Starting phenix.real_space_refine on Tue Sep 24 22:34:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_0252.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_0252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_0252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_0252.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/09_2024/6hqe_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-5461/modules/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, s, r, u, t, w, v, y, x, z Time building chain proxies: 1.93, per 1000 atoms: 0.21 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: 2.29 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: 1.03 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: 2.28 Time building geometry restraints manager: 2.65 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 19.020 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 1.101 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: 0.3480 time to fit residues: 233.3684 Evaluate side-chains 396 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8461 (ttm110) REVERT: B 10 ASP cc_start: 0.9229 (t0) cc_final: 0.9020 (t0) REVERT: E 5 GLU cc_start: 0.9136 (mp0) cc_final: 0.8886 (mm-30) REVERT: E 10 ASP cc_start: 0.9095 (t0) cc_final: 0.8663 (t0) REVERT: F 10 ASP cc_start: 0.9143 (t0) cc_final: 0.8897 (t0) REVERT: G 21 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8802 (mmm-85) REVERT: H 21 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8480 (mmm-85) REVERT: I 21 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8792 (mmm-85) REVERT: K 10 ASP cc_start: 0.9393 (t0) cc_final: 0.9038 (t0) REVERT: N 10 ASP cc_start: 0.9231 (t0) cc_final: 0.8784 (t0) REVERT: N 21 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8718 (mmm-85) REVERT: O 10 ASP cc_start: 0.9267 (t0) cc_final: 0.8825 (t0) REVERT: S 12 ASP cc_start: 0.7766 (t0) cc_final: 0.7531 (t0) REVERT: U 5 GLU cc_start: 0.9034 (mp0) cc_final: 0.8818 (mm-30) REVERT: V 5 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8742 (mm-30) REVERT: W 21 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8455 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9234 (t0) cc_final: 0.8901 (t0) REVERT: b 5 GLU cc_start: 0.8805 (mp0) cc_final: 0.8591 (mm-30) REVERT: b 10 ASP cc_start: 0.9124 (t0) cc_final: 0.8618 (t0) REVERT: c 12 ASP cc_start: 0.8377 (t70) cc_final: 0.7845 (t70) REVERT: d 10 ASP cc_start: 0.9240 (t0) cc_final: 0.9013 (t0) REVERT: f 10 ASP cc_start: 0.9137 (t0) cc_final: 0.8905 (t0) REVERT: f 21 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8603 (mmm-85) REVERT: g 10 ASP cc_start: 0.9083 (t0) cc_final: 0.8570 (t0) REVERT: i 5 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8783 (mm-30) REVERT: i 10 ASP cc_start: 0.9101 (t0) cc_final: 0.8575 (t0) REVERT: j 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8856 (t0) REVERT: k 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8857 (t0) REVERT: l 6 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8649 (ttm110) REVERT: m 21 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8552 (mmm-85) REVERT: o 5 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8923 (mm-30) REVERT: o 10 ASP cc_start: 0.9375 (t0) cc_final: 0.8813 (t0) REVERT: p 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8767 (t0) REVERT: q 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8749 (t0) REVERT: s 19 VAL cc_start: 0.9619 (t) cc_final: 0.9416 (t) REVERT: u 10 ASP cc_start: 0.9237 (t0) cc_final: 0.8730 (t0) REVERT: v 12 ASP cc_start: 0.7796 (t70) cc_final: 0.7461 (t70) REVERT: x 10 ASP cc_start: 0.9128 (t0) cc_final: 0.8766 (t0) REVERT: x 23 LEU cc_start: 0.8426 (mt) cc_final: 0.8197 (mt) REVERT: y 5 GLU cc_start: 0.8850 (mp0) cc_final: 0.8617 (mm-30) REVERT: y 22 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8704 (ttm110) REVERT: z 5 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8844 (mm-30) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.3594 time to fit residues: 236.8444 Evaluate side-chains 500 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5418 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= 0.227 Angle : 0.610 5.127 12636 Z= 0.316 Chirality : 0.040 0.124 1456 Planarity : 0.009 0.048 1716 Dihedral : 3.925 11.516 1404 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -1.29 (0.25), residues: 1092 helix: -0.63 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.12 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 550 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 1.188 Fit side-chains REVERT: A 12 ASP cc_start: 0.7614 (t70) cc_final: 0.7402 (t70) REVERT: B 6 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8454 (ttm110) REVERT: B 10 ASP cc_start: 0.9254 (t0) cc_final: 0.9026 (t0) REVERT: E 10 ASP cc_start: 0.9065 (t0) cc_final: 0.8669 (t0) REVERT: F 6 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.8622 (ttp-110) REVERT: F 10 ASP cc_start: 0.9175 (t0) cc_final: 0.8869 (t0) REVERT: F 19 VAL cc_start: 0.9473 (t) cc_final: 0.9263 (t) REVERT: G 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8862 (t0) REVERT: G 21 ARG cc_start: 0.9065 (mmm-85) cc_final: 0.8852 (mmm-85) REVERT: H 21 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8606 (mmm-85) REVERT: J 5 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8643 (mm-30) REVERT: J 6 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8269 (ttm110) REVERT: J 21 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8610 (mmm-85) REVERT: K 5 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8707 (mm-30) REVERT: K 10 ASP cc_start: 0.9286 (t0) cc_final: 0.9013 (t0) REVERT: M 10 ASP cc_start: 0.9169 (t0) cc_final: 0.8833 (t0) REVERT: N 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8767 (t0) REVERT: O 10 ASP cc_start: 0.9270 (t0) cc_final: 0.8764 (t0) REVERT: S 22 ARG cc_start: 0.9217 (tpp80) cc_final: 0.8890 (ttm-80) REVERT: V 5 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8662 (mm-30) REVERT: W 21 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8575 (mmm-85) REVERT: X 5 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8588 (mm-30) REVERT: Y 10 ASP cc_start: 0.9215 (t0) cc_final: 0.8866 (t0) REVERT: Z 10 ASP cc_start: 0.9206 (t0) cc_final: 0.8880 (t0) REVERT: Z 21 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: a 22 ARG cc_start: 0.9321 (tpp80) cc_final: 0.9118 (tpp80) REVERT: b 6 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8516 (ttm110) REVERT: b 10 ASP cc_start: 0.9113 (t0) cc_final: 0.8624 (t0) REVERT: d 10 ASP cc_start: 0.9255 (t0) cc_final: 0.8952 (t0) REVERT: f 10 ASP cc_start: 0.9164 (t0) cc_final: 0.8894 (t0) REVERT: g 10 ASP cc_start: 0.9042 (t0) cc_final: 0.8485 (t0) REVERT: h 23 LEU cc_start: 0.8496 (mt) cc_final: 0.8173 (mm) REVERT: i 10 ASP cc_start: 0.9104 (t0) cc_final: 0.8571 (t0) REVERT: j 10 ASP cc_start: 0.9117 (t0) cc_final: 0.8728 (t0) REVERT: k 10 ASP cc_start: 0.9252 (t0) cc_final: 0.8793 (t0) REVERT: k 21 ARG cc_start: 0.8935 (mmm-85) cc_final: 0.8482 (mmm-85) REVERT: l 6 ARG cc_start: 0.8974 (ttm110) cc_final: 0.8663 (ttm110) REVERT: m 21 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.8714 (mmm-85) REVERT: n 21 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8490 (mmm-85) REVERT: o 10 ASP cc_start: 0.9304 (t0) cc_final: 0.8843 (t0) REVERT: p 10 ASP cc_start: 0.9245 (t0) cc_final: 0.8768 (t0) REVERT: q 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8644 (t0) REVERT: q 14 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8446 (tp30) REVERT: u 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8829 (t0) REVERT: v 6 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8427 (ttm-80) REVERT: w 12 ASP cc_start: 0.7992 (t70) cc_final: 0.7743 (t70) REVERT: x 6 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8505 (ttm110) REVERT: x 10 ASP cc_start: 0.9125 (t0) cc_final: 0.8766 (t0) REVERT: y 5 GLU cc_start: 0.8881 (mp0) cc_final: 0.8629 (mm-30) REVERT: z 5 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8856 (mm-30) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 0.3544 time to fit residues: 238.8362 Evaluate side-chains 509 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5810 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= 0.186 Angle : 0.591 4.556 12636 Z= 0.308 Chirality : 0.039 0.129 1456 Planarity : 0.008 0.047 1716 Dihedral : 3.682 11.328 1404 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % 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: -0.21 (0.26), residues: 1092 helix: 0.14 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.03 (0.67), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 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 552 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 1.111 Fit side-chains REVERT: B 6 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8384 (ttm110) REVERT: B 10 ASP cc_start: 0.9296 (t0) cc_final: 0.9033 (t0) REVERT: B 15 VAL cc_start: 0.9318 (p) cc_final: 0.9056 (p) REVERT: E 10 ASP cc_start: 0.9140 (t0) cc_final: 0.8636 (t0) REVERT: F 10 ASP cc_start: 0.9151 (t0) cc_final: 0.8868 (t0) REVERT: G 10 ASP cc_start: 0.9170 (t0) cc_final: 0.8836 (t0) REVERT: G 22 ARG cc_start: 0.9112 (tpp80) cc_final: 0.8280 (tpp-160) REVERT: H 21 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8662 (mmm-85) REVERT: I 5 GLU cc_start: 0.9015 (mp0) cc_final: 0.8773 (mm-30) REVERT: J 6 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8251 (ttm110) REVERT: J 21 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8561 (mmm-85) REVERT: K 5 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8710 (mm-30) REVERT: K 10 ASP cc_start: 0.9313 (t0) cc_final: 0.8940 (t0) REVERT: M 10 ASP cc_start: 0.9148 (t0) cc_final: 0.8799 (t0) REVERT: N 6 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8292 (ttm110) REVERT: N 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8803 (t0) REVERT: O 10 ASP cc_start: 0.9247 (t0) cc_final: 0.8694 (t0) REVERT: S 6 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8249 (ttm-80) REVERT: V 5 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8594 (mm-30) REVERT: W 21 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: X 5 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8597 (mm-30) REVERT: Y 10 ASP cc_start: 0.9246 (t0) cc_final: 0.8888 (t0) REVERT: Z 10 ASP cc_start: 0.9194 (t0) cc_final: 0.8894 (t0) REVERT: Z 21 ARG cc_start: 0.8964 (mmm-85) cc_final: 0.8761 (mmm-85) REVERT: b 10 ASP cc_start: 0.9040 (t0) cc_final: 0.8525 (t0) REVERT: c 12 ASP cc_start: 0.8388 (t70) cc_final: 0.8176 (t70) REVERT: d 10 ASP cc_start: 0.9250 (t0) cc_final: 0.8992 (t0) REVERT: f 23 LEU cc_start: 0.8142 (mm) cc_final: 0.7477 (pp) REVERT: g 10 ASP cc_start: 0.9120 (t0) cc_final: 0.8643 (t0) REVERT: i 21 ARG cc_start: 0.8872 (mmm-85) cc_final: 0.8366 (mmm-85) REVERT: j 10 ASP cc_start: 0.9078 (t0) cc_final: 0.8696 (t0) REVERT: k 10 ASP cc_start: 0.9307 (t0) cc_final: 0.8821 (t0) REVERT: l 23 LEU cc_start: 0.7922 (mm) cc_final: 0.6922 (pp) REVERT: m 10 ASP cc_start: 0.9361 (t0) cc_final: 0.9026 (t0) REVERT: n 21 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8578 (mmm-85) REVERT: n 23 LEU cc_start: 0.8256 (mm) cc_final: 0.7343 (pp) REVERT: o 10 ASP cc_start: 0.9322 (t0) cc_final: 0.8880 (t0) REVERT: p 5 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8701 (mm-30) REVERT: p 10 ASP cc_start: 0.9219 (t0) cc_final: 0.8690 (t0) REVERT: p 23 LEU cc_start: 0.8231 (mm) cc_final: 0.7489 (pp) REVERT: q 10 ASP cc_start: 0.9047 (t0) cc_final: 0.8613 (t0) REVERT: q 22 ARG cc_start: 0.9085 (tpp-160) cc_final: 0.8744 (tpp-160) REVERT: r 10 ASP cc_start: 0.9237 (t0) cc_final: 0.8859 (t0) REVERT: r 23 LEU cc_start: 0.8086 (mm) cc_final: 0.7491 (pp) REVERT: u 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8846 (t0) REVERT: v 6 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8215 (ttm-80) REVERT: v 10 ASP cc_start: 0.9204 (t0) cc_final: 0.8853 (t0) REVERT: w 12 ASP cc_start: 0.7954 (t70) cc_final: 0.7728 (t70) REVERT: x 6 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8498 (ttm110) REVERT: x 10 ASP cc_start: 0.9109 (t0) cc_final: 0.8740 (t0) REVERT: y 5 GLU cc_start: 0.8806 (mp0) cc_final: 0.8582 (mm-30) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.3496 time to fit residues: 235.6364 Evaluate side-chains 513 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 69 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 3.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.234 Angle : 0.648 4.762 12636 Z= 0.332 Chirality : 0.040 0.209 1456 Planarity : 0.008 0.047 1716 Dihedral : 3.682 12.419 1404 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.26), residues: 1092 helix: 0.62 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.91 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 539 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 1.167 Fit side-chains REVERT: B 6 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8425 (ttm110) REVERT: B 10 ASP cc_start: 0.9296 (t0) cc_final: 0.8981 (t0) REVERT: C 21 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: E 10 ASP cc_start: 0.9185 (t0) cc_final: 0.8685 (t0) REVERT: F 10 ASP cc_start: 0.9223 (t0) cc_final: 0.8943 (t0) REVERT: G 10 ASP cc_start: 0.9265 (t0) cc_final: 0.8861 (t0) REVERT: I 5 GLU cc_start: 0.9042 (mp0) cc_final: 0.8716 (mm-30) REVERT: K 10 ASP cc_start: 0.9328 (t0) cc_final: 0.8982 (t0) REVERT: M 10 ASP cc_start: 0.9247 (t0) cc_final: 0.8796 (t0) REVERT: N 6 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8322 (ttm110) REVERT: N 10 ASP cc_start: 0.9157 (t0) cc_final: 0.8828 (t0) REVERT: O 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8779 (t0) REVERT: Q 12 ASP cc_start: 0.8084 (t70) cc_final: 0.7869 (t0) REVERT: Q 14 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8675 (tp30) REVERT: S 6 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8238 (ttm-80) REVERT: V 12 ASP cc_start: 0.7836 (t0) cc_final: 0.7627 (t0) REVERT: W 21 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8733 (mmm-85) REVERT: X 10 ASP cc_start: 0.9072 (t0) cc_final: 0.8785 (t0) REVERT: X 21 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8646 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9233 (t0) cc_final: 0.9007 (t0) REVERT: Z 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8949 (t0) REVERT: b 10 ASP cc_start: 0.9089 (t0) cc_final: 0.8547 (t0) REVERT: d 10 ASP cc_start: 0.9285 (t0) cc_final: 0.8968 (t0) REVERT: e 10 ASP cc_start: 0.9290 (t0) cc_final: 0.9088 (t0) REVERT: g 10 ASP cc_start: 0.9152 (t0) cc_final: 0.8727 (t0) REVERT: h 12 ASP cc_start: 0.8152 (t70) cc_final: 0.7944 (t70) REVERT: i 10 ASP cc_start: 0.9215 (t0) cc_final: 0.8708 (t0) REVERT: j 10 ASP cc_start: 0.9148 (t0) cc_final: 0.8836 (t0) REVERT: k 10 ASP cc_start: 0.9350 (t0) cc_final: 0.8866 (t0) REVERT: m 10 ASP cc_start: 0.9363 (t0) cc_final: 0.9035 (t0) REVERT: n 21 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8532 (mmm-85) REVERT: o 10 ASP cc_start: 0.9316 (t0) cc_final: 0.8899 (t0) REVERT: p 5 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8710 (mm-30) REVERT: p 10 ASP cc_start: 0.9256 (t0) cc_final: 0.8710 (t0) REVERT: p 23 LEU cc_start: 0.8331 (mm) cc_final: 0.7527 (pp) REVERT: q 5 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8480 (mm-30) REVERT: q 10 ASP cc_start: 0.9117 (t0) cc_final: 0.8665 (t0) REVERT: q 22 ARG cc_start: 0.9121 (tpp-160) cc_final: 0.8917 (tpp-160) REVERT: r 10 ASP cc_start: 0.9214 (t0) cc_final: 0.8893 (t0) REVERT: t 12 ASP cc_start: 0.7614 (t0) cc_final: 0.7299 (t0) REVERT: u 10 ASP cc_start: 0.9437 (t0) cc_final: 0.8884 (t0) REVERT: v 6 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8342 (ttm-80) REVERT: v 10 ASP cc_start: 0.9260 (t0) cc_final: 0.8964 (t0) REVERT: w 5 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8242 (mm-30) REVERT: w 12 ASP cc_start: 0.7881 (t70) cc_final: 0.7632 (t70) REVERT: x 6 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8539 (ttm110) REVERT: x 10 ASP cc_start: 0.9064 (t0) cc_final: 0.8763 (t0) REVERT: z 5 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8484 (mm-30) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.3553 time to fit residues: 233.9904 Evaluate side-chains 512 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.6219 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= 0.205 Angle : 0.647 4.803 12636 Z= 0.335 Chirality : 0.039 0.122 1456 Planarity : 0.008 0.047 1716 Dihedral : 3.550 10.864 1404 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1092 helix: 1.00 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.88 (0.68), 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 536 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 1.124 Fit side-chains REVERT: A 12 ASP cc_start: 0.7643 (t70) cc_final: 0.7428 (t0) REVERT: B 6 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8457 (ttm110) REVERT: B 10 ASP cc_start: 0.9290 (t0) cc_final: 0.9000 (t0) REVERT: E 10 ASP cc_start: 0.9157 (t0) cc_final: 0.8706 (t0) REVERT: F 10 ASP cc_start: 0.9211 (t0) cc_final: 0.8955 (t0) REVERT: G 10 ASP cc_start: 0.9178 (t0) cc_final: 0.8838 (t0) REVERT: I 5 GLU cc_start: 0.8973 (mp0) cc_final: 0.8592 (mm-30) REVERT: K 10 ASP cc_start: 0.9348 (t0) cc_final: 0.9055 (t0) REVERT: M 6 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8499 (ttm110) REVERT: M 10 ASP cc_start: 0.9206 (t0) cc_final: 0.8786 (t0) REVERT: N 6 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8296 (ttm110) REVERT: O 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8788 (t0) REVERT: S 6 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8222 (ttm-80) REVERT: T 23 LEU cc_start: 0.8052 (mm) cc_final: 0.6498 (pp) REVERT: V 12 ASP cc_start: 0.7764 (t0) cc_final: 0.7540 (t0) REVERT: W 5 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8425 (mm-30) REVERT: W 21 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8668 (mmm-85) REVERT: X 21 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8600 (mmm-85) REVERT: X 23 LEU cc_start: 0.7732 (mt) cc_final: 0.7532 (mt) REVERT: Y 10 ASP cc_start: 0.9247 (t0) cc_final: 0.8989 (t0) REVERT: Z 10 ASP cc_start: 0.9146 (t0) cc_final: 0.8875 (t0) REVERT: b 6 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8508 (ttm110) REVERT: b 10 ASP cc_start: 0.9054 (t0) cc_final: 0.8537 (t0) REVERT: d 10 ASP cc_start: 0.9258 (t0) cc_final: 0.8994 (t0) REVERT: d 23 LEU cc_start: 0.8412 (mm) cc_final: 0.7685 (pp) REVERT: e 10 ASP cc_start: 0.9268 (t0) cc_final: 0.9031 (t0) REVERT: f 23 LEU cc_start: 0.7988 (mm) cc_final: 0.7466 (pp) REVERT: g 10 ASP cc_start: 0.9167 (t0) cc_final: 0.8734 (t0) REVERT: j 10 ASP cc_start: 0.9160 (t0) cc_final: 0.8835 (t0) REVERT: k 10 ASP cc_start: 0.9342 (t0) cc_final: 0.8911 (t0) REVERT: l 6 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8268 (ttm110) REVERT: l 23 LEU cc_start: 0.8063 (mm) cc_final: 0.7282 (pp) REVERT: m 10 ASP cc_start: 0.9319 (t0) cc_final: 0.8996 (t0) REVERT: n 21 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8583 (mmm-85) REVERT: o 10 ASP cc_start: 0.9297 (t0) cc_final: 0.8940 (t0) REVERT: p 10 ASP cc_start: 0.9121 (t0) cc_final: 0.8685 (t0) REVERT: q 10 ASP cc_start: 0.9122 (t0) cc_final: 0.8736 (t0) REVERT: r 10 ASP cc_start: 0.9256 (t0) cc_final: 0.8994 (t0) REVERT: t 12 ASP cc_start: 0.7583 (t0) cc_final: 0.7322 (t0) REVERT: u 10 ASP cc_start: 0.9446 (t0) cc_final: 0.9114 (t0) REVERT: v 6 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: v 10 ASP cc_start: 0.9171 (t0) cc_final: 0.8888 (t0) REVERT: w 12 ASP cc_start: 0.7781 (t70) cc_final: 0.7574 (t0) REVERT: x 10 ASP cc_start: 0.9059 (t0) cc_final: 0.8724 (t0) REVERT: y 22 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8471 (ttm110) REVERT: z 5 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8459 (mm-30) REVERT: z 12 ASP cc_start: 0.8365 (t0) cc_final: 0.8075 (t0) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.3595 time to fit residues: 233.7068 Evaluate side-chains 503 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 0.0770 chunk 40 optimal weight: 0.0370 chunk 59 optimal weight: 9.9990 overall best weight: 3.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9412 Z= 0.235 Angle : 0.683 6.402 12636 Z= 0.352 Chirality : 0.039 0.122 1456 Planarity : 0.009 0.057 1716 Dihedral : 3.634 12.560 1404 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 1.27 (0.27), residues: 1092 helix: 1.17 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.79 (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 514 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 1.656 Fit side-chains REVERT: A 12 ASP cc_start: 0.7590 (t70) cc_final: 0.7383 (t0) REVERT: B 6 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8490 (ttm110) REVERT: B 10 ASP cc_start: 0.9310 (t0) cc_final: 0.9004 (t0) REVERT: C 21 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8707 (mmm-85) REVERT: E 10 ASP cc_start: 0.9207 (t0) cc_final: 0.8710 (t0) REVERT: F 10 ASP cc_start: 0.9237 (t0) cc_final: 0.8977 (t0) REVERT: G 10 ASP cc_start: 0.9246 (t0) cc_final: 0.8869 (t0) REVERT: I 5 GLU cc_start: 0.8962 (mp0) cc_final: 0.8615 (mm-30) REVERT: K 10 ASP cc_start: 0.9306 (t0) cc_final: 0.9018 (t0) REVERT: M 6 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8273 (ttm110) REVERT: M 10 ASP cc_start: 0.9254 (t0) cc_final: 0.8865 (t0) REVERT: O 10 ASP cc_start: 0.9269 (t0) cc_final: 0.8818 (t0) REVERT: R 14 GLU cc_start: 0.8964 (tp30) cc_final: 0.8754 (tp30) REVERT: T 23 LEU cc_start: 0.8199 (mm) cc_final: 0.7942 (mt) REVERT: V 10 ASP cc_start: 0.9226 (t0) cc_final: 0.8866 (t0) REVERT: W 5 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8490 (mm-30) REVERT: W 21 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8772 (mmm-85) REVERT: X 10 ASP cc_start: 0.9047 (t0) cc_final: 0.8841 (t0) REVERT: Y 10 ASP cc_start: 0.9269 (t0) cc_final: 0.9036 (t0) REVERT: Z 10 ASP cc_start: 0.9173 (t0) cc_final: 0.8900 (t0) REVERT: b 10 ASP cc_start: 0.9100 (t0) cc_final: 0.8581 (t0) REVERT: c 12 ASP cc_start: 0.8415 (t70) cc_final: 0.8092 (t70) REVERT: d 10 ASP cc_start: 0.9264 (t0) cc_final: 0.9044 (t0) REVERT: g 10 ASP cc_start: 0.9165 (t0) cc_final: 0.8737 (t0) REVERT: i 10 ASP cc_start: 0.9193 (t0) cc_final: 0.8677 (t0) REVERT: j 10 ASP cc_start: 0.9158 (t0) cc_final: 0.8870 (t0) REVERT: k 10 ASP cc_start: 0.9362 (t0) cc_final: 0.8959 (t0) REVERT: m 10 ASP cc_start: 0.9339 (t0) cc_final: 0.9028 (t0) REVERT: n 21 ARG cc_start: 0.8839 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: o 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8964 (t0) REVERT: p 10 ASP cc_start: 0.9160 (t0) cc_final: 0.8652 (t0) REVERT: q 10 ASP cc_start: 0.9176 (t0) cc_final: 0.8764 (t0) REVERT: r 10 ASP cc_start: 0.9223 (t0) cc_final: 0.9008 (t0) REVERT: t 6 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8473 (ttm110) REVERT: t 12 ASP cc_start: 0.7709 (t0) cc_final: 0.7433 (t0) REVERT: u 10 ASP cc_start: 0.9412 (t0) cc_final: 0.9076 (t0) REVERT: v 6 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8424 (ttm-80) REVERT: v 10 ASP cc_start: 0.9155 (t0) cc_final: 0.8805 (t0) REVERT: w 12 ASP cc_start: 0.7797 (t70) cc_final: 0.7546 (t0) REVERT: w 21 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8621 (tmm-80) REVERT: w 22 ARG cc_start: 0.9248 (tpp-160) cc_final: 0.8897 (tpp-160) REVERT: x 10 ASP cc_start: 0.9063 (t0) cc_final: 0.8743 (t0) REVERT: y 22 ARG cc_start: 0.9203 (tpp80) cc_final: 0.8646 (ttm110) REVERT: z 14 GLU cc_start: 0.8534 (tp30) cc_final: 0.8162 (mt-10) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.3629 time to fit residues: 228.3843 Evaluate side-chains 493 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 78 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9412 Z= 0.234 Angle : 0.704 8.515 12636 Z= 0.362 Chirality : 0.039 0.141 1456 Planarity : 0.009 0.059 1716 Dihedral : 3.603 10.857 1404 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: 1.47 (0.27), residues: 1092 helix: 1.32 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.79 (0.68), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 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 516 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 1.317 Fit side-chains REVERT: A 12 ASP cc_start: 0.7549 (t70) cc_final: 0.7343 (t0) REVERT: B 6 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8501 (ttm110) REVERT: B 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8997 (t0) REVERT: E 10 ASP cc_start: 0.9182 (t0) cc_final: 0.8694 (t0) REVERT: F 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8978 (t0) REVERT: G 10 ASP cc_start: 0.9235 (t0) cc_final: 0.8879 (t0) REVERT: I 5 GLU cc_start: 0.8947 (mp0) cc_final: 0.8599 (mm-30) REVERT: K 10 ASP cc_start: 0.9285 (t0) cc_final: 0.9014 (t0) REVERT: M 6 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8296 (ttm110) REVERT: M 10 ASP cc_start: 0.9186 (t0) cc_final: 0.8874 (t0) REVERT: M 23 LEU cc_start: 0.8484 (mm) cc_final: 0.8252 (mm) REVERT: O 10 ASP cc_start: 0.9255 (t0) cc_final: 0.8875 (t0) REVERT: V 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8814 (t0) REVERT: V 23 LEU cc_start: 0.6899 (tt) cc_final: 0.6630 (pp) REVERT: W 21 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8689 (mmm-85) REVERT: X 6 ARG cc_start: 0.8957 (ttp-110) cc_final: 0.8630 (ttm110) REVERT: Y 10 ASP cc_start: 0.9268 (t0) cc_final: 0.9046 (t0) REVERT: Z 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8890 (t0) REVERT: Z 21 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8577 (mmm-85) REVERT: b 10 ASP cc_start: 0.9089 (t0) cc_final: 0.8613 (t0) REVERT: d 10 ASP cc_start: 0.9270 (t0) cc_final: 0.9043 (t0) REVERT: e 10 ASP cc_start: 0.9279 (t0) cc_final: 0.9040 (t0) REVERT: f 23 LEU cc_start: 0.8116 (mm) cc_final: 0.7758 (pp) REVERT: g 10 ASP cc_start: 0.9143 (t0) cc_final: 0.8733 (t0) REVERT: h 5 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8829 (mm-30) REVERT: i 5 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8451 (mm-30) REVERT: i 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8683 (t0) REVERT: j 10 ASP cc_start: 0.9143 (t0) cc_final: 0.8860 (t0) REVERT: k 10 ASP cc_start: 0.9326 (t0) cc_final: 0.8953 (t0) REVERT: m 10 ASP cc_start: 0.9345 (t0) cc_final: 0.9022 (t0) REVERT: n 21 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8588 (mmm-85) REVERT: o 10 ASP cc_start: 0.9289 (t0) cc_final: 0.8993 (t0) REVERT: p 5 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8795 (mm-30) REVERT: p 10 ASP cc_start: 0.9105 (t0) cc_final: 0.8717 (t0) REVERT: q 10 ASP cc_start: 0.9165 (t0) cc_final: 0.8789 (t0) REVERT: r 10 ASP cc_start: 0.9166 (t0) cc_final: 0.8949 (t0) REVERT: r 21 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8658 (mmm-85) REVERT: t 12 ASP cc_start: 0.7734 (t0) cc_final: 0.7441 (t0) REVERT: u 10 ASP cc_start: 0.9419 (t0) cc_final: 0.9074 (t0) REVERT: v 6 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8354 (ttm-80) REVERT: v 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8799 (t0) REVERT: w 12 ASP cc_start: 0.7785 (t70) cc_final: 0.7541 (t0) REVERT: x 10 ASP cc_start: 0.9070 (t0) cc_final: 0.8723 (t0) REVERT: y 22 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8663 (ttm110) REVERT: z 5 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8574 (mm-30) REVERT: z 14 GLU cc_start: 0.8587 (tp30) cc_final: 0.7992 (mt-10) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.3557 time to fit residues: 223.4365 Evaluate side-chains 489 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 0.0070 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 1.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9412 Z= 0.228 Angle : 0.707 6.820 12636 Z= 0.364 Chirality : 0.038 0.130 1456 Planarity : 0.009 0.066 1716 Dihedral : 3.574 11.413 1404 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1092 helix: 1.70 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -1.91 (0.53), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 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 511 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 1.117 Fit side-chains REVERT: B 10 ASP cc_start: 0.9286 (t0) cc_final: 0.8983 (t0) REVERT: E 10 ASP cc_start: 0.9172 (t0) cc_final: 0.8725 (t0) REVERT: G 10 ASP cc_start: 0.9218 (t0) cc_final: 0.8864 (t0) REVERT: I 5 GLU cc_start: 0.8831 (mp0) cc_final: 0.8515 (mm-30) REVERT: K 10 ASP cc_start: 0.9290 (t0) cc_final: 0.8996 (t0) REVERT: M 10 ASP cc_start: 0.9233 (t0) cc_final: 0.8978 (t0) REVERT: M 15 VAL cc_start: 0.8888 (p) cc_final: 0.8561 (t) REVERT: N 21 ARG cc_start: 0.8987 (mmm-85) cc_final: 0.8669 (mmm-85) REVERT: O 10 ASP cc_start: 0.9229 (t0) cc_final: 0.9007 (t0) REVERT: V 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8822 (t0) REVERT: W 5 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8519 (mm-30) REVERT: W 21 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8708 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9244 (t0) cc_final: 0.8999 (t0) REVERT: Z 10 ASP cc_start: 0.9151 (t0) cc_final: 0.8878 (t0) REVERT: Z 21 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8603 (mmm-85) REVERT: b 10 ASP cc_start: 0.9048 (t0) cc_final: 0.8580 (t0) REVERT: d 10 ASP cc_start: 0.9324 (t0) cc_final: 0.9034 (t0) REVERT: d 23 LEU cc_start: 0.8322 (mm) cc_final: 0.8120 (mt) REVERT: e 10 ASP cc_start: 0.9289 (t0) cc_final: 0.9028 (t0) REVERT: f 23 LEU cc_start: 0.7883 (mm) cc_final: 0.7547 (pp) REVERT: g 10 ASP cc_start: 0.9169 (t0) cc_final: 0.8924 (t0) REVERT: g 13 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7924 (ttm170) REVERT: i 5 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8469 (mm-30) REVERT: i 10 ASP cc_start: 0.9181 (t0) cc_final: 0.8699 (t0) REVERT: j 10 ASP cc_start: 0.9141 (t0) cc_final: 0.8859 (t0) REVERT: k 10 ASP cc_start: 0.9325 (t0) cc_final: 0.8952 (t0) REVERT: m 10 ASP cc_start: 0.9323 (t0) cc_final: 0.9026 (t0) REVERT: n 12 ASP cc_start: 0.7266 (t0) cc_final: 0.6661 (t0) REVERT: n 21 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8550 (mmm-85) REVERT: o 10 ASP cc_start: 0.9264 (t0) cc_final: 0.8999 (t0) REVERT: p 10 ASP cc_start: 0.9070 (t0) cc_final: 0.8600 (t0) REVERT: q 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8772 (t0) REVERT: r 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8945 (t0) REVERT: r 21 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8570 (mmm-85) REVERT: t 12 ASP cc_start: 0.7714 (t0) cc_final: 0.7399 (t0) REVERT: u 10 ASP cc_start: 0.9425 (t0) cc_final: 0.9116 (t0) REVERT: u 19 VAL cc_start: 0.9494 (t) cc_final: 0.9288 (p) REVERT: v 6 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8418 (ttm-80) REVERT: v 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8886 (t0) REVERT: w 12 ASP cc_start: 0.7757 (t70) cc_final: 0.7537 (t0) REVERT: x 10 ASP cc_start: 0.9016 (t0) cc_final: 0.8732 (t0) REVERT: y 22 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8717 (ttm110) REVERT: z 12 ASP cc_start: 0.7785 (t70) cc_final: 0.7337 (t0) REVERT: z 14 GLU cc_start: 0.8725 (tp30) cc_final: 0.8141 (mt-10) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.3481 time to fit residues: 217.0731 Evaluate side-chains 481 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 overall best weight: 2.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6639 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= 0.246 Angle : 0.745 8.733 12636 Z= 0.380 Chirality : 0.039 0.120 1456 Planarity : 0.009 0.065 1716 Dihedral : 3.631 11.690 1404 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.53 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: 1.53 (0.27), residues: 1092 helix: 1.34 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.67 (0.69), 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 496 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 1.127 Fit side-chains REVERT: B 10 ASP cc_start: 0.9311 (t0) cc_final: 0.8990 (t0) REVERT: D 5 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8695 (mm-30) REVERT: E 10 ASP cc_start: 0.9198 (t0) cc_final: 0.8762 (t0) REVERT: F 12 ASP cc_start: 0.7873 (t70) cc_final: 0.7417 (t70) REVERT: G 10 ASP cc_start: 0.9246 (t0) cc_final: 0.8877 (t0) REVERT: I 5 GLU cc_start: 0.8803 (mp0) cc_final: 0.8520 (mm-30) REVERT: K 10 ASP cc_start: 0.9272 (t0) cc_final: 0.9013 (t0) REVERT: L 22 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8711 (ttm110) REVERT: M 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8848 (t0) REVERT: O 10 ASP cc_start: 0.9308 (t0) cc_final: 0.9070 (t0) REVERT: S 10 ASP cc_start: 0.9299 (t0) cc_final: 0.8956 (t0) REVERT: V 10 ASP cc_start: 0.9161 (t0) cc_final: 0.8699 (t0) REVERT: W 21 ARG cc_start: 0.9018 (mmm-85) cc_final: 0.8721 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9269 (t0) cc_final: 0.9009 (t0) REVERT: Z 10 ASP cc_start: 0.9150 (t0) cc_final: 0.8865 (t0) REVERT: Z 21 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8615 (mmm-85) REVERT: b 10 ASP cc_start: 0.9061 (t0) cc_final: 0.8643 (t0) REVERT: c 12 ASP cc_start: 0.8456 (t70) cc_final: 0.8226 (t0) REVERT: d 10 ASP cc_start: 0.9256 (t0) cc_final: 0.9053 (t0) REVERT: d 23 LEU cc_start: 0.8466 (mm) cc_final: 0.8202 (mt) REVERT: e 10 ASP cc_start: 0.9294 (t0) cc_final: 0.9024 (t0) REVERT: g 10 ASP cc_start: 0.9169 (t0) cc_final: 0.8915 (t0) REVERT: g 13 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7902 (ttm170) REVERT: h 21 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8309 (mmm-85) REVERT: i 5 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8476 (mm-30) REVERT: i 10 ASP cc_start: 0.9196 (t0) cc_final: 0.8701 (t0) REVERT: j 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8855 (t0) REVERT: k 10 ASP cc_start: 0.9330 (t0) cc_final: 0.8963 (t0) REVERT: l 6 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8438 (ttm110) REVERT: m 10 ASP cc_start: 0.9340 (t0) cc_final: 0.9043 (t0) REVERT: o 10 ASP cc_start: 0.9302 (t0) cc_final: 0.8999 (t0) REVERT: p 5 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8713 (mm-30) REVERT: p 10 ASP cc_start: 0.9062 (t0) cc_final: 0.8606 (t0) REVERT: q 10 ASP cc_start: 0.9076 (t0) cc_final: 0.8694 (t0) REVERT: q 14 GLU cc_start: 0.8857 (tp30) cc_final: 0.8607 (tp30) REVERT: r 10 ASP cc_start: 0.9140 (t0) cc_final: 0.8861 (t0) REVERT: t 6 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8422 (ttm110) REVERT: t 12 ASP cc_start: 0.7764 (t0) cc_final: 0.7514 (t0) REVERT: u 10 ASP cc_start: 0.9416 (t0) cc_final: 0.9101 (t0) REVERT: v 10 ASP cc_start: 0.9124 (t0) cc_final: 0.8875 (t0) REVERT: w 12 ASP cc_start: 0.7792 (t70) cc_final: 0.7573 (t0) REVERT: x 10 ASP cc_start: 0.9038 (t0) cc_final: 0.8707 (t0) REVERT: z 12 ASP cc_start: 0.7756 (t70) cc_final: 0.7311 (t0) REVERT: z 14 GLU cc_start: 0.8721 (tp30) cc_final: 0.8126 (mt-10) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3480 time to fit residues: 210.4010 Evaluate side-chains 476 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081741 restraints weight = 20147.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083858 restraints weight = 10855.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085317 restraints weight = 6652.539| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9412 Z= 0.329 Angle : 0.808 9.168 12636 Z= 0.407 Chirality : 0.042 0.142 1456 Planarity : 0.010 0.079 1716 Dihedral : 4.006 15.791 1404 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.46 (0.27), residues: 1092 helix: 1.65 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.03 (0.52), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 6 =============================================================================== Job complete usr+sys time: 3425.03 seconds wall clock time: 60 minutes 5.39 seconds (3605.39 seconds total)