Starting phenix.real_space_refine on Thu Feb 13 11:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hqe_0252/02_2025/6hqe_0252.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hqe_0252/02_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_0252/02_2025/6hqe_0252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hqe_0252/02_2025/6hqe_0252.map" model { file = "/net/cci-nas-00/data/ceres_data/6hqe_0252/02_2025/6hqe_0252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hqe_0252/02_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-5592/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: 2.12, per 1000 atoms: 0.23 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: 2.26 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: 0.94 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: 2.34 Time building geometry restraints manager: 2.58 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: 0.11 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: 0.140 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.330 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- 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= 0.618 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 *********************** 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 : 1.113 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: 0.3627 time to fit residues: 242.4893 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 : 1.139 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.082923 restraints weight = 10501.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084411 restraints weight = 6333.402| |-----------------------------------------------------------------------------| 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= 0.254 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 *********************** 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 : 1.125 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: 0.9159 (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: 0.8797 (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: 0.8746 (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: 0.8436 (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: 0.8646 (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: 0.9201 (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: 0.8717 (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: 0.7859 (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: 0.8186 (mt) REVERT: y 5 GLU cc_start: 0.8945 (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: 0.3799 time to fit residues: 251.0416 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 : 1.201 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 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 = 0.093176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085758 restraints weight = 19013.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087900 restraints weight = 10160.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089326 restraints weight = 6059.672| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5553 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= 0.172 Angle : 0.571 4.395 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 : 9.30 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 *********************** 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 : 1.167 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: 0.8678 (ttp-110) cc_final: 0.8370 (ttm110) REVERT: B 10 ASP cc_start: 0.9151 (t0) cc_final: 0.8812 (t0) REVERT: D 22 ARG cc_start: 0.8524 (mmt180) cc_final: 0.8303 (mmt-90) REVERT: E 10 ASP cc_start: 0.9035 (t0) cc_final: 0.8579 (t0) REVERT: F 10 ASP cc_start: 0.9130 (t0) cc_final: 0.8746 (t0) REVERT: H 21 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8587 (mmm-85) REVERT: I 5 GLU cc_start: 0.9059 (mp0) cc_final: 0.8786 (mm-30) REVERT: J 5 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8616 (mm-30) REVERT: J 6 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8380 (ttm110) REVERT: J 21 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8667 (mmm-85) REVERT: K 5 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8594 (mm-30) REVERT: K 10 ASP cc_start: 0.9228 (t0) cc_final: 0.8928 (t0) REVERT: L 7 LEU cc_start: 0.9139 (mt) cc_final: 0.8925 (mt) REVERT: N 5 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8744 (mm-30) REVERT: N 10 ASP cc_start: 0.9188 (t0) cc_final: 0.8797 (t0) REVERT: N 21 ARG cc_start: 0.8964 (mmm-85) cc_final: 0.8709 (mmm-85) REVERT: O 10 ASP cc_start: 0.9216 (t0) cc_final: 0.8626 (t0) REVERT: P 22 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.8044 (mmt-90) REVERT: R 5 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8559 (mm-30) REVERT: V 5 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8729 (mm-30) REVERT: W 5 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8632 (mm-30) REVERT: W 21 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8693 (mmm-85) REVERT: X 23 LEU cc_start: 0.7781 (mt) cc_final: 0.6931 (pp) REVERT: Z 5 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8856 (mm-30) REVERT: Z 23 LEU cc_start: 0.8532 (mm) cc_final: 0.7794 (pp) REVERT: a 22 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8941 (ttm110) REVERT: b 10 ASP cc_start: 0.9023 (t0) cc_final: 0.8533 (t0) REVERT: d 10 ASP cc_start: 0.9226 (t0) cc_final: 0.8967 (t0) REVERT: f 10 ASP cc_start: 0.9098 (t0) cc_final: 0.8740 (t0) REVERT: f 23 LEU cc_start: 0.7947 (mm) cc_final: 0.7324 (pp) REVERT: g 10 ASP cc_start: 0.9040 (t0) cc_final: 0.8449 (t0) REVERT: i 6 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8305 (ttm-80) REVERT: j 10 ASP cc_start: 0.9052 (t0) cc_final: 0.8579 (t0) REVERT: k 10 ASP cc_start: 0.9253 (t0) cc_final: 0.8708 (t0) REVERT: k 21 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: l 6 ARG cc_start: 0.8993 (ttm110) cc_final: 0.8714 (ttm110) REVERT: l 23 LEU cc_start: 0.7903 (mm) cc_final: 0.6864 (pp) REVERT: m 10 ASP cc_start: 0.9302 (t0) cc_final: 0.8841 (t0) REVERT: n 21 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8478 (mmm-85) REVERT: n 23 LEU cc_start: 0.8070 (mm) cc_final: 0.7174 (pp) REVERT: o 10 ASP cc_start: 0.9260 (t0) cc_final: 0.8700 (t0) REVERT: p 10 ASP cc_start: 0.9093 (t0) cc_final: 0.8701 (t0) REVERT: p 23 LEU cc_start: 0.8078 (mm) cc_final: 0.7368 (pp) REVERT: q 10 ASP cc_start: 0.9100 (t0) cc_final: 0.8598 (t0) REVERT: r 10 ASP cc_start: 0.9140 (t0) cc_final: 0.8718 (t0) REVERT: s 5 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8588 (mm-30) REVERT: u 10 ASP cc_start: 0.9296 (t0) cc_final: 0.8702 (t0) REVERT: w 12 ASP cc_start: 0.7999 (t70) cc_final: 0.7734 (t70) REVERT: x 6 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8475 (ttm110) REVERT: x 10 ASP cc_start: 0.9064 (t0) cc_final: 0.8602 (t0) REVERT: z 23 LEU cc_start: 0.7890 (mt) cc_final: 0.7333 (pp) outliers start: 1 outliers final: 0 residues processed: 574 average time/residue: 0.3854 time to fit residues: 268.7730 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 : 1.097 ------------------------------------------------------------------------------- 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: 8.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.089291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081246 restraints weight = 19501.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083419 restraints weight = 10403.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084864 restraints weight = 6299.657| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5775 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= 0.225 Angle : 0.619 4.513 12636 Z= 0.320 Chirality : 0.040 0.137 1456 Planarity : 0.008 0.046 1716 Dihedral : 3.736 17.477 1404 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -0.33 (0.26), residues: 1092 helix: 0.03 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.90 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 6 *********************** 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 536 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7584 (t70) cc_final: 0.7363 (t70) REVERT: B 6 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8484 (ttm110) REVERT: B 10 ASP cc_start: 0.9250 (t0) cc_final: 0.8919 (t0) REVERT: C 21 ARG cc_start: 0.8899 (mmm-85) cc_final: 0.8670 (mmm-85) REVERT: E 10 ASP cc_start: 0.9191 (t0) cc_final: 0.8668 (t0) REVERT: F 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8889 (t0) REVERT: F 22 ARG cc_start: 0.9170 (tpp-160) cc_final: 0.8879 (tpp-160) REVERT: G 10 ASP cc_start: 0.9224 (t0) cc_final: 0.8831 (t0) REVERT: H 21 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8607 (mmm-85) REVERT: I 12 ASP cc_start: 0.7904 (t0) cc_final: 0.7696 (t0) REVERT: J 6 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8385 (ttm110) REVERT: K 5 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8749 (mm-30) REVERT: K 10 ASP cc_start: 0.9328 (t0) cc_final: 0.8949 (t0) REVERT: L 7 LEU cc_start: 0.9188 (mt) cc_final: 0.8971 (mt) REVERT: L 23 LEU cc_start: 0.8644 (mm) cc_final: 0.8428 (mm) REVERT: N 6 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8217 (ttm110) REVERT: N 10 ASP cc_start: 0.9209 (t0) cc_final: 0.8810 (t0) REVERT: O 10 ASP cc_start: 0.9225 (t0) cc_final: 0.8625 (t0) REVERT: O 22 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8529 (mmt-90) REVERT: Q 12 ASP cc_start: 0.8311 (t70) cc_final: 0.8073 (t70) REVERT: S 6 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8422 (ttm-80) REVERT: U 12 ASP cc_start: 0.7827 (t70) cc_final: 0.7580 (t0) REVERT: V 5 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8687 (mm-30) REVERT: V 14 GLU cc_start: 0.9195 (tp30) cc_final: 0.8987 (tp30) REVERT: W 21 ARG cc_start: 0.8952 (mmm-85) cc_final: 0.8566 (mmm-85) REVERT: W 22 ARG cc_start: 0.8930 (tpp-160) cc_final: 0.8598 (ttm110) REVERT: X 21 ARG cc_start: 0.9050 (mmm-85) cc_final: 0.8682 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9269 (t0) cc_final: 0.8891 (t0) REVERT: Z 10 ASP cc_start: 0.9194 (t0) cc_final: 0.8913 (t0) REVERT: Z 23 LEU cc_start: 0.8607 (mm) cc_final: 0.8361 (mt) REVERT: b 10 ASP cc_start: 0.9087 (t0) cc_final: 0.8562 (t0) REVERT: c 12 ASP cc_start: 0.8504 (t70) cc_final: 0.8245 (t70) REVERT: d 10 ASP cc_start: 0.9289 (t0) cc_final: 0.8920 (t0) REVERT: d 23 LEU cc_start: 0.7455 (mt) cc_final: 0.7217 (mt) REVERT: f 10 ASP cc_start: 0.9184 (t0) cc_final: 0.8891 (t0) REVERT: g 10 ASP cc_start: 0.9130 (t0) cc_final: 0.8644 (t0) REVERT: i 5 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8571 (mm-30) REVERT: i 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8555 (t0) REVERT: j 6 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8721 (ttm110) REVERT: j 10 ASP cc_start: 0.9089 (t0) cc_final: 0.8657 (t0) REVERT: k 10 ASP cc_start: 0.9353 (t0) cc_final: 0.8822 (t0) REVERT: k 14 GLU cc_start: 0.8946 (tp30) cc_final: 0.8700 (tp30) REVERT: k 21 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8595 (mmm-85) REVERT: l 6 ARG cc_start: 0.8952 (ttm110) cc_final: 0.8514 (ttm110) REVERT: m 10 ASP cc_start: 0.9368 (t0) cc_final: 0.9005 (t0) REVERT: n 21 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8649 (mmm-85) REVERT: o 10 ASP cc_start: 0.9345 (t0) cc_final: 0.8843 (t0) REVERT: p 5 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8827 (mm-30) REVERT: p 10 ASP cc_start: 0.9210 (t0) cc_final: 0.8686 (t0) REVERT: q 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8659 (t0) REVERT: q 22 ARG cc_start: 0.8990 (tpp-160) cc_final: 0.8728 (tpp-160) REVERT: r 10 ASP cc_start: 0.9233 (t0) cc_final: 0.8801 (t0) REVERT: s 12 ASP cc_start: 0.7714 (t70) cc_final: 0.7501 (t70) REVERT: t 12 ASP cc_start: 0.7593 (t0) cc_final: 0.7277 (t0) REVERT: u 10 ASP cc_start: 0.9342 (t0) cc_final: 0.8848 (t0) REVERT: v 6 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.8267 (ttm-80) REVERT: v 10 ASP cc_start: 0.9184 (t0) cc_final: 0.8810 (t0) REVERT: w 12 ASP cc_start: 0.8179 (t70) cc_final: 0.7885 (t70) REVERT: x 6 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8513 (ttm110) REVERT: x 10 ASP cc_start: 0.9063 (t0) cc_final: 0.8720 (t0) REVERT: y 12 ASP cc_start: 0.7712 (t70) cc_final: 0.7488 (t0) REVERT: z 23 LEU cc_start: 0.8184 (mt) cc_final: 0.7952 (mt) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.3816 time to fit residues: 249.7686 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 : 1.053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 54 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.087671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079495 restraints weight = 19765.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081701 restraints weight = 10373.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083211 restraints weight = 6229.278| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.6026 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= 0.253 Angle : 0.654 5.615 12636 Z= 0.334 Chirality : 0.041 0.210 1456 Planarity : 0.008 0.045 1716 Dihedral : 3.702 13.995 1404 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.26), residues: 1092 helix: 0.53 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.92 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG m 6 *********************** 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 543 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 1.019 Fit side-chains REVERT: A 12 ASP cc_start: 0.7743 (t70) cc_final: 0.7463 (t70) REVERT: B 6 ARG cc_start: 0.8827 (ttp-110) cc_final: 0.8543 (ttm110) REVERT: B 10 ASP cc_start: 0.9294 (t0) cc_final: 0.8996 (t0) REVERT: E 10 ASP cc_start: 0.9238 (t0) cc_final: 0.8711 (t0) REVERT: F 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8840 (t0) REVERT: F 22 ARG cc_start: 0.9097 (tpp-160) cc_final: 0.8823 (tpp-160) REVERT: G 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8826 (t0) REVERT: H 21 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8638 (mmm-85) REVERT: I 21 ARG cc_start: 0.9268 (mmm-85) cc_final: 0.9016 (mmm-85) REVERT: J 6 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8491 (ttm110) REVERT: J 10 ASP cc_start: 0.9291 (t0) cc_final: 0.8993 (t0) REVERT: J 22 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8546 (tpp-160) REVERT: K 5 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8884 (mm-30) REVERT: K 10 ASP cc_start: 0.9364 (t0) cc_final: 0.8954 (t0) REVERT: K 21 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8483 (tmm-80) REVERT: L 21 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8737 (mmm-85) REVERT: M 6 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8585 (ttm110) REVERT: M 10 ASP cc_start: 0.9305 (t0) cc_final: 0.8884 (t0) REVERT: N 6 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8378 (ttm110) REVERT: N 10 ASP cc_start: 0.9220 (t0) cc_final: 0.8911 (t0) REVERT: O 10 ASP cc_start: 0.9304 (t0) cc_final: 0.8703 (t0) REVERT: Q 12 ASP cc_start: 0.8369 (t70) cc_final: 0.8113 (t0) REVERT: S 6 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8406 (ttm-80) REVERT: T 6 ARG cc_start: 0.8979 (ttp-110) cc_final: 0.8735 (ttm110) REVERT: V 5 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8721 (mm-30) REVERT: V 10 ASP cc_start: 0.9308 (t0) cc_final: 0.8703 (t0) REVERT: V 23 LEU cc_start: 0.7862 (mt) cc_final: 0.7653 (mt) REVERT: W 5 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8623 (mm-30) REVERT: W 21 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8614 (mmm-85) REVERT: W 22 ARG cc_start: 0.8866 (tpp-160) cc_final: 0.8348 (ttm110) REVERT: X 10 ASP cc_start: 0.9109 (t0) cc_final: 0.8770 (t0) REVERT: X 21 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8740 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8975 (t0) REVERT: Z 10 ASP cc_start: 0.9193 (t0) cc_final: 0.8906 (t0) REVERT: Z 23 LEU cc_start: 0.8575 (mm) cc_final: 0.8359 (mt) REVERT: b 10 ASP cc_start: 0.9166 (t0) cc_final: 0.8611 (t0) REVERT: c 12 ASP cc_start: 0.8509 (t70) cc_final: 0.8264 (t70) REVERT: d 10 ASP cc_start: 0.9320 (t0) cc_final: 0.8945 (t0) REVERT: d 23 LEU cc_start: 0.7613 (mt) cc_final: 0.7319 (mt) REVERT: e 10 ASP cc_start: 0.9284 (t0) cc_final: 0.9040 (t0) REVERT: f 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8937 (t0) REVERT: f 23 LEU cc_start: 0.8392 (mm) cc_final: 0.8085 (pp) REVERT: g 10 ASP cc_start: 0.9155 (t0) cc_final: 0.8701 (t0) REVERT: i 10 ASP cc_start: 0.9211 (t0) cc_final: 0.8650 (t0) REVERT: j 6 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8700 (ttm110) REVERT: j 10 ASP cc_start: 0.9189 (t0) cc_final: 0.8790 (t0) REVERT: k 10 ASP cc_start: 0.9390 (t0) cc_final: 0.8864 (t0) REVERT: k 21 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8580 (mmm-85) REVERT: l 6 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8754 (ttm110) REVERT: l 10 ASP cc_start: 0.9305 (t0) cc_final: 0.8930 (t0) REVERT: m 10 ASP cc_start: 0.9398 (t0) cc_final: 0.8969 (t0) REVERT: n 6 ARG cc_start: 0.9082 (ttm110) cc_final: 0.8835 (ttm110) REVERT: n 21 ARG cc_start: 0.9021 (mmm-85) cc_final: 0.8731 (mmm-85) REVERT: o 10 ASP cc_start: 0.9329 (t0) cc_final: 0.8771 (t0) REVERT: p 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8713 (t0) REVERT: q 10 ASP cc_start: 0.9187 (t0) cc_final: 0.8736 (t0) REVERT: r 6 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8561 (ttm110) REVERT: r 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8982 (t0) REVERT: t 12 ASP cc_start: 0.7807 (t0) cc_final: 0.7456 (t0) REVERT: u 10 ASP cc_start: 0.9408 (t0) cc_final: 0.8836 (t0) REVERT: v 6 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: v 10 ASP cc_start: 0.9287 (t0) cc_final: 0.8890 (t0) REVERT: w 12 ASP cc_start: 0.8268 (t70) cc_final: 0.7874 (t0) REVERT: x 6 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8631 (ttm110) REVERT: x 10 ASP cc_start: 0.9093 (t0) cc_final: 0.8713 (t0) REVERT: y 12 ASP cc_start: 0.7907 (t70) cc_final: 0.7641 (t0) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.3659 time to fit residues: 242.5837 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 : 1.075 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084924 restraints weight = 19424.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087115 restraints weight = 10126.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088564 restraints weight = 5955.663| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.210 Angle : 0.639 4.888 12636 Z= 0.332 Chirality : 0.039 0.122 1456 Planarity : 0.008 0.052 1716 Dihedral : 3.632 13.151 1404 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 0.89 (0.26), residues: 1092 helix: 0.91 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.91 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG m 6 *********************** 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 : 1.119 Fit side-chains REVERT: A 12 ASP cc_start: 0.7706 (t70) cc_final: 0.7430 (t70) REVERT: A 22 ARG cc_start: 0.9357 (tpp-160) cc_final: 0.8882 (tpp-160) REVERT: B 6 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8478 (ttm110) REVERT: B 10 ASP cc_start: 0.9268 (t0) cc_final: 0.8953 (t0) REVERT: B 15 VAL cc_start: 0.9320 (p) cc_final: 0.9113 (p) REVERT: C 22 ARG cc_start: 0.9075 (tpp80) cc_final: 0.8457 (ttm110) REVERT: E 10 ASP cc_start: 0.9228 (t0) cc_final: 0.8696 (t0) REVERT: E 23 LEU cc_start: 0.8755 (mm) cc_final: 0.8264 (mm) REVERT: F 10 ASP cc_start: 0.9189 (t0) cc_final: 0.8897 (t0) REVERT: F 22 ARG cc_start: 0.9074 (tpp-160) cc_final: 0.8870 (tpp-160) REVERT: G 10 ASP cc_start: 0.9206 (t0) cc_final: 0.8867 (t0) REVERT: G 22 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8750 (ttm-80) REVERT: H 21 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8612 (mmm-85) REVERT: I 5 GLU cc_start: 0.9063 (mp0) cc_final: 0.8736 (mm-30) REVERT: I 12 ASP cc_start: 0.7929 (t0) cc_final: 0.7701 (t0) REVERT: J 6 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8413 (ttm110) REVERT: J 22 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8527 (tpp-160) REVERT: K 5 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8805 (mm-30) REVERT: K 10 ASP cc_start: 0.9371 (t0) cc_final: 0.9027 (t0) REVERT: L 10 ASP cc_start: 0.9206 (t0) cc_final: 0.8917 (t0) REVERT: L 23 LEU cc_start: 0.8702 (mm) cc_final: 0.8497 (mm) REVERT: M 6 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8550 (ttm110) REVERT: M 10 ASP cc_start: 0.9300 (t0) cc_final: 0.8891 (t0) REVERT: N 6 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8364 (ttm110) REVERT: N 10 ASP cc_start: 0.9220 (t0) cc_final: 0.8950 (t0) REVERT: O 10 ASP cc_start: 0.9255 (t0) cc_final: 0.8679 (t0) REVERT: Q 12 ASP cc_start: 0.8244 (t70) cc_final: 0.8034 (t70) REVERT: S 6 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: V 5 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8604 (mm-30) REVERT: W 5 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8576 (mm-30) REVERT: W 21 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8667 (mmm-85) REVERT: W 22 ARG cc_start: 0.8876 (tpp-160) cc_final: 0.8531 (ttm110) REVERT: X 21 ARG cc_start: 0.8969 (mmm-85) cc_final: 0.8693 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9263 (t0) cc_final: 0.8976 (t0) REVERT: Z 10 ASP cc_start: 0.9139 (t0) cc_final: 0.8822 (t0) REVERT: b 10 ASP cc_start: 0.9144 (t0) cc_final: 0.8572 (t0) REVERT: b 12 ASP cc_start: 0.7814 (t0) cc_final: 0.7443 (t0) REVERT: c 12 ASP cc_start: 0.8452 (t70) cc_final: 0.8242 (t0) REVERT: d 10 ASP cc_start: 0.9254 (t0) cc_final: 0.8929 (t0) REVERT: d 23 LEU cc_start: 0.7854 (mt) cc_final: 0.7486 (mt) REVERT: e 10 ASP cc_start: 0.9262 (t0) cc_final: 0.9003 (t0) REVERT: f 10 ASP cc_start: 0.9234 (t0) cc_final: 0.8923 (t0) REVERT: g 10 ASP cc_start: 0.9174 (t0) cc_final: 0.8777 (t0) REVERT: i 10 ASP cc_start: 0.9204 (t0) cc_final: 0.8627 (t0) REVERT: j 6 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8671 (ttm110) REVERT: j 10 ASP cc_start: 0.9145 (t0) cc_final: 0.8811 (t0) REVERT: k 10 ASP cc_start: 0.9376 (t0) cc_final: 0.8923 (t0) REVERT: l 10 ASP cc_start: 0.9291 (t0) cc_final: 0.8946 (t0) REVERT: l 21 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7943 (tpp80) REVERT: m 10 ASP cc_start: 0.9355 (t0) cc_final: 0.8971 (t0) REVERT: n 6 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8774 (ttm110) REVERT: n 21 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8519 (mmm-85) REVERT: n 23 LEU cc_start: 0.8278 (mm) cc_final: 0.7427 (pp) REVERT: o 10 ASP cc_start: 0.9310 (t0) cc_final: 0.8830 (t0) REVERT: p 10 ASP cc_start: 0.9235 (t0) cc_final: 0.8705 (t0) REVERT: q 10 ASP cc_start: 0.9132 (t0) cc_final: 0.8706 (t0) REVERT: r 10 ASP cc_start: 0.9294 (t0) cc_final: 0.8976 (t0) REVERT: u 10 ASP cc_start: 0.9319 (t0) cc_final: 0.8947 (t0) REVERT: u 22 ARG cc_start: 0.9265 (tpp80) cc_final: 0.8970 (ttm-80) REVERT: v 6 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8247 (ttm-80) REVERT: v 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8832 (t0) REVERT: w 5 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8419 (mm-30) REVERT: w 12 ASP cc_start: 0.8141 (t70) cc_final: 0.7799 (t0) REVERT: x 6 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8510 (ttm110) REVERT: x 10 ASP cc_start: 0.9069 (t0) cc_final: 0.8712 (t0) REVERT: z 12 ASP cc_start: 0.8429 (t70) cc_final: 0.8216 (t0) REVERT: z 15 VAL cc_start: 0.9045 (p) cc_final: 0.8801 (m) outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 0.3759 time to fit residues: 243.2946 Evaluate side-chains 506 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.0270 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.0060 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.0060 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.091455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083210 restraints weight = 19651.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085530 restraints weight = 10167.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.087086 restraints weight = 5998.198| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9412 Z= 0.229 Angle : 0.672 5.112 12636 Z= 0.349 Chirality : 0.039 0.118 1456 Planarity : 0.009 0.057 1716 Dihedral : 3.690 11.455 1404 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.14 (0.27), residues: 1092 helix: 1.08 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.85 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG m 6 *********************** 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 523 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.062 Fit side-chains REVERT: A 12 ASP cc_start: 0.7525 (t70) cc_final: 0.7287 (t70) REVERT: A 22 ARG cc_start: 0.9295 (tpp-160) cc_final: 0.9006 (tpp-160) REVERT: B 6 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8564 (ttm110) REVERT: B 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8932 (t0) REVERT: C 22 ARG cc_start: 0.9058 (tpp80) cc_final: 0.8567 (ttm110) REVERT: D 22 ARG cc_start: 0.9204 (tpp-160) cc_final: 0.8898 (tpp-160) REVERT: E 10 ASP cc_start: 0.9267 (t0) cc_final: 0.8700 (t0) REVERT: F 10 ASP cc_start: 0.9227 (t0) cc_final: 0.8889 (t0) REVERT: F 22 ARG cc_start: 0.9002 (tpp-160) cc_final: 0.8799 (tpp-160) REVERT: G 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8878 (t0) REVERT: H 21 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8611 (mmm-85) REVERT: H 23 LEU cc_start: 0.8448 (mm) cc_final: 0.7732 (mm) REVERT: I 5 GLU cc_start: 0.9097 (mp0) cc_final: 0.8726 (mm-30) REVERT: J 6 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8465 (ttm110) REVERT: K 5 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8876 (mm-30) REVERT: K 10 ASP cc_start: 0.9372 (t0) cc_final: 0.9036 (t0) REVERT: L 10 ASP cc_start: 0.9198 (t0) cc_final: 0.8942 (t0) REVERT: M 6 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8540 (ttm110) REVERT: M 10 ASP cc_start: 0.9267 (t0) cc_final: 0.8814 (t0) REVERT: N 6 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8466 (ttm110) REVERT: N 10 ASP cc_start: 0.9203 (t0) cc_final: 0.8952 (t0) REVERT: O 10 ASP cc_start: 0.9274 (t0) cc_final: 0.8689 (t0) REVERT: V 10 ASP cc_start: 0.9287 (t0) cc_final: 0.8835 (t0) REVERT: W 5 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8666 (mm-30) REVERT: W 21 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8749 (mmm-85) REVERT: X 10 ASP cc_start: 0.9072 (t0) cc_final: 0.8765 (t0) REVERT: Y 10 ASP cc_start: 0.9314 (t0) cc_final: 0.9030 (t0) REVERT: Z 10 ASP cc_start: 0.9138 (t0) cc_final: 0.8823 (t0) REVERT: b 10 ASP cc_start: 0.9112 (t0) cc_final: 0.8547 (t0) REVERT: b 12 ASP cc_start: 0.7786 (t0) cc_final: 0.7338 (t0) REVERT: c 12 ASP cc_start: 0.8631 (t70) cc_final: 0.8380 (t0) REVERT: d 10 ASP cc_start: 0.9314 (t0) cc_final: 0.8980 (t0) REVERT: d 23 LEU cc_start: 0.7940 (mt) cc_final: 0.7613 (mt) REVERT: e 10 ASP cc_start: 0.9283 (t0) cc_final: 0.8983 (t0) REVERT: f 2 GLU cc_start: 0.8503 (mp0) cc_final: 0.8190 (mm-30) REVERT: f 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8889 (t0) REVERT: f 23 LEU cc_start: 0.8185 (mm) cc_final: 0.7843 (pp) REVERT: g 10 ASP cc_start: 0.9186 (t0) cc_final: 0.8744 (t0) REVERT: i 10 ASP cc_start: 0.9218 (t0) cc_final: 0.8642 (t0) REVERT: j 6 ARG cc_start: 0.8991 (ttm110) cc_final: 0.8663 (ttm110) REVERT: j 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8765 (t0) REVERT: k 10 ASP cc_start: 0.9379 (t0) cc_final: 0.8943 (t0) REVERT: l 21 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7961 (tpp80) REVERT: m 10 ASP cc_start: 0.9408 (t0) cc_final: 0.8985 (t0) REVERT: n 21 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8563 (mmm-85) REVERT: o 10 ASP cc_start: 0.9296 (t0) cc_final: 0.8844 (t0) REVERT: p 10 ASP cc_start: 0.9238 (t0) cc_final: 0.8603 (t0) REVERT: p 23 LEU cc_start: 0.8081 (mm) cc_final: 0.7393 (pp) REVERT: q 10 ASP cc_start: 0.9173 (t0) cc_final: 0.8710 (t0) REVERT: r 10 ASP cc_start: 0.9279 (t0) cc_final: 0.8948 (t0) REVERT: r 21 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8713 (mmm-85) REVERT: u 10 ASP cc_start: 0.9459 (t0) cc_final: 0.8982 (t0) REVERT: v 10 ASP cc_start: 0.9181 (t0) cc_final: 0.8772 (t0) REVERT: w 5 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8519 (mm-30) REVERT: w 12 ASP cc_start: 0.8102 (t70) cc_final: 0.7743 (t0) REVERT: x 10 ASP cc_start: 0.9091 (t0) cc_final: 0.8700 (t0) REVERT: z 12 ASP cc_start: 0.8184 (t70) cc_final: 0.7935 (t0) REVERT: z 14 GLU cc_start: 0.8958 (tp30) cc_final: 0.8454 (mt-10) REVERT: z 15 VAL cc_start: 0.8952 (p) cc_final: 0.8750 (m) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.3648 time to fit residues: 231.5604 Evaluate side-chains 504 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.088084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.079433 restraints weight = 20477.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081745 restraints weight = 10817.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083301 restraints weight = 6567.548| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 0.027 9412 Z= 0.299 Angle : 0.742 6.275 12636 Z= 0.379 Chirality : 0.041 0.128 1456 Planarity : 0.009 0.063 1716 Dihedral : 3.882 12.943 1404 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.06 (0.26), residues: 1092 helix: 1.05 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.01 (0.66), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG n 6 *********************** 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 515 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.152 Fit side-chains REVERT: A 12 ASP cc_start: 0.7723 (t70) cc_final: 0.7427 (t70) REVERT: B 6 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8604 (ttm110) REVERT: B 10 ASP cc_start: 0.9327 (t0) cc_final: 0.9026 (t0) REVERT: C 5 GLU cc_start: 0.9046 (mp0) cc_final: 0.8568 (mp0) REVERT: C 22 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8503 (ttm-80) REVERT: E 10 ASP cc_start: 0.9262 (t0) cc_final: 0.8709 (t0) REVERT: F 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8928 (t0) REVERT: F 22 ARG cc_start: 0.9122 (tpp-160) cc_final: 0.8882 (tpp-160) REVERT: G 10 ASP cc_start: 0.9278 (t0) cc_final: 0.8877 (t0) REVERT: H 21 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8683 (mmm-85) REVERT: J 6 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8504 (ttm110) REVERT: J 10 ASP cc_start: 0.9254 (t0) cc_final: 0.8991 (t0) REVERT: K 5 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8874 (mm-30) REVERT: K 10 ASP cc_start: 0.9370 (t0) cc_final: 0.9067 (t0) REVERT: L 10 ASP cc_start: 0.9165 (t0) cc_final: 0.8905 (t0) REVERT: M 6 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8422 (ttm110) REVERT: M 10 ASP cc_start: 0.9262 (t0) cc_final: 0.8813 (t0) REVERT: N 6 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8522 (ttm110) REVERT: N 10 ASP cc_start: 0.9191 (t0) cc_final: 0.8954 (t0) REVERT: O 10 ASP cc_start: 0.9308 (t0) cc_final: 0.8760 (t0) REVERT: Q 12 ASP cc_start: 0.8329 (t70) cc_final: 0.8003 (t0) REVERT: T 6 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8641 (ttm110) REVERT: T 10 ASP cc_start: 0.9215 (t0) cc_final: 0.8765 (t0) REVERT: V 10 ASP cc_start: 0.9329 (t0) cc_final: 0.8842 (t0) REVERT: V 23 LEU cc_start: 0.7220 (tt) cc_final: 0.7017 (pp) REVERT: W 21 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8774 (mmm-85) REVERT: X 10 ASP cc_start: 0.9103 (t0) cc_final: 0.8847 (t0) REVERT: Y 10 ASP cc_start: 0.9257 (t0) cc_final: 0.9005 (t0) REVERT: Z 10 ASP cc_start: 0.9203 (t0) cc_final: 0.8950 (t0) REVERT: b 10 ASP cc_start: 0.9129 (t0) cc_final: 0.8593 (t0) REVERT: c 12 ASP cc_start: 0.8373 (t70) cc_final: 0.8041 (t70) REVERT: d 10 ASP cc_start: 0.9318 (t0) cc_final: 0.9117 (t0) REVERT: d 23 LEU cc_start: 0.7752 (mt) cc_final: 0.7372 (mt) REVERT: e 10 ASP cc_start: 0.9260 (t0) cc_final: 0.8972 (t0) REVERT: f 2 GLU cc_start: 0.8503 (mp0) cc_final: 0.8174 (mm-30) REVERT: f 10 ASP cc_start: 0.9204 (t0) cc_final: 0.8857 (t0) REVERT: g 10 ASP cc_start: 0.9305 (t0) cc_final: 0.8777 (t0) REVERT: h 5 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8884 (mm-30) REVERT: i 5 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8516 (mm-30) REVERT: i 10 ASP cc_start: 0.9295 (t0) cc_final: 0.8703 (t0) REVERT: j 10 ASP cc_start: 0.9233 (t0) cc_final: 0.8962 (t0) REVERT: k 10 ASP cc_start: 0.9371 (t0) cc_final: 0.8913 (t0) REVERT: l 10 ASP cc_start: 0.9359 (t0) cc_final: 0.9059 (t0) REVERT: l 21 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7942 (tpp80) REVERT: m 10 ASP cc_start: 0.9455 (t0) cc_final: 0.9049 (t0) REVERT: n 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8873 (t0) REVERT: n 21 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8559 (mmm-85) REVERT: o 10 ASP cc_start: 0.9366 (t0) cc_final: 0.8917 (t0) REVERT: p 5 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8878 (mm-30) REVERT: p 10 ASP cc_start: 0.9363 (t0) cc_final: 0.8794 (t0) REVERT: q 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8728 (t0) REVERT: r 10 ASP cc_start: 0.9264 (t0) cc_final: 0.8948 (t0) REVERT: u 10 ASP cc_start: 0.9411 (t0) cc_final: 0.8885 (t0) REVERT: v 6 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8420 (ttm-80) REVERT: v 10 ASP cc_start: 0.9252 (t0) cc_final: 0.8837 (t0) REVERT: w 5 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8581 (mm-30) REVERT: w 12 ASP cc_start: 0.8210 (t70) cc_final: 0.7837 (t0) REVERT: x 10 ASP cc_start: 0.9133 (t0) cc_final: 0.8765 (t0) REVERT: z 12 ASP cc_start: 0.8205 (t70) cc_final: 0.7907 (t0) REVERT: z 14 GLU cc_start: 0.8952 (tp30) cc_final: 0.8509 (mt-10) REVERT: z 15 VAL cc_start: 0.9039 (p) cc_final: 0.8784 (m) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.3694 time to fit residues: 231.4131 Evaluate side-chains 495 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.0060 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.094483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086557 restraints weight = 19270.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088822 restraints weight = 10037.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090370 restraints weight = 5924.200| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9412 Z= 0.234 Angle : 0.724 5.523 12636 Z= 0.373 Chirality : 0.039 0.184 1456 Planarity : 0.009 0.068 1716 Dihedral : 3.729 15.539 1404 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 1.32 (0.27), residues: 1092 helix: 1.21 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.82 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG p 6 *********************** 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 513 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.128 Fit side-chains REVERT: A 22 ARG cc_start: 0.9353 (tpp-160) cc_final: 0.9152 (tpp-160) REVERT: B 10 ASP cc_start: 0.9279 (t0) cc_final: 0.8954 (t0) REVERT: E 6 ARG cc_start: 0.8701 (ttm110) cc_final: 0.8443 (ttm-80) REVERT: E 10 ASP cc_start: 0.9249 (t0) cc_final: 0.8730 (t0) REVERT: F 10 ASP cc_start: 0.9210 (t0) cc_final: 0.8858 (t0) REVERT: F 14 GLU cc_start: 0.8960 (tp30) cc_final: 0.8598 (tp30) REVERT: G 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8888 (t0) REVERT: H 21 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8611 (mmm-85) REVERT: H 23 LEU cc_start: 0.8353 (mm) cc_final: 0.8118 (mm) REVERT: I 5 GLU cc_start: 0.8958 (mp0) cc_final: 0.8680 (mm-30) REVERT: I 21 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8427 (tpt-90) REVERT: J 6 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8418 (ttm110) REVERT: K 5 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8842 (mm-30) REVERT: K 10 ASP cc_start: 0.9304 (t0) cc_final: 0.8981 (t0) REVERT: L 10 ASP cc_start: 0.9102 (t0) cc_final: 0.8810 (t0) REVERT: M 6 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8406 (ttm110) REVERT: M 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8795 (t0) REVERT: N 5 GLU cc_start: 0.9025 (mp0) cc_final: 0.8812 (mm-30) REVERT: N 6 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8374 (ttm110) REVERT: O 10 ASP cc_start: 0.9230 (t0) cc_final: 0.8685 (t0) REVERT: Q 21 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8865 (mmm-85) REVERT: R 14 GLU cc_start: 0.9110 (tp30) cc_final: 0.8881 (tp30) REVERT: S 5 GLU cc_start: 0.9034 (mp0) cc_final: 0.8812 (mp0) REVERT: T 6 ARG cc_start: 0.8880 (ttm110) cc_final: 0.8548 (ttm110) REVERT: V 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8904 (t0) REVERT: W 21 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9295 (t0) cc_final: 0.8984 (t0) REVERT: Z 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8808 (t0) REVERT: b 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8540 (t0) REVERT: b 23 LEU cc_start: 0.8486 (mm) cc_final: 0.8206 (pp) REVERT: d 10 ASP cc_start: 0.9320 (t0) cc_final: 0.8826 (t0) REVERT: d 23 LEU cc_start: 0.7891 (mt) cc_final: 0.7638 (mt) REVERT: e 10 ASP cc_start: 0.9275 (t0) cc_final: 0.8961 (t0) REVERT: f 2 GLU cc_start: 0.8531 (mp0) cc_final: 0.8315 (mm-30) REVERT: f 10 ASP cc_start: 0.9166 (t0) cc_final: 0.8878 (t0) REVERT: f 23 LEU cc_start: 0.8032 (mm) cc_final: 0.7532 (pp) REVERT: g 10 ASP cc_start: 0.9284 (t0) cc_final: 0.8946 (t0) REVERT: g 13 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7830 (ttm170) REVERT: i 10 ASP cc_start: 0.9196 (t0) cc_final: 0.8616 (t0) REVERT: j 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8797 (t0) REVERT: k 10 ASP cc_start: 0.9329 (t0) cc_final: 0.8969 (t0) REVERT: l 6 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8612 (ttm110) REVERT: l 21 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7981 (tpp80) REVERT: l 23 LEU cc_start: 0.8045 (mm) cc_final: 0.7156 (pp) REVERT: m 10 ASP cc_start: 0.9392 (t0) cc_final: 0.8975 (t0) REVERT: o 10 ASP cc_start: 0.9291 (t0) cc_final: 0.8887 (t0) REVERT: p 6 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8642 (ttp-110) REVERT: p 10 ASP cc_start: 0.9213 (t0) cc_final: 0.8640 (t0) REVERT: q 10 ASP cc_start: 0.9144 (t0) cc_final: 0.8711 (t0) REVERT: r 10 ASP cc_start: 0.9185 (t0) cc_final: 0.8951 (t0) REVERT: r 21 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8516 (mmm-85) REVERT: t 6 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8282 (ttm110) REVERT: u 10 ASP cc_start: 0.9458 (t0) cc_final: 0.9092 (t0) REVERT: v 6 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8253 (ttm-80) REVERT: v 10 ASP cc_start: 0.9195 (t0) cc_final: 0.8822 (t0) REVERT: w 5 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8605 (mm-30) REVERT: w 12 ASP cc_start: 0.8050 (t70) cc_final: 0.7714 (t0) REVERT: x 10 ASP cc_start: 0.9037 (t0) cc_final: 0.8647 (t0) REVERT: x 23 LEU cc_start: 0.7333 (mt) cc_final: 0.6998 (mt) REVERT: z 14 GLU cc_start: 0.8862 (tp30) cc_final: 0.8356 (mt-10) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3831 time to fit residues: 237.8396 Evaluate side-chains 490 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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: 8.9990 chunk 98 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.094681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.086137 restraints weight = 19709.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088512 restraints weight = 10317.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090141 restraints weight = 6152.592| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6666 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= 0.250 Angle : 0.749 8.486 12636 Z= 0.385 Chirality : 0.039 0.171 1456 Planarity : 0.009 0.065 1716 Dihedral : 3.774 13.740 1404 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 1.32 (0.27), residues: 1092 helix: 1.19 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.70 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 6 ********************** 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 499 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 1.065 Fit side-chains REVERT: A 12 ASP cc_start: 0.7702 (t70) cc_final: 0.7406 (t0) REVERT: A 22 ARG cc_start: 0.9337 (tpp-160) cc_final: 0.9107 (tpp-160) REVERT: A 23 LEU cc_start: 0.8130 (mm) cc_final: 0.7885 (mm) REVERT: B 10 ASP cc_start: 0.9288 (t0) cc_final: 0.8987 (t0) REVERT: B 15 VAL cc_start: 0.9198 (p) cc_final: 0.8984 (p) REVERT: E 10 ASP cc_start: 0.9267 (t0) cc_final: 0.8772 (t0) REVERT: F 10 ASP cc_start: 0.9223 (t0) cc_final: 0.8845 (t0) REVERT: G 10 ASP cc_start: 0.9243 (t0) cc_final: 0.8862 (t0) REVERT: H 21 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8653 (mmm-85) REVERT: I 14 GLU cc_start: 0.8804 (tp30) cc_final: 0.8469 (tp30) REVERT: J 6 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8453 (ttm110) REVERT: K 10 ASP cc_start: 0.9332 (t0) cc_final: 0.8993 (t0) REVERT: K 23 LEU cc_start: 0.8325 (mm) cc_final: 0.8092 (mm) REVERT: L 10 ASP cc_start: 0.9084 (t0) cc_final: 0.8788 (t0) REVERT: L 23 LEU cc_start: 0.8626 (mm) cc_final: 0.8171 (mm) REVERT: M 6 ARG cc_start: 0.8664 (ttm110) cc_final: 0.8432 (ttm110) REVERT: M 10 ASP cc_start: 0.9238 (t0) cc_final: 0.8827 (t0) REVERT: N 6 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8379 (ttm110) REVERT: O 10 ASP cc_start: 0.9256 (t0) cc_final: 0.8729 (t0) REVERT: R 14 GLU cc_start: 0.9165 (tp30) cc_final: 0.8922 (tp30) REVERT: V 10 ASP cc_start: 0.9345 (t0) cc_final: 0.8914 (t0) REVERT: W 21 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8116 (tpt-90) REVERT: Y 10 ASP cc_start: 0.9322 (t0) cc_final: 0.9058 (t0) REVERT: Z 4 LEU cc_start: 0.9308 (mm) cc_final: 0.9092 (mm) REVERT: Z 10 ASP cc_start: 0.9096 (t0) cc_final: 0.8845 (t0) REVERT: b 10 ASP cc_start: 0.9072 (t0) cc_final: 0.8567 (t0) REVERT: b 23 LEU cc_start: 0.8253 (mm) cc_final: 0.8021 (tt) REVERT: d 10 ASP cc_start: 0.9376 (t0) cc_final: 0.8864 (t0) REVERT: d 23 LEU cc_start: 0.7927 (mt) cc_final: 0.7650 (mt) REVERT: e 5 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8649 (mm-30) REVERT: e 10 ASP cc_start: 0.9292 (t0) cc_final: 0.8996 (t0) REVERT: f 2 GLU cc_start: 0.8592 (mp0) cc_final: 0.8321 (mm-30) REVERT: f 10 ASP cc_start: 0.9082 (t0) cc_final: 0.8716 (t0) REVERT: f 23 LEU cc_start: 0.8123 (mm) cc_final: 0.7910 (mt) REVERT: g 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8937 (t0) REVERT: i 10 ASP cc_start: 0.9221 (t0) cc_final: 0.8645 (t0) REVERT: j 10 ASP cc_start: 0.9208 (t0) cc_final: 0.8816 (t0) REVERT: k 10 ASP cc_start: 0.9376 (t0) cc_final: 0.8973 (t0) REVERT: l 6 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8570 (ttm110) REVERT: l 21 ARG cc_start: 0.8232 (tpp80) cc_final: 0.8021 (tpp80) REVERT: m 10 ASP cc_start: 0.9406 (t0) cc_final: 0.9058 (t0) REVERT: n 10 ASP cc_start: 0.9084 (t0) cc_final: 0.8724 (t0) REVERT: n 15 VAL cc_start: 0.9240 (m) cc_final: 0.8989 (m) REVERT: o 10 ASP cc_start: 0.9349 (t0) cc_final: 0.8879 (t0) REVERT: p 6 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8646 (ttp-110) REVERT: p 10 ASP cc_start: 0.9243 (t0) cc_final: 0.8689 (t0) REVERT: q 10 ASP cc_start: 0.9161 (t0) cc_final: 0.8699 (t0) REVERT: r 10 ASP cc_start: 0.9183 (t0) cc_final: 0.8900 (t0) REVERT: r 12 ASP cc_start: 0.7723 (t0) cc_final: 0.7466 (t0) REVERT: t 6 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8436 (ttm110) REVERT: u 10 ASP cc_start: 0.9447 (t0) cc_final: 0.9095 (t0) REVERT: v 6 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8294 (ttm-80) REVERT: v 10 ASP cc_start: 0.9165 (t0) cc_final: 0.8804 (t0) REVERT: w 5 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8654 (mm-30) REVERT: w 12 ASP cc_start: 0.8099 (t70) cc_final: 0.7750 (t0) REVERT: w 21 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8910 (mmm-85) REVERT: x 10 ASP cc_start: 0.9049 (t0) cc_final: 0.8680 (t0) REVERT: x 23 LEU cc_start: 0.7294 (mt) cc_final: 0.7029 (mt) REVERT: z 14 GLU cc_start: 0.8942 (tp30) cc_final: 0.8516 (mt-10) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3656 time to fit residues: 222.1321 Evaluate side-chains 478 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 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 = 0.3208 r_free = 0.3208 target = 0.091726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083061 restraints weight = 19806.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085409 restraints weight = 10501.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087024 restraints weight = 6323.861| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.6674 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= 0.294 Angle : 0.776 8.625 12636 Z= 0.396 Chirality : 0.041 0.124 1456 Planarity : 0.009 0.070 1716 Dihedral : 3.938 16.157 1404 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.27), residues: 1092 helix: 1.16 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.84 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 6 =============================================================================== Job complete usr+sys time: 3832.83 seconds wall clock time: 68 minutes 26.53 seconds (4106.53 seconds total)