cc_final: 0.8820 (mmm-85) REVERT: H 21 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8495 (mmm-85) REVERT: I 21 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: K 10 ASP cc_start: 0.9421 (t0) cc_final: 0.9045 (t0) REVERT: N 10 ASP cc_start: 0.9243 (t0) cc_final: 0.8777 (t0) REVERT: N 21 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: O 10 ASP cc_start: 0.9276 (t0) cc_final: 0.8808 (t0) REVERT: S 12 ASP cc_start: 0.7867 (t0) cc_final: 0.7618 (t0) REVERT: U 5 GLU cc_start: 0.9097 (mp0) cc_final: 0.8894 (mm-30) REVERT: V 5 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8814 (mm-30) REVERT: W 21 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8494 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9242 (t0) cc_final: 0.8884 (t0) REVERT: b 10 ASP cc_start: 0.9133 (t0) cc_final: 0.8604 (t0) REVERT: c 12 ASP cc_start: 0.8437 (t70) cc_final: 0.7824 (t70) REVERT: d 10 ASP cc_start: 0.9258 (t0) cc_final: 0.9002 (t0) REVERT: f 10 ASP cc_start: 0.9148 (t0) cc_final: 0.8897 (t0) REVERT: f 21 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8647 (mmm-85) REVERT: g 10 ASP cc_start: 0.9062 (t0) cc_final: 0.8526 (t0) REVERT: h 12 ASP cc_start: 0.8390 (t70) cc_final: 0.8164 (t70) REVERT: i 5 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8794 (mm-30) REVERT: i 10 ASP cc_start: 0.9095 (t0) cc_final: 0.8570 (t0) REVERT: j 10 ASP cc_start: 0.9202 (t0) cc_final: 0.8840 (t0) REVERT: k 10 ASP cc_start: 0.9275 (t0) cc_final: 0.8885 (t0) REVERT: l 6 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8695 (ttm110) REVERT: m 21 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8609 (mmm-85) REVERT: o 10 ASP cc_start: 0.9393 (t0) cc_final: 0.8779 (t0) REVERT: p 10 ASP cc_start: 0.9248 (t0) cc_final: 0.8760 (t0) REVERT: q 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8732 (t0) REVERT: s 19 VAL cc_start: 0.9599 (t) cc_final: 0.9391 (t) REVERT: u 6 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8549 (ttm110) REVERT: u 10 ASP cc_start: 0.9250 (t0) cc_final: 0.8716 (t0) REVERT: v 12 ASP cc_start: 0.7875 (t70) cc_final: 0.7541 (t70) REVERT: w 12 ASP cc_start: 0.8089 (t70) cc_final: 0.7858 (t70) REVERT: x 10 ASP cc_start: 0.9146 (t0) cc_final: 0.8766 (t0) REVERT: x 23 LEU cc_start: 0.8405 (mt) cc_final: 0.8185 (mt) REVERT: y 5 GLU cc_start: 0.8944 (mp0) cc_final: 0.8738 (mm-30) REVERT: y 22 ARG cc_start: 0.9220 (tpp80) cc_final: 0.8689 (ttm110) REVERT: z 5 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8922 (mm-30) REVERT: z 12 ASP cc_start: 0.7702 (t70) cc_final: 0.7475 (t70) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.3539 time to fit residues: 233.1237 Evaluate side-chains 500 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 90 optimal weight: 0.0870 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085740 restraints weight = 19012.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087854 restraints weight = 10149.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089271 restraints weight = 6105.248| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9412 Z= 0.115 Angle : 0.572 4.393 12636 Z= 0.301 Chirality : 0.038 0.118 1456 Planarity : 0.008 0.047 1716 Dihedral : 3.894 11.413 1404 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.11 % Allowed : 1.24 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1092 helix: -0.66 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -1.12 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 6 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 468) hydrogen bonds : angle 5.96598 ( 1404) covalent geometry : bond 0.00260 ( 9412) covalent geometry : angle 0.57152 (12636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 574 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8376 (ttm110) REVERT: B 10 ASP cc_start: 0.9151 (t0) cc_final: 0.8811 (t0) REVERT: D 22 ARG cc_start: 0.8523 (mmt180) cc_final: 0.8301 (mmt-90) REVERT: E 10 ASP cc_start: 0.9037 (t0) cc_final: 0.8578 (t0) REVERT: F 10 ASP cc_start: 0.9130 (t0) cc_final: 0.8744 (t0) REVERT: H 21 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8589 (mmm-85) REVERT: I 5 GLU cc_start: 0.9061 (mp0) cc_final: 0.8793 (mm-30) REVERT: J 5 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8622 (mm-30) REVERT: J 6 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8385 (ttm110) REVERT: J 21 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8672 (mmm-85) REVERT: K 5 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8599 (mm-30) REVERT: K 10 ASP cc_start: 0.9228 (t0) cc_final: 0.8925 (t0) REVERT: L 7 LEU cc_start: 0.9136 (mt) cc_final: 0.8922 (mt) REVERT: N 5 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8751 (mm-30) REVERT: N 10 ASP cc_start: 0.9188 (t0) cc_final: 0.8796 (t0) REVERT: N 21 ARG cc_start: 0.8969 (mmm-85) cc_final: 0.8715 (mmm-85) REVERT: O 10 ASP cc_start: 0.9214 (t0) cc_final: 0.8622 (t0) REVERT: P 22 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8042 (mmt-90) REVERT: R 5 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8565 (mm-30) REVERT: V 5 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8736 (mm-30) REVERT: W 5 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8638 (mm-30) REVERT: W 21 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: X 23 LEU cc_start: 0.7784 (mt) cc_final: 0.6934 (pp) REVERT: Z 5 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8863 (mm-30) REVERT: Z 23 LEU cc_start: 0.8533 (mm) cc_final: 0.7796 (pp) REVERT: a 22 ARG cc_start: 0.9198 (tpp80) cc_final: 0.8939 (ttm110) REVERT: b 10 ASP cc_start: 0.9022 (t0) cc_final: 0.8531 (t0) REVERT: d 10 ASP cc_start: 0.9226 (t0) cc_final: 0.8965 (t0) REVERT: f 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8734 (t0) REVERT: f 23 LEU cc_start: 0.7949 (mm) cc_final: 0.7326 (pp) REVERT: g 10 ASP cc_start: 0.9040 (t0) cc_final: 0.8446 (t0) REVERT: i 6 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8311 (ttm-80) REVERT: j 10 ASP cc_start: 0.9053 (t0) cc_final: 0.8578 (t0) REVERT: k 10 ASP cc_start: 0.9253 (t0) cc_final: 0.8706 (t0) REVERT: k 21 ARG cc_start: 0.8814 (mmm-85) cc_final: 0.8435 (mmm-85) REVERT: l 6 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8721 (ttm110) REVERT: l 23 LEU cc_start: 0.7906 (mm) cc_final: 0.6865 (pp) REVERT: m 10 ASP cc_start: 0.9301 (t0) cc_final: 0.8838 (t0) REVERT: n 21 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8484 (mmm-85) REVERT: n 23 LEU cc_start: 0.8074 (mm) cc_final: 0.7177 (pp) REVERT: o 10 ASP cc_start: 0.9259 (t0) cc_final: 0.8696 (t0) REVERT: p 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8702 (t0) REVERT: p 23 LEU cc_start: 0.8082 (mm) cc_final: 0.7372 (pp) REVERT: q 10 ASP cc_start: 0.9099 (t0) cc_final: 0.8595 (t0) REVERT: r 10 ASP cc_start: 0.9140 (t0) cc_final: 0.8716 (t0) REVERT: s 5 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8594 (mm-30) REVERT: u 10 ASP cc_start: 0.9296 (t0) cc_final: 0.8699 (t0) REVERT: w 12 ASP cc_start: 0.8008 (t70) cc_final: 0.7740 (t70) REVERT: x 6 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8481 (ttm110) REVERT: x 10 ASP cc_start: 0.9066 (t0) cc_final: 0.8601 (t0) REVERT: z 23 LEU cc_start: 0.7892 (mt) cc_final: 0.7335 (pp) outliers start: 1 outliers final: 0 residues processed: 574 average time/residue: 0.3728 time to fit residues: 258.6683 Evaluate side-chains 515 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.076951 restraints weight = 20212.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079027 restraints weight = 11013.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080466 restraints weight = 6801.067| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9412 Z= 0.202 Angle : 0.691 4.862 12636 Z= 0.351 Chirality : 0.042 0.126 1456 Planarity : 0.009 0.047 1716 Dihedral : 3.938 17.931 1404 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1092 helix: -0.03 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.98 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG k 6 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 468) hydrogen bonds : angle 7.12991 ( 1404) covalent geometry : bond 0.00471 ( 9412) covalent geometry : angle 0.69063 (12636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 1.020 Fit side-chains REVERT: A 12 ASP cc_start: 0.7716 (t70) cc_final: 0.7467 (t70) REVERT: B 6 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8497 (ttm110) REVERT: B 10 ASP cc_start: 0.9298 (t0) cc_final: 0.9031 (t0) REVERT: C 5 GLU cc_start: 0.8844 (mp0) cc_final: 0.8624 (mp0) REVERT: C 21 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8690 (mmm-85) REVERT: E 10 ASP cc_start: 0.9216 (t0) cc_final: 0.8718 (t0) REVERT: F 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8886 (t0) REVERT: F 22 ARG cc_start: 0.9219 (tpp-160) cc_final: 0.8939 (tpp-160) REVERT: G 10 ASP cc_start: 0.9283 (t0) cc_final: 0.8909 (t0) REVERT: H 21 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8547 (mmm-85) REVERT: I 12 ASP cc_start: 0.8115 (t0) cc_final: 0.7844 (t0) REVERT: J 6 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8423 (ttm110) REVERT: J 10 ASP cc_start: 0.9302 (t0) cc_final: 0.9082 (t0) REVERT: K 5 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8819 (mm-30) REVERT: K 10 ASP cc_start: 0.9348 (t0) cc_final: 0.9066 (t0) REVERT: L 21 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8691 (mmm-85) REVERT: M 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8893 (t0) REVERT: N 6 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8237 (ttm110) REVERT: N 10 ASP cc_start: 0.9194 (t0) cc_final: 0.8823 (t0) REVERT: O 10 ASP cc_start: 0.9263 (t0) cc_final: 0.8710 (t0) REVERT: Q 12 ASP cc_start: 0.8419 (t70) cc_final: 0.8184 (t70) REVERT: Q 14 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8847 (tp30) REVERT: U 12 ASP cc_start: 0.7925 (t70) cc_final: 0.7700 (t0) REVERT: V 5 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8680 (mm-30) REVERT: W 21 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8592 (mmm-85) REVERT: W 22 ARG cc_start: 0.8986 (tpp-160) cc_final: 0.8606 (ttm110) REVERT: X 21 ARG cc_start: 0.9126 (mmm-85) cc_final: 0.8802 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9225 (t0) cc_final: 0.8934 (t0) REVERT: Z 10 ASP cc_start: 0.9250 (t0) cc_final: 0.8919 (t0) REVERT: b 10 ASP cc_start: 0.9184 (t0) cc_final: 0.8660 (t0) REVERT: c 12 ASP cc_start: 0.8535 (t70) cc_final: 0.8035 (t70) REVERT: d 10 ASP cc_start: 0.9281 (t0) cc_final: 0.8937 (t0) REVERT: e 10 ASP cc_start: 0.9270 (t0) cc_final: 0.9030 (t0) REVERT: f 10 ASP cc_start: 0.9224 (t0) cc_final: 0.8964 (t0) REVERT: g 10 ASP cc_start: 0.9149 (t0) cc_final: 0.8694 (t0) REVERT: i 5 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8529 (mm-30) REVERT: i 10 ASP cc_start: 0.9179 (t0) cc_final: 0.8692 (t0) REVERT: j 6 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8778 (ttm110) REVERT: j 10 ASP cc_start: 0.9128 (t0) cc_final: 0.8721 (t0) REVERT: k 10 ASP cc_start: 0.9345 (t0) cc_final: 0.8865 (t0) REVERT: k 14 GLU cc_start: 0.8909 (tp30) cc_final: 0.8668 (tp30) REVERT: l 6 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8701 (ttm110) REVERT: n 21 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8648 (mmm-85) REVERT: o 10 ASP cc_start: 0.9348 (t0) cc_final: 0.8856 (t0) REVERT: o 22 ARG cc_start: 0.9092 (tpp-160) cc_final: 0.8758 (ttm110) REVERT: p 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8771 (t0) REVERT: q 10 ASP cc_start: 0.9159 (t0) cc_final: 0.8691 (t0) REVERT: r 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8943 (t0) REVERT: t 12 ASP cc_start: 0.7839 (t0) cc_final: 0.7495 (t0) REVERT: u 10 ASP cc_start: 0.9308 (t0) cc_final: 0.8839 (t0) REVERT: v 6 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: v 10 ASP cc_start: 0.9205 (t0) cc_final: 0.8852 (t0) REVERT: w 12 ASP cc_start: 0.8134 (t70) cc_final: 0.7849 (t0) REVERT: x 6 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8567 (ttm110) REVERT: x 10 ASP cc_start: 0.9102 (t0) cc_final: 0.8805 (t0) REVERT: z 23 LEU cc_start: 0.8324 (mt) cc_final: 0.8046 (mt) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.3551 time to fit residues: 234.5750 Evaluate side-chains 508 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080575 restraints weight = 19976.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082830 restraints weight = 10456.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084374 restraints weight = 6239.211| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9412 Z= 0.154 Angle : 0.660 5.188 12636 Z= 0.341 Chirality : 0.041 0.122 1456 Planarity : 0.008 0.046 1716 Dihedral : 3.769 16.723 1404 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1092 helix: 0.67 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 468) hydrogen bonds : angle 6.72359 ( 1404) covalent geometry : bond 0.00367 ( 9412) covalent geometry : angle 0.66044 (12636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.148 Fit side-chains REVERT: A 12 ASP cc_start: 0.7793 (t70) cc_final: 0.7519 (t70) REVERT: B 6 ARG cc_start: 0.8830 (ttp-110) cc_final: 0.8569 (ttm110) REVERT: B 10 ASP cc_start: 0.9289 (t0) cc_final: 0.8998 (t0) REVERT: E 10 ASP cc_start: 0.9273 (t0) cc_final: 0.8702 (t0) REVERT: F 10 ASP cc_start: 0.9228 (t0) cc_final: 0.8903 (t0) REVERT: F 22 ARG cc_start: 0.9159 (tpp-160) cc_final: 0.8827 (tpp-160) REVERT: G 10 ASP cc_start: 0.9223 (t0) cc_final: 0.8842 (t0) REVERT: H 21 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8656 (mmm-85) REVERT: J 6 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8496 (ttm110) REVERT: J 22 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8753 (tpp-160) REVERT: K 5 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8920 (mm-30) REVERT: K 10 ASP cc_start: 0.9350 (t0) cc_final: 0.8996 (t0) REVERT: L 21 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8698 (mmm-85) REVERT: M 6 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8608 (ttm110) REVERT: N 6 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8432 (ttm110) REVERT: N 10 ASP cc_start: 0.9255 (t0) cc_final: 0.8867 (t0) REVERT: O 10 ASP cc_start: 0.9253 (t0) cc_final: 0.8776 (t0) REVERT: Q 6 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8362 (ttm110) REVERT: Q 12 ASP cc_start: 0.8391 (t70) cc_final: 0.8175 (t70) REVERT: S 6 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8518 (ttm-80) REVERT: V 5 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8751 (mm-30) REVERT: V 12 ASP cc_start: 0.8108 (t0) cc_final: 0.7887 (t0) REVERT: W 5 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8602 (mm-30) REVERT: W 21 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8669 (mmm-85) REVERT: W 22 ARG cc_start: 0.8881 (tpp-160) cc_final: 0.8323 (ttm110) REVERT: X 21 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8814 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9235 (t0) cc_final: 0.8947 (t0) REVERT: Z 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8917 (t0) REVERT: b 10 ASP cc_start: 0.9149 (t0) cc_final: 0.8526 (t0) REVERT: c 12 ASP cc_start: 0.8542 (t70) cc_final: 0.8295 (t70) REVERT: d 10 ASP cc_start: 0.9341 (t0) cc_final: 0.8960 (t0) REVERT: e 10 ASP cc_start: 0.9281 (t0) cc_final: 0.9023 (t0) REVERT: f 10 ASP cc_start: 0.9243 (t0) cc_final: 0.8948 (t0) REVERT: f 23 LEU cc_start: 0.8338 (mm) cc_final: 0.8032 (pp) REVERT: g 10 ASP cc_start: 0.9238 (t0) cc_final: 0.8752 (t0) REVERT: i 10 ASP cc_start: 0.9214 (t0) cc_final: 0.8673 (t0) REVERT: i 21 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8570 (mmm-85) REVERT: j 6 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8687 (ttm110) REVERT: j 10 ASP cc_start: 0.9190 (t0) cc_final: 0.8799 (t0) REVERT: k 10 ASP cc_start: 0.9380 (t0) cc_final: 0.8890 (t0) REVERT: k 14 GLU cc_start: 0.8944 (tp30) cc_final: 0.8718 (tp30) REVERT: k 21 ARG cc_start: 0.9045 (mmm-85) cc_final: 0.8769 (mmm-85) REVERT: l 6 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8754 (ttm110) REVERT: l 10 ASP cc_start: 0.9295 (t0) cc_final: 0.8957 (t0) REVERT: m 10 ASP cc_start: 0.9414 (t0) cc_final: 0.8978 (t0) REVERT: n 21 ARG cc_start: 0.8992 (mmm-85) cc_final: 0.8704 (mmm-85) REVERT: o 10 ASP cc_start: 0.9352 (t0) cc_final: 0.8780 (t0) REVERT: p 10 ASP cc_start: 0.9253 (t0) cc_final: 0.8660 (t0) REVERT: q 10 ASP cc_start: 0.9160 (t0) cc_final: 0.8683 (t0) REVERT: r 23 LEU cc_start: 0.8087 (mm) cc_final: 0.7529 (pp) REVERT: t 12 ASP cc_start: 0.7891 (t0) cc_final: 0.7551 (t0) REVERT: u 10 ASP cc_start: 0.9388 (t0) cc_final: 0.8822 (t0) REVERT: u 22 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8971 (ttm-80) REVERT: v 6 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8359 (ttm-80) REVERT: v 10 ASP cc_start: 0.9216 (t0) cc_final: 0.8872 (t0) REVERT: v 12 ASP cc_start: 0.7901 (t70) cc_final: 0.7606 (t70) REVERT: w 12 ASP cc_start: 0.8150 (t70) cc_final: 0.7820 (t70) REVERT: x 6 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8599 (ttm110) REVERT: x 10 ASP cc_start: 0.9167 (t0) cc_final: 0.8762 (t0) REVERT: z 23 LEU cc_start: 0.7852 (mt) cc_final: 0.7646 (mt) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.3620 time to fit residues: 237.1072 Evaluate side-chains 512 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080583 restraints weight = 20191.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.082796 restraints weight = 10794.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084324 restraints weight = 6554.930| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9412 Z= 0.169 Angle : 0.697 7.772 12636 Z= 0.356 Chirality : 0.042 0.295 1456 Planarity : 0.009 0.052 1716 Dihedral : 3.855 14.884 1404 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1092 helix: 0.92 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.04 (0.66), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG m 6 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 468) hydrogen bonds : angle 6.87480 ( 1404) covalent geometry : bond 0.00399 ( 9412) covalent geometry : angle 0.69696 (12636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.118 Fit side-chains REVERT: A 12 ASP cc_start: 0.7780 (t70) cc_final: 0.7492 (t70) REVERT: A 23 LEU cc_start: 0.8523 (mm) cc_final: 0.8220 (mm) REVERT: B 6 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8581 (ttm110) REVERT: B 10 ASP cc_start: 0.9337 (t0) cc_final: 0.9074 (t0) REVERT: C 12 ASP cc_start: 0.7867 (t0) cc_final: 0.7657 (t0) REVERT: C 22 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8621 (tpp-160) REVERT: E 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8694 (t0) REVERT: F 10 ASP cc_start: 0.9227 (t0) cc_final: 0.8906 (t0) REVERT: G 10 ASP cc_start: 0.9259 (t0) cc_final: 0.8843 (t0) REVERT: I 5 GLU cc_start: 0.9137 (mp0) cc_final: 0.8847 (mm-30) REVERT: J 6 ARG cc_start: 0.9008 (ttm110) cc_final: 0.8580 (ttm110) REVERT: J 10 ASP cc_start: 0.9248 (t0) cc_final: 0.9005 (t0) REVERT: K 5 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8852 (mm-30) REVERT: K 10 ASP cc_start: 0.9376 (t0) cc_final: 0.9002 (t0) REVERT: L 22 ARG cc_start: 0.9057 (tpp-160) cc_final: 0.8827 (tpp-160) REVERT: M 6 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8500 (ttm110) REVERT: M 10 ASP cc_start: 0.9347 (t0) cc_final: 0.8896 (t0) REVERT: N 6 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8415 (ttm110) REVERT: N 10 ASP cc_start: 0.9252 (t0) cc_final: 0.8986 (t0) REVERT: O 10 ASP cc_start: 0.9233 (t0) cc_final: 0.8868 (t0) REVERT: Q 6 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8485 (ttm110) REVERT: S 5 GLU cc_start: 0.9060 (mp0) cc_final: 0.8825 (mp0) REVERT: S 6 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8386 (ttm-80) REVERT: V 10 ASP cc_start: 0.9313 (t0) cc_final: 0.8835 (t0) REVERT: W 5 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8622 (mm-30) REVERT: W 21 ARG cc_start: 0.9045 (mmm-85) cc_final: 0.8683 (mmm-85) REVERT: W 22 ARG cc_start: 0.8868 (tpp-160) cc_final: 0.8639 (ttm-80) REVERT: X 10 ASP cc_start: 0.9141 (t0) cc_final: 0.8775 (t0) REVERT: X 21 ARG cc_start: 0.9023 (mmm-85) cc_final: 0.8811 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9225 (t0) cc_final: 0.8981 (t0) REVERT: Z 10 ASP cc_start: 0.9239 (t0) cc_final: 0.8916 (t0) REVERT: b 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8661 (t0) REVERT: c 12 ASP cc_start: 0.8569 (t70) cc_final: 0.8200 (t70) REVERT: d 10 ASP cc_start: 0.9286 (t0) cc_final: 0.8965 (t0) REVERT: e 10 ASP cc_start: 0.9319 (t0) cc_final: 0.9077 (t0) REVERT: f 10 ASP cc_start: 0.9247 (t0) cc_final: 0.8982 (t0) REVERT: g 10 ASP cc_start: 0.9260 (t0) cc_final: 0.8720 (t0) REVERT: h 12 ASP cc_start: 0.8529 (t70) cc_final: 0.8260 (t70) REVERT: i 10 ASP cc_start: 0.9257 (t0) cc_final: 0.8725 (t0) REVERT: j 6 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8692 (ttm110) REVERT: j 10 ASP cc_start: 0.9215 (t0) cc_final: 0.8833 (t0) REVERT: k 10 ASP cc_start: 0.9374 (t0) cc_final: 0.8954 (t0) REVERT: l 10 ASP cc_start: 0.9336 (t0) cc_final: 0.8965 (t0) REVERT: l 21 ARG cc_start: 0.8248 (tpp80) cc_final: 0.8005 (tpp80) REVERT: m 5 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8787 (mm-30) REVERT: m 10 ASP cc_start: 0.9445 (t0) cc_final: 0.9097 (t0) REVERT: n 21 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: o 10 ASP cc_start: 0.9344 (t0) cc_final: 0.8857 (t0) REVERT: p 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8712 (t0) REVERT: q 10 ASP cc_start: 0.9158 (t0) cc_final: 0.8670 (t0) REVERT: r 10 ASP cc_start: 0.9268 (t0) cc_final: 0.9024 (t0) REVERT: r 23 LEU cc_start: 0.8114 (mm) cc_final: 0.7490 (pp) REVERT: t 12 ASP cc_start: 0.7876 (t0) cc_final: 0.7619 (t0) REVERT: u 10 ASP cc_start: 0.9383 (t0) cc_final: 0.9069 (t0) REVERT: v 6 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8340 (ttm-80) REVERT: v 10 ASP cc_start: 0.9342 (t0) cc_final: 0.8971 (t0) REVERT: w 5 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8511 (mm-30) REVERT: w 12 ASP cc_start: 0.8151 (t70) cc_final: 0.7890 (t0) REVERT: x 10 ASP cc_start: 0.9056 (t0) cc_final: 0.8784 (t0) REVERT: z 23 LEU cc_start: 0.7925 (mt) cc_final: 0.7666 (mt) outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 0.3807 time to fit residues: 247.1311 Evaluate side-chains 507 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.083268 restraints weight = 19903.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085569 restraints weight = 10432.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087087 restraints weight = 6179.063| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.144 Angle : 0.686 5.579 12636 Z= 0.355 Chirality : 0.040 0.122 1456 Planarity : 0.009 0.056 1716 Dihedral : 3.758 16.569 1404 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1092 helix: 1.20 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.98 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG p 6 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 468) hydrogen bonds : angle 6.42962 ( 1404) covalent geometry : bond 0.00350 ( 9412) covalent geometry : angle 0.68574 (12636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 1.181 Fit side-chains REVERT: A 22 ARG cc_start: 0.9394 (tpp80) cc_final: 0.8882 (tpp-160) REVERT: B 6 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8577 (ttm110) REVERT: B 10 ASP cc_start: 0.9293 (t0) cc_final: 0.9033 (t0) REVERT: C 22 ARG cc_start: 0.9288 (tpp80) cc_final: 0.8487 (ttm110) REVERT: E 10 ASP cc_start: 0.9252 (t0) cc_final: 0.8679 (t0) REVERT: F 10 ASP cc_start: 0.9190 (t0) cc_final: 0.8888 (t0) REVERT: G 10 ASP cc_start: 0.9250 (t0) cc_final: 0.8863 (t0) REVERT: G 23 LEU cc_start: 0.8003 (mm) cc_final: 0.7755 (mm) REVERT: I 5 GLU cc_start: 0.9123 (mp0) cc_final: 0.8825 (mm-30) REVERT: J 6 ARG cc_start: 0.8916 (ttm110) cc_final: 0.8440 (ttm110) REVERT: K 5 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8859 (mm-30) REVERT: K 10 ASP cc_start: 0.9347 (t0) cc_final: 0.9041 (t0) REVERT: L 23 LEU cc_start: 0.8760 (mm) cc_final: 0.8541 (mm) REVERT: M 6 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8474 (ttm110) REVERT: M 10 ASP cc_start: 0.9319 (t0) cc_final: 0.8887 (t0) REVERT: N 6 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8465 (ttm110) REVERT: N 10 ASP cc_start: 0.9253 (t0) cc_final: 0.8957 (t0) REVERT: O 10 ASP cc_start: 0.9191 (t0) cc_final: 0.8860 (t0) REVERT: Q 12 ASP cc_start: 0.8322 (t70) cc_final: 0.7980 (t70) REVERT: S 6 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8444 (ttm-80) REVERT: V 10 ASP cc_start: 0.9309 (t0) cc_final: 0.8831 (t0) REVERT: V 23 LEU cc_start: 0.7056 (tt) cc_final: 0.6822 (pp) REVERT: W 5 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8620 (mm-30) REVERT: W 21 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9302 (t0) cc_final: 0.9069 (t0) REVERT: Z 10 ASP cc_start: 0.9197 (t0) cc_final: 0.8907 (t0) REVERT: b 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8583 (t0) REVERT: b 12 ASP cc_start: 0.7883 (t0) cc_final: 0.7454 (t0) REVERT: b 23 LEU cc_start: 0.8565 (mm) cc_final: 0.8001 (pp) REVERT: c 12 ASP cc_start: 0.8375 (t70) cc_final: 0.8047 (t70) REVERT: d 10 ASP cc_start: 0.9328 (t0) cc_final: 0.9029 (t0) REVERT: f 10 ASP cc_start: 0.9243 (t0) cc_final: 0.9011 (t0) REVERT: f 23 LEU cc_start: 0.8292 (mm) cc_final: 0.7866 (pp) REVERT: g 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8749 (t0) REVERT: i 10 ASP cc_start: 0.9221 (t0) cc_final: 0.8672 (t0) REVERT: j 6 ARG cc_start: 0.8947 (ttm110) cc_final: 0.8644 (ttm110) REVERT: j 10 ASP cc_start: 0.9217 (t0) cc_final: 0.8821 (t0) REVERT: k 10 ASP cc_start: 0.9376 (t0) cc_final: 0.8934 (t0) REVERT: l 10 ASP cc_start: 0.9300 (t0) cc_final: 0.9022 (t0) REVERT: l 23 LEU cc_start: 0.8114 (mm) cc_final: 0.7301 (pp) REVERT: m 5 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8810 (mm-30) REVERT: m 10 ASP cc_start: 0.9375 (t0) cc_final: 0.8989 (t0) REVERT: n 21 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8564 (mmm-85) REVERT: o 5 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8490 (mm-30) REVERT: o 10 ASP cc_start: 0.9324 (t0) cc_final: 0.8897 (t0) REVERT: p 6 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8596 (ttp-110) REVERT: p 10 ASP cc_start: 0.9272 (t0) cc_final: 0.8707 (t0) REVERT: q 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8761 (t0) REVERT: r 10 ASP cc_start: 0.9246 (t0) cc_final: 0.9007 (t0) REVERT: t 6 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8372 (ttm110) REVERT: t 12 ASP cc_start: 0.7713 (t0) cc_final: 0.7447 (t0) REVERT: u 5 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8741 (mm-30) REVERT: u 10 ASP cc_start: 0.9384 (t0) cc_final: 0.9028 (t0) REVERT: v 6 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8288 (ttm-80) REVERT: v 10 ASP cc_start: 0.9335 (t0) cc_final: 0.8878 (t0) REVERT: w 5 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8521 (mm-30) REVERT: w 12 ASP cc_start: 0.8178 (t70) cc_final: 0.7766 (t70) REVERT: x 10 ASP cc_start: 0.9069 (t0) cc_final: 0.8742 (t0) REVERT: z 12 ASP cc_start: 0.8273 (t70) cc_final: 0.8036 (t0) REVERT: z 14 GLU cc_start: 0.8799 (tp30) cc_final: 0.8483 (mt-10) REVERT: z 15 VAL cc_start: 0.8971 (p) cc_final: 0.8751 (m) REVERT: z 23 LEU cc_start: 0.7887 (mt) cc_final: 0.7606 (mt) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.3570 time to fit residues: 225.0819 Evaluate side-chains 499 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 overall best weight: 2.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084799 restraints weight = 19676.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087164 restraints weight = 10129.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088757 restraints weight = 5984.392| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9412 Z= 0.137 Angle : 0.694 4.965 12636 Z= 0.359 Chirality : 0.039 0.138 1456 Planarity : 0.009 0.058 1716 Dihedral : 3.687 17.054 1404 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1092 helix: 1.31 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.80 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG m 6 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 468) hydrogen bonds : angle 6.14335 ( 1404) covalent geometry : bond 0.00339 ( 9412) covalent geometry : angle 0.69433 (12636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 1.050 Fit side-chains REVERT: A 12 ASP cc_start: 0.7629 (t70) cc_final: 0.7382 (t0) REVERT: A 22 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8916 (tpp-160) REVERT: B 10 ASP cc_start: 0.9309 (t0) cc_final: 0.8971 (t0) REVERT: C 22 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8599 (ttm110) REVERT: D 22 ARG cc_start: 0.9288 (tpp-160) cc_final: 0.8928 (tpp-160) REVERT: E 10 ASP cc_start: 0.9221 (t0) cc_final: 0.8693 (t0) REVERT: F 10 ASP cc_start: 0.9208 (t0) cc_final: 0.8859 (t0) REVERT: G 10 ASP cc_start: 0.9239 (t0) cc_final: 0.8834 (t0) REVERT: G 21 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8807 (mmm-85) REVERT: G 23 LEU cc_start: 0.7999 (mm) cc_final: 0.7667 (mm) REVERT: H 23 LEU cc_start: 0.8365 (mm) cc_final: 0.7491 (mm) REVERT: J 6 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8480 (ttm110) REVERT: K 5 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8911 (mm-30) REVERT: K 10 ASP cc_start: 0.9324 (t0) cc_final: 0.8999 (t0) REVERT: L 21 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8894 (mmm-85) REVERT: M 10 ASP cc_start: 0.9305 (t0) cc_final: 0.8855 (t0) REVERT: N 6 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8490 (ttm110) REVERT: N 10 ASP cc_start: 0.9210 (t0) cc_final: 0.8983 (t0) REVERT: O 10 ASP cc_start: 0.9257 (t0) cc_final: 0.8831 (t0) REVERT: R 7 LEU cc_start: 0.9316 (mt) cc_final: 0.9101 (mp) REVERT: S 6 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8466 (ttm-80) REVERT: V 10 ASP cc_start: 0.9378 (t0) cc_final: 0.8908 (t0) REVERT: W 5 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8651 (mm-30) REVERT: W 21 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8477 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9324 (t0) cc_final: 0.9066 (t0) REVERT: Z 10 ASP cc_start: 0.9183 (t0) cc_final: 0.8869 (t0) REVERT: b 10 ASP cc_start: 0.9077 (t0) cc_final: 0.8535 (t0) REVERT: b 12 ASP cc_start: 0.7791 (t0) cc_final: 0.7189 (t0) REVERT: c 12 ASP cc_start: 0.8428 (t70) cc_final: 0.8212 (t0) REVERT: d 10 ASP cc_start: 0.9387 (t0) cc_final: 0.8999 (t0) REVERT: e 10 ASP cc_start: 0.9284 (t0) cc_final: 0.8974 (t0) REVERT: f 10 ASP cc_start: 0.9221 (t0) cc_final: 0.8951 (t0) REVERT: f 23 LEU cc_start: 0.8119 (mm) cc_final: 0.7904 (mt) REVERT: g 10 ASP cc_start: 0.9280 (t0) cc_final: 0.8921 (t0) REVERT: g 13 ARG cc_start: 0.8440 (ttp80) cc_final: 0.7812 (ttm170) REVERT: h 5 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8872 (mm-30) REVERT: h 12 ASP cc_start: 0.8382 (t70) cc_final: 0.8180 (t70) REVERT: i 5 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8503 (mm-30) REVERT: i 10 ASP cc_start: 0.9217 (t0) cc_final: 0.8652 (t0) REVERT: j 10 ASP cc_start: 0.9195 (t0) cc_final: 0.8796 (t0) REVERT: k 10 ASP cc_start: 0.9373 (t0) cc_final: 0.8923 (t0) REVERT: l 6 ARG cc_start: 0.8868 (ttm110) cc_final: 0.8650 (ttm110) REVERT: l 10 ASP cc_start: 0.9322 (t0) cc_final: 0.8965 (t0) REVERT: m 10 ASP cc_start: 0.9358 (t0) cc_final: 0.8987 (t0) REVERT: n 12 ASP cc_start: 0.7309 (t0) cc_final: 0.7006 (t0) REVERT: n 21 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8541 (mmm-85) REVERT: o 5 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8492 (mm-30) REVERT: o 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8891 (t0) REVERT: p 5 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8841 (mm-30) REVERT: p 6 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8696 (ttp-110) REVERT: p 10 ASP cc_start: 0.9081 (t0) cc_final: 0.8493 (t0) REVERT: q 10 ASP cc_start: 0.9162 (t0) cc_final: 0.8758 (t0) REVERT: r 10 ASP cc_start: 0.9251 (t0) cc_final: 0.8948 (t0) REVERT: t 6 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8514 (ttm110) REVERT: u 10 ASP cc_start: 0.9400 (t0) cc_final: 0.9035 (t0) REVERT: v 6 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8366 (ttm-80) REVERT: v 10 ASP cc_start: 0.9323 (t0) cc_final: 0.8868 (t0) REVERT: w 5 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8639 (mm-30) REVERT: w 12 ASP cc_start: 0.8102 (t70) cc_final: 0.7751 (t0) REVERT: x 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8743 (t0) REVERT: z 14 GLU cc_start: 0.8781 (tp30) cc_final: 0.8322 (mt-10) REVERT: z 23 LEU cc_start: 0.7875 (mt) cc_final: 0.7514 (mt) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.3528 time to fit residues: 221.7745 Evaluate side-chains 489 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083463 restraints weight = 19668.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085590 restraints weight = 10579.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087033 restraints weight = 6413.831| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9412 Z= 0.158 Angle : 0.731 5.752 12636 Z= 0.375 Chirality : 0.040 0.131 1456 Planarity : 0.009 0.066 1716 Dihedral : 3.801 16.811 1404 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1092 helix: 1.33 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.78 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 6 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 468) hydrogen bonds : angle 6.48155 ( 1404) covalent geometry : bond 0.00391 ( 9412) covalent geometry : angle 0.73051 (12636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.230 Fit side-chains REVERT: A 12 ASP cc_start: 0.7747 (t70) cc_final: 0.7485 (t70) REVERT: A 22 ARG cc_start: 0.9362 (tpp80) cc_final: 0.9037 (tpp-160) REVERT: B 10 ASP cc_start: 0.9330 (t0) cc_final: 0.9048 (t0) REVERT: C 22 ARG cc_start: 0.9247 (tpp80) cc_final: 0.8801 (tpp-160) REVERT: E 6 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8475 (ttm-80) REVERT: E 10 ASP cc_start: 0.9222 (t0) cc_final: 0.8756 (t0) REVERT: F 10 ASP cc_start: 0.9227 (t0) cc_final: 0.8917 (t0) REVERT: G 10 ASP cc_start: 0.9257 (t0) cc_final: 0.8800 (t0) REVERT: G 21 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8872 (mmm-85) REVERT: H 23 LEU cc_start: 0.8424 (mm) cc_final: 0.7733 (mm) REVERT: I 12 ASP cc_start: 0.7883 (t0) cc_final: 0.7625 (t0) REVERT: J 6 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8474 (ttm110) REVERT: K 10 ASP cc_start: 0.9312 (t0) cc_final: 0.9039 (t0) REVERT: K 23 LEU cc_start: 0.8196 (mm) cc_final: 0.7994 (mm) REVERT: M 10 ASP cc_start: 0.9315 (t0) cc_final: 0.8889 (t0) REVERT: N 6 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8398 (ttm110) REVERT: N 10 ASP cc_start: 0.9212 (t0) cc_final: 0.8983 (t0) REVERT: O 10 ASP cc_start: 0.9251 (t0) cc_final: 0.8878 (t0) REVERT: Q 14 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8702 (tp30) REVERT: S 5 GLU cc_start: 0.8988 (mp0) cc_final: 0.8608 (mp0) REVERT: S 6 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8371 (ttm-80) REVERT: S 10 ASP cc_start: 0.9381 (t0) cc_final: 0.8973 (t0) REVERT: V 10 ASP cc_start: 0.9371 (t0) cc_final: 0.8990 (t0) REVERT: W 5 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8578 (mm-30) REVERT: W 21 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8760 (mmm-85) REVERT: X 10 ASP cc_start: 0.9091 (t0) cc_final: 0.8860 (t0) REVERT: Z 10 ASP cc_start: 0.9169 (t0) cc_final: 0.8917 (t0) REVERT: b 10 ASP cc_start: 0.9068 (t0) cc_final: 0.8567 (t0) REVERT: b 12 ASP cc_start: 0.7864 (t0) cc_final: 0.7333 (t0) REVERT: c 12 ASP cc_start: 0.8438 (t70) cc_final: 0.8227 (t0) REVERT: d 10 ASP cc_start: 0.9310 (t0) cc_final: 0.8875 (t0) REVERT: e 10 ASP cc_start: 0.9311 (t0) cc_final: 0.9049 (t0) REVERT: f 10 ASP cc_start: 0.9189 (t0) cc_final: 0.8834 (t0) REVERT: f 23 LEU cc_start: 0.8286 (mm) cc_final: 0.8002 (mt) REVERT: g 10 ASP cc_start: 0.9285 (t0) cc_final: 0.8789 (t0) REVERT: i 10 ASP cc_start: 0.9282 (t0) cc_final: 0.8740 (t0) REVERT: j 10 ASP cc_start: 0.9197 (t0) cc_final: 0.8842 (t0) REVERT: k 10 ASP cc_start: 0.9353 (t0) cc_final: 0.9050 (t0) REVERT: l 10 ASP cc_start: 0.9387 (t0) cc_final: 0.9096 (t0) REVERT: m 10 ASP cc_start: 0.9412 (t0) cc_final: 0.9039 (t0) REVERT: n 12 ASP cc_start: 0.7311 (t0) cc_final: 0.7007 (t0) REVERT: o 5 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8448 (mm-30) REVERT: o 10 ASP cc_start: 0.9366 (t0) cc_final: 0.8927 (t0) REVERT: p 5 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8852 (mm-30) REVERT: p 10 ASP cc_start: 0.9229 (t0) cc_final: 0.8660 (t0) REVERT: q 10 ASP cc_start: 0.9211 (t0) cc_final: 0.8801 (t0) REVERT: r 10 ASP cc_start: 0.9197 (t0) cc_final: 0.8947 (t0) REVERT: r 21 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8627 (mmm-85) REVERT: t 6 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8455 (ttm-80) REVERT: u 10 ASP cc_start: 0.9395 (t0) cc_final: 0.9063 (t0) REVERT: v 10 ASP cc_start: 0.9308 (t0) cc_final: 0.8909 (t0) REVERT: v 23 LEU cc_start: 0.7738 (mt) cc_final: 0.7464 (mt) REVERT: w 12 ASP cc_start: 0.8139 (t70) cc_final: 0.7771 (t0) REVERT: x 10 ASP cc_start: 0.9099 (t0) cc_final: 0.8822 (t0) REVERT: z 5 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8430 (mm-30) REVERT: z 14 GLU cc_start: 0.8828 (tp30) cc_final: 0.8591 (mt-10) REVERT: z 23 LEU cc_start: 0.7901 (mt) cc_final: 0.7654 (mt) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.3548 time to fit residues: 215.3965 Evaluate side-chains 482 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087307 restraints weight = 19949.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089558 restraints weight = 10519.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091048 restraints weight = 6236.502| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9412 Z= 0.143 Angle : 0.734 5.431 12636 Z= 0.380 Chirality : 0.039 0.137 1456 Planarity : 0.009 0.063 1716 Dihedral : 3.720 17.885 1404 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1092 helix: 1.28 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.65 (0.69), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.02349 ( 468) hydrogen bonds : angle 5.91754 ( 1404) covalent geometry : bond 0.00354 ( 9412) covalent geometry : angle 0.73393 (12636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8902 (tpp-160) REVERT: B 10 ASP cc_start: 0.9289 (t0) cc_final: 0.8987 (t0) REVERT: C 22 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8589 (ttm110) REVERT: D 21 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8498 (tpp80) REVERT: E 10 ASP cc_start: 0.9216 (t0) cc_final: 0.8723 (t0) REVERT: F 10 ASP cc_start: 0.9206 (t0) cc_final: 0.8869 (t0) REVERT: G 10 ASP cc_start: 0.9161 (t0) cc_final: 0.8858 (t0) REVERT: H 23 LEU cc_start: 0.8224 (mm) cc_final: 0.6769 (mm) REVERT: I 12 ASP cc_start: 0.7823 (t0) cc_final: 0.7598 (t0) REVERT: K 10 ASP cc_start: 0.9327 (t0) cc_final: 0.9005 (t0) REVERT: M 10 ASP cc_start: 0.9241 (t0) cc_final: 0.8853 (t0) REVERT: N 6 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8278 (ttm110) REVERT: N 10 ASP cc_start: 0.9243 (t0) cc_final: 0.8940 (t0) REVERT: O 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8924 (t0) REVERT: O 15 VAL cc_start: 0.9172 (p) cc_final: 0.8934 (t) REVERT: S 5 GLU cc_start: 0.8970 (mp0) cc_final: 0.8698 (mp0) REVERT: S 10 ASP cc_start: 0.9381 (t0) cc_final: 0.8933 (t0) REVERT: T 6 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8581 (ttm110) REVERT: V 10 ASP cc_start: 0.9287 (t0) cc_final: 0.8907 (t0) REVERT: W 5 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8647 (mm-30) REVERT: W 21 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8221 (tpt-90) REVERT: Y 23 LEU cc_start: 0.8405 (mm) cc_final: 0.7778 (mm) REVERT: Z 10 ASP cc_start: 0.9114 (t0) cc_final: 0.8841 (t0) REVERT: b 10 ASP cc_start: 0.9048 (t0) cc_final: 0.8485 (t0) REVERT: b 12 ASP cc_start: 0.7619 (t0) cc_final: 0.6980 (t0) REVERT: c 12 ASP cc_start: 0.8538 (t70) cc_final: 0.8284 (t70) REVERT: d 10 ASP cc_start: 0.9321 (t0) cc_final: 0.8793 (t0) REVERT: e 5 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8608 (mm-30) REVERT: e 10 ASP cc_start: 0.9260 (t0) cc_final: 0.8948 (t0) REVERT: f 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8839 (t0) REVERT: g 10 ASP cc_start: 0.9119 (t0) cc_final: 0.8715 (t0) REVERT: g 13 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7443 (ttm170) REVERT: j 10 ASP cc_start: 0.9175 (t0) cc_final: 0.8793 (t0) REVERT: k 10 ASP cc_start: 0.9353 (t0) cc_final: 0.8978 (t0) REVERT: l 6 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8574 (ttm110) REVERT: l 23 LEU cc_start: 0.7998 (mm) cc_final: 0.7275 (pp) REVERT: m 10 ASP cc_start: 0.9320 (t0) cc_final: 0.8995 (t0) REVERT: n 12 ASP cc_start: 0.7194 (t0) cc_final: 0.6904 (t0) REVERT: o 5 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8491 (mm-30) REVERT: o 10 ASP cc_start: 0.9302 (t0) cc_final: 0.8939 (t0) REVERT: p 10 ASP cc_start: 0.9080 (t0) cc_final: 0.8570 (t0) REVERT: q 10 ASP cc_start: 0.9137 (t0) cc_final: 0.8748 (t0) REVERT: q 14 GLU cc_start: 0.8943 (tp30) cc_final: 0.8695 (tp30) REVERT: r 10 ASP cc_start: 0.9171 (t0) cc_final: 0.8927 (t0) REVERT: t 6 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8407 (ttm-80) REVERT: t 12 ASP cc_start: 0.7663 (t70) cc_final: 0.7410 (t0) REVERT: u 10 ASP cc_start: 0.9412 (t0) cc_final: 0.9089 (t0) REVERT: v 6 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8374 (ttm-80) REVERT: v 10 ASP cc_start: 0.9271 (t0) cc_final: 0.8837 (t0) REVERT: v 23 LEU cc_start: 0.8091 (mt) cc_final: 0.7842 (mt) REVERT: w 12 ASP cc_start: 0.8095 (t70) cc_final: 0.7737 (t0) REVERT: x 10 ASP cc_start: 0.9043 (t0) cc_final: 0.8775 (t0) REVERT: z 12 ASP cc_start: 0.8016 (t70) cc_final: 0.7787 (t0) REVERT: z 14 GLU cc_start: 0.8755 (tp30) cc_final: 0.8425 (mt-10) REVERT: z 23 LEU cc_start: 0.7710 (mt) cc_final: 0.7384 (mt) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3571 time to fit residues: 213.8953 Evaluate side-chains 473 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.083136 restraints weight = 20036.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085260 restraints weight = 10832.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.086686 restraints weight = 6599.558| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9412 Z= 0.178 Angle : 0.770 9.148 12636 Z= 0.394 Chirality : 0.041 0.125 1456 Planarity : 0.010 0.071 1716 Dihedral : 3.923 16.298 1404 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1092 helix: 1.29 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.65 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 6 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 468) hydrogen bonds : angle 6.71909 ( 1404) covalent geometry : bond 0.00434 ( 9412) covalent geometry : angle 0.77004 (12636) =============================================================================== Job complete usr+sys time: 4039.49 seconds wall clock time: 70 minutes 4.38 seconds (4204.38 seconds total)