Starting phenix.real_space_refine on Thu Feb 5 03:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.map" model { file = "/net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lji_63154/02_2026/9lji_63154.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 9765 2.51 5 N 2478 2.21 5 O 2751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15057 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 717 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Restraints were copied for chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, S, T, U Time building chain proxies: 1.12, per 1000 atoms: 0.07 Number of scatterers: 15057 At special positions: 0 Unit cell: (87.648, 87.648, 160.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2751 8.00 N 2478 7.00 C 9765 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: 0.94 Conformation dependent library (CDL) restraints added in 653.3 milliseconds 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'R' and resid 5 through 14 Processing helix chain 'R' and resid 18 through 29 Processing helix chain 'R' and resid 36 through 42 Processing helix chain 'R' and resid 44 through 56 Processing helix chain 'R' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP R 71 " --> pdb=" O LYS R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU R 87 " --> pdb=" O LYS R 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.511A pdb=" N ASP A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 4.044A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.511A pdb=" N ASP E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 36 through 42 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 36 through 42 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP G 71 " --> pdb=" O LYS G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 36 through 42 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 61 through 71 removed outlier: 3.511A pdb=" N ASP H 71 " --> pdb=" O LYS H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 removed outlier: 4.046A pdb=" N LEU H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 14 Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 36 through 42 Processing helix chain 'I' and resid 44 through 56 Processing helix chain 'I' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU I 87 " --> pdb=" O LYS I 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 18 through 29 Processing helix chain 'J' and resid 36 through 42 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP J 71 " --> pdb=" O LYS J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'K' and resid 18 through 29 Processing helix chain 'K' and resid 36 through 42 Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU K 87 " --> pdb=" O LYS K 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 18 through 29 Processing helix chain 'L' and resid 36 through 42 Processing helix chain 'L' and resid 44 through 56 Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP L 71 " --> pdb=" O LYS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 87 removed outlier: 4.046A pdb=" N LEU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 14 Processing helix chain 'M' and resid 18 through 29 Processing helix chain 'M' and resid 36 through 42 Processing helix chain 'M' and resid 44 through 56 Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.511A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 18 through 29 Processing helix chain 'N' and resid 36 through 42 Processing helix chain 'N' and resid 44 through 56 Processing helix chain 'N' and resid 61 through 71 removed outlier: 3.511A pdb=" N ASP N 71 " --> pdb=" O LYS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'O' and resid 18 through 29 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP O 71 " --> pdb=" O LYS O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 14 Processing helix chain 'P' and resid 18 through 29 Processing helix chain 'P' and resid 36 through 42 Processing helix chain 'P' and resid 44 through 56 Processing helix chain 'P' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP P 71 " --> pdb=" O LYS P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 36 through 42 Processing helix chain 'Q' and resid 44 through 56 Processing helix chain 'Q' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP Q 71 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 4.045A pdb=" N LEU Q 87 " --> pdb=" O LYS Q 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 14 Processing helix chain 'S' and resid 18 through 29 Processing helix chain 'S' and resid 36 through 42 Processing helix chain 'S' and resid 44 through 56 Processing helix chain 'S' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP S 71 " --> pdb=" O LYS S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 4.046A pdb=" N LEU S 87 " --> pdb=" O LYS S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 14 Processing helix chain 'T' and resid 18 through 29 Processing helix chain 'T' and resid 36 through 42 Processing helix chain 'T' and resid 44 through 56 Processing helix chain 'T' and resid 61 through 71 removed outlier: 3.510A pdb=" N ASP T 71 " --> pdb=" O LYS T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 removed outlier: 4.044A pdb=" N LEU T 87 " --> pdb=" O LYS T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 14 Processing helix chain 'U' and resid 18 through 29 Processing helix chain 'U' and resid 36 through 42 Processing helix chain 'U' and resid 44 through 56 Processing helix chain 'U' and resid 61 through 71 removed outlier: 3.509A pdb=" N ASP U 71 " --> pdb=" O LYS U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 removed outlier: 4.044A pdb=" N LEU U 87 " --> pdb=" O LYS U 83 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2520 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: 2.17 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4746 1.34 - 1.46: 1850 1.46 - 1.57: 8482 1.57 - 1.69: 0 1.69 - 1.80: 126 Bond restraints: 15204 Sorted by residual: bond pdb=" CA THR C 81 " pdb=" CB THR C 81 " ideal model delta sigma weight residual 1.528 1.534 -0.005 1.66e-02 3.63e+03 1.09e-01 bond pdb=" CA THR B 81 " pdb=" CB THR B 81 " ideal model delta sigma weight residual 1.528 1.534 -0.005 1.66e-02 3.63e+03 1.08e-01 bond pdb=" CA THR Q 81 " pdb=" CB THR Q 81 " ideal model delta sigma weight residual 1.528 1.534 -0.005 1.66e-02 3.63e+03 1.04e-01 bond pdb=" CA THR L 81 " pdb=" CB THR L 81 " ideal model delta sigma weight residual 1.528 1.534 -0.005 1.66e-02 3.63e+03 1.00e-01 bond pdb=" CA THR S 81 " pdb=" CB THR S 81 " ideal model delta sigma weight residual 1.528 1.534 -0.005 1.66e-02 3.63e+03 9.99e-02 ... (remaining 15199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.60: 19205 0.60 - 1.20: 841 1.20 - 1.79: 73 1.79 - 2.39: 83 2.39 - 2.99: 21 Bond angle restraints: 20223 Sorted by residual: angle pdb=" C LYS K 12 " pdb=" N GLY K 13 " pdb=" CA GLY K 13 " ideal model delta sigma weight residual 121.41 119.38 2.03 1.96e+00 2.60e-01 1.08e+00 angle pdb=" C LYS T 12 " pdb=" N GLY T 13 " pdb=" CA GLY T 13 " ideal model delta sigma weight residual 121.41 119.39 2.02 1.96e+00 2.60e-01 1.06e+00 angle pdb=" C LYS S 12 " pdb=" N GLY S 13 " pdb=" CA GLY S 13 " ideal model delta sigma weight residual 121.41 119.41 2.00 1.96e+00 2.60e-01 1.04e+00 angle pdb=" C LYS B 12 " pdb=" N GLY B 13 " pdb=" CA GLY B 13 " ideal model delta sigma weight residual 121.41 119.41 2.00 1.96e+00 2.60e-01 1.04e+00 angle pdb=" C LYS L 12 " pdb=" N GLY L 13 " pdb=" CA GLY L 13 " ideal model delta sigma weight residual 121.41 119.42 1.99 1.96e+00 2.60e-01 1.04e+00 ... (remaining 20218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7501 14.99 - 29.97: 1277 29.97 - 44.96: 651 44.96 - 59.95: 189 59.95 - 74.93: 42 Dihedral angle restraints: 9660 sinusoidal: 4305 harmonic: 5355 Sorted by residual: dihedral pdb=" CA LYS D 3 " pdb=" CB LYS D 3 " pdb=" CG LYS D 3 " pdb=" CD LYS D 3 " ideal model delta sinusoidal sigma weight residual -180.00 -123.94 -56.06 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS G 3 " pdb=" CB LYS G 3 " pdb=" CG LYS G 3 " pdb=" CD LYS G 3 " ideal model delta sinusoidal sigma weight residual -180.00 -123.94 -56.06 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS P 3 " pdb=" CB LYS P 3 " pdb=" CG LYS P 3 " pdb=" CD LYS P 3 " ideal model delta sinusoidal sigma weight residual 180.00 -123.96 -56.04 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 9657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1450 0.025 - 0.051: 499 0.051 - 0.076: 338 0.076 - 0.102: 23 0.102 - 0.127: 21 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CA ILE R 72 " pdb=" N ILE R 72 " pdb=" C ILE R 72 " pdb=" CB ILE R 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE T 72 " pdb=" N ILE T 72 " pdb=" C ILE T 72 " pdb=" CB ILE T 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2328 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 10 " 0.004 2.00e-02 2.50e+03 7.28e-03 5.30e-01 pdb=" C LEU O 10 " -0.013 2.00e-02 2.50e+03 pdb=" O LEU O 10 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU O 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 10 " -0.004 2.00e-02 2.50e+03 7.24e-03 5.24e-01 pdb=" C LEU A 10 " 0.013 2.00e-02 2.50e+03 pdb=" O LEU A 10 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU A 11 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 10 " -0.004 2.00e-02 2.50e+03 7.22e-03 5.21e-01 pdb=" C LEU J 10 " 0.012 2.00e-02 2.50e+03 pdb=" O LEU J 10 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU J 11 " -0.004 2.00e-02 2.50e+03 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3585 2.80 - 3.33: 14184 3.33 - 3.85: 23424 3.85 - 4.38: 28274 4.38 - 4.90: 49379 Nonbonded interactions: 118846 Sorted by model distance: nonbonded pdb=" NH2 ARG H 23 " pdb=" OD2 ASP M 44 " model vdw 2.280 3.120 nonbonded pdb=" OD2 ASP N 44 " pdb=" NH2 ARG O 23 " model vdw 2.287 3.120 nonbonded pdb=" OD2 ASP I 44 " pdb=" NH2 ARG P 23 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP R 44 " pdb=" NH2 ARG J 23 " model vdw 2.304 3.120 nonbonded pdb=" OD2 ASP B 44 " pdb=" NH2 ARG C 23 " model vdw 2.305 3.120 ... (remaining 118841 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: 0.03 Found NCS groups: ncs_group { reference = chain 'R' 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 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic 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: 0.250 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 10.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.001 0.008 15204 Z= 0.058 Angle : 0.306 2.990 20223 Z= 0.167 Chirality : 0.035 0.127 2331 Planarity : 0.001 0.007 2478 Dihedral : 19.445 74.935 6174 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 38.75 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1785 helix: 1.73 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -0.64 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 40 TYR 0.002 0.000 TYR S 20 PHE 0.001 0.000 PHE U 56 HIS 0.001 0.000 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00105 (15204) covalent geometry : angle 0.30609 (20223) hydrogen bonds : bond 0.05815 ( 840) hydrogen bonds : angle 4.32947 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8171 (ttp-170) REVERT: A 42 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 52 MET cc_start: 0.8227 (mtp) cc_final: 0.7948 (mtp) REVERT: A 59 ASP cc_start: 0.8017 (t0) cc_final: 0.7773 (t0) REVERT: A 67 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7698 (mtmt) REVERT: B 67 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7226 (mtmt) REVERT: C 41 GLU cc_start: 0.8482 (tp30) cc_final: 0.8185 (mm-30) REVERT: C 50 ASP cc_start: 0.8126 (m-30) cc_final: 0.7750 (m-30) REVERT: C 52 MET cc_start: 0.8508 (mtp) cc_final: 0.8223 (mtp) REVERT: C 59 ASP cc_start: 0.8402 (t0) cc_final: 0.7936 (t0) REVERT: C 67 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7406 (mtmp) REVERT: D 24 MET cc_start: 0.8748 (mtm) cc_final: 0.8492 (mtp) REVERT: D 67 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7780 (mtmm) REVERT: E 40 ARG cc_start: 0.8281 (ttp80) cc_final: 0.8045 (ttm-80) REVERT: E 67 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7073 (mtmt) REVERT: G 30 SER cc_start: 0.8279 (t) cc_final: 0.8015 (p) REVERT: G 52 MET cc_start: 0.8288 (mtp) cc_final: 0.8066 (mtp) REVERT: G 67 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7893 (mtmt) REVERT: H 24 MET cc_start: 0.8852 (mtm) cc_final: 0.8357 (mtp) REVERT: I 50 ASP cc_start: 0.7990 (m-30) cc_final: 0.7594 (m-30) REVERT: I 67 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7722 (mtpt) REVERT: J 24 MET cc_start: 0.8736 (mtm) cc_final: 0.8420 (mtm) REVERT: J 41 GLU cc_start: 0.8569 (tp30) cc_final: 0.8208 (tp30) REVERT: J 59 ASP cc_start: 0.8126 (t0) cc_final: 0.7838 (t70) REVERT: K 34 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7814 (mtmm) REVERT: L 50 ASP cc_start: 0.8338 (m-30) cc_final: 0.8116 (m-30) REVERT: L 67 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7797 (mtpt) REVERT: N 67 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7670 (mtmt) REVERT: O 8 ILE cc_start: 0.7171 (mt) cc_final: 0.6770 (pt) REVERT: O 67 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7636 (mtmm) REVERT: P 39 MET cc_start: 0.8864 (mtm) cc_final: 0.8566 (mtm) REVERT: P 50 ASP cc_start: 0.7990 (m-30) cc_final: 0.7787 (m-30) REVERT: Q 41 GLU cc_start: 0.8402 (tp30) cc_final: 0.8029 (tp30) REVERT: Q 59 ASP cc_start: 0.8398 (t0) cc_final: 0.8134 (t0) REVERT: Q 67 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7281 (mtmt) REVERT: S 59 ASP cc_start: 0.8051 (t0) cc_final: 0.7787 (t70) REVERT: S 67 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7506 (mtpt) REVERT: S 84 LYS cc_start: 0.7748 (ptpp) cc_final: 0.7261 (pttt) REVERT: T 24 MET cc_start: 0.8610 (mtm) cc_final: 0.8165 (mtp) REVERT: T 56 PHE cc_start: 0.7979 (m-80) cc_final: 0.7760 (m-10) REVERT: T 59 ASP cc_start: 0.7880 (t0) cc_final: 0.7483 (t0) REVERT: U 24 MET cc_start: 0.8809 (mtm) cc_final: 0.8571 (mtp) REVERT: U 52 MET cc_start: 0.8383 (mtp) cc_final: 0.8182 (mtm) REVERT: U 67 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7593 (mtpt) outliers start: 0 outliers final: 2 residues processed: 470 average time/residue: 0.8232 time to fit residues: 411.0363 Evaluate side-chains 332 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain S residue 7 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.113578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097545 restraints weight = 17232.963| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.65 r_work: 0.2931 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15204 Z= 0.153 Angle : 0.527 7.893 20223 Z= 0.277 Chirality : 0.041 0.137 2331 Planarity : 0.003 0.026 2478 Dihedral : 3.179 13.695 1936 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.63 % Allowed : 32.26 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1785 helix: 1.26 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.80 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 23 TYR 0.007 0.001 TYR F 5 PHE 0.012 0.001 PHE R 22 HIS 0.003 0.001 HIS K 21 Details of bonding type rmsd covalent geometry : bond 0.00378 (15204) covalent geometry : angle 0.52734 (20223) hydrogen bonds : bond 0.02745 ( 840) hydrogen bonds : angle 4.55322 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 385 time to evaluate : 0.441 Fit side-chains REVERT: R 8 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7279 (mt) REVERT: R 40 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8401 (ttm-80) REVERT: A 4 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7082 (tptp) REVERT: A 40 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8520 (ttp-170) REVERT: A 42 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 50 ASP cc_start: 0.8420 (m-30) cc_final: 0.8038 (m-30) REVERT: A 52 MET cc_start: 0.8803 (mtp) cc_final: 0.8337 (mtp) REVERT: A 54 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 59 ASP cc_start: 0.8578 (t0) cc_final: 0.8169 (t0) REVERT: A 67 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8045 (mtmt) REVERT: B 53 GLU cc_start: 0.8581 (tt0) cc_final: 0.8317 (tt0) REVERT: B 67 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7914 (mtmt) REVERT: C 41 GLU cc_start: 0.8516 (tp30) cc_final: 0.8309 (mm-30) REVERT: C 42 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7904 (mt-10) REVERT: C 67 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7896 (mtmp) REVERT: D 8 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7576 (mt) REVERT: D 24 MET cc_start: 0.8999 (mtm) cc_final: 0.8733 (mtp) REVERT: D 42 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8122 (mt-10) REVERT: D 67 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8135 (mtmm) REVERT: E 40 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8177 (ttm-80) REVERT: E 67 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7866 (mtmm) REVERT: E 84 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7660 (ptpp) REVERT: F 4 LYS cc_start: 0.7392 (tmtp) cc_final: 0.6992 (mmtm) REVERT: F 83 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: G 6 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8116 (ttmt) REVERT: G 8 ILE cc_start: 0.8103 (mt) cc_final: 0.7836 (mt) REVERT: G 42 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: G 67 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8149 (mtmt) REVERT: H 24 MET cc_start: 0.8912 (mtm) cc_final: 0.8558 (mtp) REVERT: I 8 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7386 (mt) REVERT: I 9 VAL cc_start: 0.7242 (t) cc_final: 0.6918 (t) REVERT: I 42 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8051 (mt-10) REVERT: I 52 MET cc_start: 0.8894 (mtm) cc_final: 0.8634 (mtp) REVERT: I 67 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7961 (mtpt) REVERT: J 8 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7483 (mt) REVERT: J 24 MET cc_start: 0.8826 (mtm) cc_final: 0.8375 (mtm) REVERT: J 27 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (p) REVERT: J 41 GLU cc_start: 0.8442 (tp30) cc_final: 0.7976 (tp30) REVERT: J 57 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: K 4 LYS cc_start: 0.7740 (tmtp) cc_final: 0.7220 (tppp) REVERT: K 34 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8182 (mtmm) REVERT: K 54 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7096 (mt-10) REVERT: K 59 ASP cc_start: 0.7942 (t0) cc_final: 0.7733 (t0) REVERT: K 71 ASP cc_start: 0.8684 (m-30) cc_final: 0.8410 (m-30) REVERT: L 4 LYS cc_start: 0.7852 (tmtp) cc_final: 0.7262 (tppt) REVERT: L 9 VAL cc_start: 0.7743 (t) cc_final: 0.7322 (t) REVERT: L 67 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7904 (mtpt) REVERT: M 4 LYS cc_start: 0.7331 (tmtp) cc_final: 0.6698 (tppt) REVERT: M 6 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8013 (tttt) REVERT: M 8 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7461 (mt) REVERT: M 40 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8261 (ttm110) REVERT: M 42 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: M 50 ASP cc_start: 0.8293 (m-30) cc_final: 0.7577 (m-30) REVERT: M 59 ASP cc_start: 0.7927 (t70) cc_final: 0.7602 (t0) REVERT: N 50 ASP cc_start: 0.8496 (m-30) cc_final: 0.8281 (m-30) REVERT: N 54 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7178 (mt-10) REVERT: N 59 ASP cc_start: 0.8258 (t0) cc_final: 0.7868 (t0) REVERT: O 53 GLU cc_start: 0.8629 (tt0) cc_final: 0.8419 (tt0) REVERT: O 67 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7813 (mtmt) REVERT: P 4 LYS cc_start: 0.7962 (tppp) cc_final: 0.7439 (tmtp) REVERT: P 53 GLU cc_start: 0.8519 (tt0) cc_final: 0.8316 (tt0) REVERT: Q 40 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8492 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8383 (tp30) cc_final: 0.7959 (tp30) REVERT: Q 67 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7453 (mtmt) REVERT: S 8 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7451 (mt) REVERT: S 9 VAL cc_start: 0.7624 (t) cc_final: 0.7253 (t) REVERT: S 67 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7911 (mtpt) REVERT: S 71 ASP cc_start: 0.8326 (m-30) cc_final: 0.8091 (m-30) REVERT: S 83 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8135 (mtmm) REVERT: T 8 ILE cc_start: 0.7746 (mt) cc_final: 0.7402 (mt) REVERT: T 24 MET cc_start: 0.8745 (mtm) cc_final: 0.8439 (mtp) REVERT: U 6 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7617 (tttt) REVERT: U 8 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7412 (mt) REVERT: U 9 VAL cc_start: 0.7776 (t) cc_final: 0.7243 (t) REVERT: U 50 ASP cc_start: 0.8292 (m-30) cc_final: 0.8017 (m-30) REVERT: U 52 MET cc_start: 0.8915 (mtp) cc_final: 0.8491 (mtm) REVERT: U 67 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7741 (mtpt) outliers start: 61 outliers final: 16 residues processed: 424 average time/residue: 0.7939 time to fit residues: 360.6906 Evaluate side-chains 409 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 83 LYS Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 83 LYS Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097049 restraints weight = 17194.156| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.65 r_work: 0.2907 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15204 Z= 0.118 Angle : 0.438 7.767 20223 Z= 0.240 Chirality : 0.038 0.133 2331 Planarity : 0.002 0.014 2478 Dihedral : 3.060 11.406 1932 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.68 % Allowed : 31.07 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1785 helix: 1.30 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.98 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 23 TYR 0.003 0.001 TYR N 5 PHE 0.006 0.001 PHE R 22 HIS 0.002 0.001 HIS K 21 Details of bonding type rmsd covalent geometry : bond 0.00286 (15204) covalent geometry : angle 0.43788 (20223) hydrogen bonds : bond 0.02403 ( 840) hydrogen bonds : angle 4.51590 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 403 time to evaluate : 0.538 Fit side-chains REVERT: R 8 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7325 (mt) REVERT: A 4 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7132 (tptp) REVERT: A 40 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8498 (ttp-170) REVERT: A 42 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: A 50 ASP cc_start: 0.8467 (m-30) cc_final: 0.8035 (m-30) REVERT: A 52 MET cc_start: 0.8779 (mtp) cc_final: 0.8421 (mtp) REVERT: A 54 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 59 ASP cc_start: 0.8556 (t0) cc_final: 0.8157 (t0) REVERT: A 67 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8075 (mtmt) REVERT: B 67 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7877 (mtmm) REVERT: C 4 LYS cc_start: 0.7349 (tptm) cc_final: 0.6949 (tppt) REVERT: C 41 GLU cc_start: 0.8559 (tp30) cc_final: 0.8261 (mm-30) REVERT: C 67 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7984 (mtmt) REVERT: D 8 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7677 (mt) REVERT: D 24 MET cc_start: 0.9028 (mtm) cc_final: 0.8778 (mtp) REVERT: D 42 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8119 (mt-10) REVERT: E 40 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8252 (ttm-80) REVERT: E 53 GLU cc_start: 0.8507 (tt0) cc_final: 0.8247 (tt0) REVERT: E 67 LYS cc_start: 0.8294 (mtmm) cc_final: 0.8043 (mtmm) REVERT: E 84 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7872 (ptpp) REVERT: F 4 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7031 (mmtm) REVERT: G 8 ILE cc_start: 0.8177 (mt) cc_final: 0.7865 (mt) REVERT: G 42 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: G 67 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8159 (mtmt) REVERT: H 24 MET cc_start: 0.8969 (mtm) cc_final: 0.8591 (mtp) REVERT: H 71 ASP cc_start: 0.8312 (m-30) cc_final: 0.8092 (m-30) REVERT: H 84 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8081 (ttmm) REVERT: I 9 VAL cc_start: 0.7251 (t) cc_final: 0.6887 (t) REVERT: I 52 MET cc_start: 0.8912 (mtm) cc_final: 0.8651 (mtp) REVERT: I 67 LYS cc_start: 0.8238 (mtmm) cc_final: 0.8013 (mtpt) REVERT: J 8 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7637 (mt) REVERT: J 24 MET cc_start: 0.8896 (mtm) cc_final: 0.8451 (mtm) REVERT: J 27 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8661 (p) REVERT: J 42 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8098 (mt-10) REVERT: J 71 ASP cc_start: 0.8667 (m-30) cc_final: 0.8301 (m-30) REVERT: K 4 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7183 (tppp) REVERT: K 54 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7078 (mt-10) REVERT: K 71 ASP cc_start: 0.8767 (m-30) cc_final: 0.8522 (m-30) REVERT: L 9 VAL cc_start: 0.7784 (t) cc_final: 0.7394 (t) REVERT: L 42 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: L 67 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7886 (mtpt) REVERT: M 4 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6737 (tppt) REVERT: M 6 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8011 (tttt) REVERT: M 8 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7462 (mt) REVERT: M 40 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8348 (ttp-110) REVERT: M 42 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: M 50 ASP cc_start: 0.8217 (m-30) cc_final: 0.7651 (m-30) REVERT: M 59 ASP cc_start: 0.8145 (t70) cc_final: 0.7647 (t0) REVERT: N 39 MET cc_start: 0.9043 (mtm) cc_final: 0.8813 (mtm) REVERT: N 50 ASP cc_start: 0.8385 (m-30) cc_final: 0.8173 (m-30) REVERT: N 54 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7157 (mt-10) REVERT: N 59 ASP cc_start: 0.8403 (t0) cc_final: 0.7949 (t0) REVERT: O 67 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7855 (mtmt) REVERT: P 4 LYS cc_start: 0.8082 (tppp) cc_final: 0.7434 (tmtp) REVERT: Q 40 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8503 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8390 (tp30) cc_final: 0.8060 (tp30) REVERT: Q 59 ASP cc_start: 0.8626 (t0) cc_final: 0.8220 (t0) REVERT: Q 67 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7741 (mtmt) REVERT: S 8 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7550 (mt) REVERT: S 9 VAL cc_start: 0.7734 (t) cc_final: 0.7372 (t) REVERT: S 52 MET cc_start: 0.8757 (mtp) cc_final: 0.8279 (mtm) REVERT: S 67 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8103 (mtpt) REVERT: S 71 ASP cc_start: 0.8425 (m-30) cc_final: 0.8216 (m-30) REVERT: S 83 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: T 4 LYS cc_start: 0.7719 (tptm) cc_final: 0.6769 (tppt) REVERT: T 8 ILE cc_start: 0.7917 (mt) cc_final: 0.7643 (mt) REVERT: T 24 MET cc_start: 0.8776 (mtm) cc_final: 0.8503 (mtp) REVERT: U 9 VAL cc_start: 0.7867 (t) cc_final: 0.7361 (t) REVERT: U 42 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: U 52 MET cc_start: 0.8816 (mtp) cc_final: 0.8462 (mtm) REVERT: U 71 ASP cc_start: 0.8508 (m-30) cc_final: 0.8222 (m-30) outliers start: 45 outliers final: 19 residues processed: 430 average time/residue: 0.7593 time to fit residues: 350.1555 Evaluate side-chains 427 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 390 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 142 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.115305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099158 restraints weight = 17141.386| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.65 r_work: 0.2936 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15204 Z= 0.084 Angle : 0.387 6.321 20223 Z= 0.217 Chirality : 0.036 0.135 2331 Planarity : 0.002 0.013 2478 Dihedral : 2.935 11.435 1932 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.68 % Allowed : 30.48 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1785 helix: 1.61 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 40 TYR 0.003 0.000 TYR D 5 PHE 0.003 0.000 PHE R 22 HIS 0.001 0.000 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00190 (15204) covalent geometry : angle 0.38717 (20223) hydrogen bonds : bond 0.02069 ( 840) hydrogen bonds : angle 4.44646 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 395 time to evaluate : 0.636 Fit side-chains REVERT: R 8 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7421 (mt) REVERT: A 40 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8381 (ttp-170) REVERT: A 42 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: A 50 ASP cc_start: 0.8318 (m-30) cc_final: 0.7906 (m-30) REVERT: A 52 MET cc_start: 0.8733 (mtp) cc_final: 0.8445 (mtp) REVERT: A 59 ASP cc_start: 0.8515 (t0) cc_final: 0.8125 (t0) REVERT: A 67 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8206 (mtmt) REVERT: B 67 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7825 (mtmm) REVERT: C 41 GLU cc_start: 0.8574 (tp30) cc_final: 0.8308 (mm-30) REVERT: C 42 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8108 (mt-10) REVERT: C 67 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7913 (mtmt) REVERT: D 4 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (tptm) REVERT: D 8 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7744 (mt) REVERT: D 24 MET cc_start: 0.9045 (mtm) cc_final: 0.8788 (mtp) REVERT: D 42 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8207 (mt-10) REVERT: E 40 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8167 (ttm-80) REVERT: E 42 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: E 52 MET cc_start: 0.8622 (mtm) cc_final: 0.8249 (mtp) REVERT: E 53 GLU cc_start: 0.8446 (tt0) cc_final: 0.8203 (tt0) REVERT: E 67 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7972 (mtmm) REVERT: F 4 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6936 (mmtm) REVERT: G 8 ILE cc_start: 0.8181 (mt) cc_final: 0.7888 (mt) REVERT: G 67 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8122 (mtmt) REVERT: H 24 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8637 (mtp) REVERT: H 71 ASP cc_start: 0.8305 (m-30) cc_final: 0.8085 (m-30) REVERT: H 84 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7932 (ttmm) REVERT: I 52 MET cc_start: 0.8893 (mtm) cc_final: 0.8612 (mtp) REVERT: I 67 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7968 (mtpt) REVERT: I 70 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8565 (mt-10) REVERT: J 8 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7587 (mt) REVERT: J 24 MET cc_start: 0.8911 (mtm) cc_final: 0.8584 (mtm) REVERT: J 42 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7994 (mt-10) REVERT: J 84 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7922 (ttmm) REVERT: K 4 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7205 (tppp) REVERT: K 54 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6934 (mt-10) REVERT: K 71 ASP cc_start: 0.8758 (m-30) cc_final: 0.8506 (m-30) REVERT: L 4 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6640 (tppt) REVERT: L 9 VAL cc_start: 0.7696 (t) cc_final: 0.6933 (t) REVERT: L 42 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: L 67 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7837 (mtpt) REVERT: M 4 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6651 (tppt) REVERT: M 6 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8068 (tttt) REVERT: M 8 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7505 (mt) REVERT: M 40 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8253 (ttp-110) REVERT: M 42 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: M 50 ASP cc_start: 0.8249 (m-30) cc_final: 0.7720 (m-30) REVERT: M 59 ASP cc_start: 0.8109 (t70) cc_final: 0.7605 (t0) REVERT: N 39 MET cc_start: 0.9000 (mtm) cc_final: 0.8795 (mtm) REVERT: N 54 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7114 (mt-10) REVERT: N 59 ASP cc_start: 0.8373 (t0) cc_final: 0.7935 (t0) REVERT: O 67 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7786 (mtmt) REVERT: P 4 LYS cc_start: 0.8096 (tppp) cc_final: 0.7408 (tmtp) REVERT: Q 40 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8472 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8395 (tp30) cc_final: 0.8061 (tp30) REVERT: Q 59 ASP cc_start: 0.8622 (t0) cc_final: 0.8211 (t0) REVERT: Q 67 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7701 (mtmt) REVERT: S 6 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: S 8 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7483 (mt) REVERT: S 9 VAL cc_start: 0.7616 (t) cc_final: 0.7220 (t) REVERT: S 52 MET cc_start: 0.8711 (mtp) cc_final: 0.8271 (mtm) REVERT: S 67 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7982 (mtpt) REVERT: S 83 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8013 (mtmm) REVERT: T 4 LYS cc_start: 0.7431 (tptm) cc_final: 0.6562 (tppt) REVERT: T 8 ILE cc_start: 0.7914 (mt) cc_final: 0.7633 (mt) REVERT: T 24 MET cc_start: 0.8771 (mtm) cc_final: 0.8461 (mtp) REVERT: U 4 LYS cc_start: 0.7581 (tmtp) cc_final: 0.7197 (mmtm) REVERT: U 6 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7679 (tttt) REVERT: U 9 VAL cc_start: 0.7877 (t) cc_final: 0.7301 (t) REVERT: U 50 ASP cc_start: 0.8383 (m-30) cc_final: 0.8088 (m-30) REVERT: U 52 MET cc_start: 0.8755 (mtp) cc_final: 0.8414 (mtm) REVERT: U 71 ASP cc_start: 0.8486 (m-30) cc_final: 0.8178 (m-30) outliers start: 45 outliers final: 18 residues processed: 421 average time/residue: 0.7615 time to fit residues: 344.2146 Evaluate side-chains 425 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 71 ASP Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 109 optimal weight: 0.0060 chunk 6 optimal weight: 5.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.112840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.096135 restraints weight = 17146.089| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.66 r_work: 0.2871 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15204 Z= 0.138 Angle : 0.461 8.542 20223 Z= 0.247 Chirality : 0.039 0.135 2331 Planarity : 0.002 0.017 2478 Dihedral : 3.154 11.657 1932 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.21 % Allowed : 29.29 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1785 helix: 1.32 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 23 TYR 0.003 0.001 TYR C 20 PHE 0.009 0.001 PHE R 22 HIS 0.002 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00342 (15204) covalent geometry : angle 0.46084 (20223) hydrogen bonds : bond 0.02607 ( 840) hydrogen bonds : angle 4.61489 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 397 time to evaluate : 0.481 Fit side-chains REVERT: R 4 LYS cc_start: 0.7650 (tptm) cc_final: 0.7303 (tppt) REVERT: R 8 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7383 (mt) REVERT: R 42 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 4 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7156 (tptp) REVERT: A 15 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8656 (mm-30) REVERT: A 40 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8396 (ttp-170) REVERT: A 42 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: A 50 ASP cc_start: 0.8498 (m-30) cc_final: 0.8049 (m-30) REVERT: A 52 MET cc_start: 0.8716 (mtp) cc_final: 0.8448 (mtp) REVERT: A 59 ASP cc_start: 0.8564 (t0) cc_final: 0.8141 (t0) REVERT: A 67 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8255 (mtmt) REVERT: B 4 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6995 (tppp) REVERT: B 67 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7891 (mtmm) REVERT: C 41 GLU cc_start: 0.8510 (tp30) cc_final: 0.8246 (mm-30) REVERT: C 42 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: C 67 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8024 (mtmt) REVERT: D 4 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (tptm) REVERT: D 8 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7749 (mt) REVERT: D 24 MET cc_start: 0.9086 (mtm) cc_final: 0.8823 (mtp) REVERT: D 42 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8176 (mt-10) REVERT: E 40 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8251 (ttm-80) REVERT: E 42 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: E 53 GLU cc_start: 0.8510 (tt0) cc_final: 0.8267 (tt0) REVERT: E 67 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8054 (mtmm) REVERT: F 15 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8586 (mm-30) REVERT: G 8 ILE cc_start: 0.8242 (mt) cc_final: 0.7968 (mt) REVERT: G 67 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8089 (mtmt) REVERT: G 84 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8168 (ttmt) REVERT: H 24 MET cc_start: 0.8992 (mtm) cc_final: 0.8628 (mtp) REVERT: H 71 ASP cc_start: 0.8370 (m-30) cc_final: 0.8126 (m-30) REVERT: H 84 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8005 (ttmm) REVERT: I 42 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: I 67 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7982 (mtpt) REVERT: I 70 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8599 (mt-10) REVERT: I 84 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8264 (ttmm) REVERT: J 8 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7596 (mt) REVERT: J 24 MET cc_start: 0.8893 (mtm) cc_final: 0.8468 (mtm) REVERT: J 27 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8599 (p) REVERT: J 71 ASP cc_start: 0.8775 (m-30) cc_final: 0.8357 (m-30) REVERT: K 4 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7276 (tppp) REVERT: K 54 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6946 (mt-10) REVERT: K 71 ASP cc_start: 0.8714 (m-30) cc_final: 0.8418 (m-30) REVERT: K 84 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7846 (ttmm) REVERT: K 85 GLU cc_start: 0.7338 (tt0) cc_final: 0.7052 (tt0) REVERT: L 4 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6786 (tppt) REVERT: L 8 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (mt) REVERT: L 9 VAL cc_start: 0.7798 (t) cc_final: 0.7425 (t) REVERT: L 67 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7858 (mtpt) REVERT: M 4 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6893 (tppt) REVERT: M 6 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8054 (tttt) REVERT: M 8 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7541 (mt) REVERT: M 50 ASP cc_start: 0.8284 (m-30) cc_final: 0.7741 (m-30) REVERT: M 59 ASP cc_start: 0.8144 (t70) cc_final: 0.7713 (t0) REVERT: N 54 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7140 (mt-10) REVERT: N 59 ASP cc_start: 0.8406 (t0) cc_final: 0.7989 (t0) REVERT: O 42 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: O 67 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7844 (mtmt) REVERT: O 84 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8177 (ttmm) REVERT: P 23 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8284 (mtm110) REVERT: P 39 MET cc_start: 0.9105 (mtp) cc_final: 0.8798 (mtm) REVERT: Q 40 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8510 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8383 (tp30) cc_final: 0.8047 (tp30) REVERT: Q 59 ASP cc_start: 0.8669 (t0) cc_final: 0.8277 (t0) REVERT: Q 67 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7720 (mtmt) REVERT: S 8 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7496 (mt) REVERT: S 9 VAL cc_start: 0.7805 (t) cc_final: 0.7417 (t) REVERT: S 52 MET cc_start: 0.8754 (mtp) cc_final: 0.8364 (mtm) REVERT: S 67 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8081 (mtpt) REVERT: S 83 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8102 (mtmm) REVERT: T 4 LYS cc_start: 0.7763 (tptm) cc_final: 0.6896 (tppt) REVERT: T 24 MET cc_start: 0.8823 (mtm) cc_final: 0.8562 (mtp) REVERT: U 4 LYS cc_start: 0.7553 (tmtp) cc_final: 0.7190 (mmtm) REVERT: U 6 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7761 (tttt) REVERT: U 8 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7487 (mt) REVERT: U 9 VAL cc_start: 0.7893 (t) cc_final: 0.7401 (t) REVERT: U 42 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: U 52 MET cc_start: 0.8761 (mtp) cc_final: 0.8486 (mtm) REVERT: U 71 ASP cc_start: 0.8581 (m-30) cc_final: 0.8272 (m-30) outliers start: 54 outliers final: 18 residues processed: 426 average time/residue: 0.7393 time to fit residues: 337.5318 Evaluate side-chains 435 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 392 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 118 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.115192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099090 restraints weight = 16939.030| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.59 r_work: 0.2921 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15204 Z= 0.086 Angle : 0.383 5.776 20223 Z= 0.216 Chirality : 0.036 0.130 2331 Planarity : 0.002 0.014 2478 Dihedral : 3.011 11.725 1932 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.44 % Allowed : 29.82 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1785 helix: 1.61 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.23 (0.21), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 40 TYR 0.004 0.000 TYR S 5 PHE 0.003 0.000 PHE B 22 HIS 0.001 0.000 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00193 (15204) covalent geometry : angle 0.38343 (20223) hydrogen bonds : bond 0.02148 ( 840) hydrogen bonds : angle 4.51500 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 397 time to evaluate : 0.627 Fit side-chains REVERT: R 4 LYS cc_start: 0.7387 (tptm) cc_final: 0.7074 (tppp) REVERT: R 8 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7512 (mt) REVERT: R 42 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 15 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 42 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 50 ASP cc_start: 0.8447 (m-30) cc_final: 0.7982 (m-30) REVERT: A 52 MET cc_start: 0.8790 (mtp) cc_final: 0.8544 (mtp) REVERT: A 59 ASP cc_start: 0.8521 (t0) cc_final: 0.8145 (t0) REVERT: A 67 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8246 (mtmt) REVERT: B 4 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.6993 (tppp) REVERT: B 67 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7870 (mtmm) REVERT: B 84 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8202 (ttmm) REVERT: C 41 GLU cc_start: 0.8576 (tp30) cc_final: 0.8327 (mm-30) REVERT: C 59 ASP cc_start: 0.8552 (t0) cc_final: 0.8032 (t0) REVERT: C 67 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7944 (mtmt) REVERT: D 4 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (tptm) REVERT: D 8 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7817 (mt) REVERT: D 24 MET cc_start: 0.9071 (mtm) cc_final: 0.8814 (mtp) REVERT: D 42 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: E 40 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8201 (ttm-80) REVERT: E 42 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: E 52 MET cc_start: 0.8640 (mtm) cc_final: 0.8285 (mtp) REVERT: E 53 GLU cc_start: 0.8479 (tt0) cc_final: 0.8241 (tt0) REVERT: E 67 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7967 (mttp) REVERT: F 15 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8570 (mm-30) REVERT: G 8 ILE cc_start: 0.8199 (mt) cc_final: 0.7918 (mt) REVERT: G 67 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8069 (mtmt) REVERT: H 6 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7652 (tttt) REVERT: H 24 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8677 (mtp) REVERT: H 42 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8156 (mm-30) REVERT: H 50 ASP cc_start: 0.8277 (m-30) cc_final: 0.8005 (m-30) REVERT: H 71 ASP cc_start: 0.8355 (m-30) cc_final: 0.8126 (m-30) REVERT: H 84 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7984 (ttmm) REVERT: I 42 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: I 67 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8043 (mtpt) REVERT: I 70 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8529 (mt-10) REVERT: I 84 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8298 (ttmm) REVERT: J 4 LYS cc_start: 0.8184 (tppt) cc_final: 0.7526 (tmtt) REVERT: J 24 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8533 (mtm) REVERT: J 27 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8713 (p) REVERT: J 67 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8032 (mtmm) REVERT: J 71 ASP cc_start: 0.8769 (m-30) cc_final: 0.8393 (m-30) REVERT: K 4 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7337 (tppp) REVERT: K 54 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6954 (mt-10) REVERT: K 71 ASP cc_start: 0.8675 (m-30) cc_final: 0.8383 (m-30) REVERT: K 85 GLU cc_start: 0.7198 (tt0) cc_final: 0.6955 (tt0) REVERT: L 4 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6698 (mmtm) REVERT: L 8 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7796 (mt) REVERT: L 9 VAL cc_start: 0.7828 (t) cc_final: 0.7093 (t) REVERT: L 67 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7867 (mtpt) REVERT: L 81 THR cc_start: 0.8469 (t) cc_final: 0.8211 (p) REVERT: M 4 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6797 (tppt) REVERT: M 6 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8009 (tttt) REVERT: M 8 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7555 (mt) REVERT: M 50 ASP cc_start: 0.8242 (m-30) cc_final: 0.7664 (m-30) REVERT: M 59 ASP cc_start: 0.8110 (t70) cc_final: 0.7591 (t0) REVERT: M 84 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8093 (ttmm) REVERT: N 39 MET cc_start: 0.9101 (mtm) cc_final: 0.8855 (mtm) REVERT: N 54 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7100 (mt-10) REVERT: N 59 ASP cc_start: 0.8349 (t0) cc_final: 0.7925 (t0) REVERT: O 67 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7822 (mtmt) REVERT: O 84 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8244 (ttmm) REVERT: P 4 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7346 (tmtp) REVERT: P 39 MET cc_start: 0.9106 (mtp) cc_final: 0.8758 (mtm) REVERT: Q 40 ARG cc_start: 0.8738 (ttm110) cc_final: 0.8511 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8348 (tp30) cc_final: 0.8038 (tp30) REVERT: Q 59 ASP cc_start: 0.8621 (t0) cc_final: 0.8211 (t0) REVERT: Q 67 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7725 (mtmt) REVERT: S 8 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7529 (mt) REVERT: S 9 VAL cc_start: 0.7833 (t) cc_final: 0.7417 (t) REVERT: S 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7784 (m-30) REVERT: S 52 MET cc_start: 0.8728 (mtp) cc_final: 0.8258 (mtm) REVERT: S 59 ASP cc_start: 0.8103 (t0) cc_final: 0.7860 (t0) REVERT: S 67 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8051 (mtpt) REVERT: S 83 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8205 (mtmm) REVERT: T 24 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: U 4 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7116 (mmtm) REVERT: U 6 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (tttt) REVERT: U 8 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7539 (mt) REVERT: U 9 VAL cc_start: 0.7968 (t) cc_final: 0.7455 (t) REVERT: U 42 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: U 52 MET cc_start: 0.8726 (mtp) cc_final: 0.8414 (mtm) REVERT: U 71 ASP cc_start: 0.8558 (m-30) cc_final: 0.8261 (m-30) outliers start: 41 outliers final: 14 residues processed: 417 average time/residue: 0.7018 time to fit residues: 314.3075 Evaluate side-chains 431 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 392 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 24 MET Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093067 restraints weight = 17099.681| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.66 r_work: 0.2862 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15204 Z= 0.183 Angle : 0.498 5.284 20223 Z= 0.264 Chirality : 0.040 0.136 2331 Planarity : 0.003 0.020 2478 Dihedral : 3.324 11.844 1932 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.15 % Allowed : 29.05 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1785 helix: 1.23 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.11 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.006 0.001 TYR A 5 PHE 0.010 0.001 PHE R 22 HIS 0.003 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00461 (15204) covalent geometry : angle 0.49764 (20223) hydrogen bonds : bond 0.02899 ( 840) hydrogen bonds : angle 4.74641 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 400 time to evaluate : 0.456 Fit side-chains REVERT: R 8 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7441 (mt) REVERT: R 42 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8076 (mm-30) REVERT: R 53 GLU cc_start: 0.8465 (tt0) cc_final: 0.8087 (tt0) REVERT: A 4 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7236 (tptp) REVERT: A 15 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 42 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: A 52 MET cc_start: 0.8724 (mtp) cc_final: 0.8492 (mtp) REVERT: A 59 ASP cc_start: 0.8577 (t0) cc_final: 0.8194 (t0) REVERT: A 67 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8271 (mtmt) REVERT: B 4 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7018 (tppp) REVERT: B 67 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7855 (mtmm) REVERT: C 41 GLU cc_start: 0.8565 (tp30) cc_final: 0.8309 (mm-30) REVERT: C 42 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: C 59 ASP cc_start: 0.8586 (t0) cc_final: 0.8038 (t0) REVERT: C 67 LYS cc_start: 0.8328 (mtmm) cc_final: 0.8036 (mtmt) REVERT: D 4 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: D 8 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7848 (mt) REVERT: D 24 MET cc_start: 0.9089 (mtm) cc_final: 0.8834 (mtp) REVERT: D 84 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8119 (ttmm) REVERT: E 40 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8217 (ttm-80) REVERT: E 42 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: E 53 GLU cc_start: 0.8504 (tt0) cc_final: 0.8269 (tt0) REVERT: E 67 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8037 (mtmm) REVERT: F 15 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8751 (mm-30) REVERT: G 8 ILE cc_start: 0.8315 (mt) cc_final: 0.8047 (mt) REVERT: G 42 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: G 67 LYS cc_start: 0.8265 (mtmm) cc_final: 0.8043 (mtmt) REVERT: G 84 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8270 (ttmm) REVERT: H 24 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: H 42 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8321 (mm-30) REVERT: H 71 ASP cc_start: 0.8436 (m-30) cc_final: 0.8151 (m-30) REVERT: I 42 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: I 67 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8039 (mtpt) REVERT: I 70 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8515 (mt-10) REVERT: I 84 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8311 (ttmm) REVERT: J 4 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7409 (tppt) REVERT: J 24 MET cc_start: 0.8881 (mtm) cc_final: 0.8541 (mtm) REVERT: J 57 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7021 (mtp85) REVERT: K 54 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6973 (mt-10) REVERT: K 71 ASP cc_start: 0.8703 (m-30) cc_final: 0.8400 (m-30) REVERT: K 85 GLU cc_start: 0.7415 (tt0) cc_final: 0.7180 (tt0) REVERT: L 4 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6891 (mmtm) REVERT: L 8 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7782 (mt) REVERT: L 9 VAL cc_start: 0.7894 (t) cc_final: 0.7532 (t) REVERT: L 42 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: L 67 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7849 (mtpt) REVERT: L 84 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8023 (ttmm) REVERT: M 4 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7094 (tppt) REVERT: M 6 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8094 (tttt) REVERT: M 8 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7573 (mt) REVERT: M 42 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: M 50 ASP cc_start: 0.8286 (m-30) cc_final: 0.7787 (m-30) REVERT: M 59 ASP cc_start: 0.8287 (t70) cc_final: 0.7744 (t0) REVERT: M 84 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7921 (ttmm) REVERT: N 39 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8921 (mtm) REVERT: N 54 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7113 (mt-10) REVERT: N 59 ASP cc_start: 0.8462 (t0) cc_final: 0.8075 (t0) REVERT: O 42 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: O 67 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7806 (mtmt) REVERT: O 84 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8272 (ttmm) REVERT: P 4 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8039 (mmtp) REVERT: P 23 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8307 (mtm110) REVERT: P 39 MET cc_start: 0.9094 (mtp) cc_final: 0.8799 (mtm) REVERT: Q 40 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8512 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8341 (tp30) cc_final: 0.8005 (tp30) REVERT: Q 59 ASP cc_start: 0.8496 (t0) cc_final: 0.8268 (t0) REVERT: Q 67 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7733 (mtmt) REVERT: S 8 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7446 (mt) REVERT: S 9 VAL cc_start: 0.7780 (t) cc_final: 0.7389 (t) REVERT: S 52 MET cc_start: 0.8780 (mtp) cc_final: 0.8418 (mtm) REVERT: S 67 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8049 (mtpt) REVERT: T 4 LYS cc_start: 0.7642 (tptm) cc_final: 0.7064 (tppt) REVERT: T 24 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8590 (mtp) REVERT: U 4 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7170 (mmtm) REVERT: U 6 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7786 (tttt) REVERT: U 8 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7479 (mt) REVERT: U 9 VAL cc_start: 0.7877 (t) cc_final: 0.7403 (t) REVERT: U 42 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: U 52 MET cc_start: 0.8675 (mtp) cc_final: 0.8418 (mtm) REVERT: U 71 ASP cc_start: 0.8598 (m-30) cc_final: 0.8268 (m-30) outliers start: 53 outliers final: 16 residues processed: 428 average time/residue: 0.8153 time to fit residues: 373.5552 Evaluate side-chains 443 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.112649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.095816 restraints weight = 17027.866| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.67 r_work: 0.2849 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15204 Z= 0.123 Angle : 0.439 6.727 20223 Z= 0.238 Chirality : 0.038 0.134 2331 Planarity : 0.002 0.015 2478 Dihedral : 3.224 12.033 1932 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.56 % Allowed : 29.70 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1785 helix: 1.29 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 40 TYR 0.005 0.001 TYR I 20 PHE 0.005 0.001 PHE B 22 HIS 0.001 0.000 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00301 (15204) covalent geometry : angle 0.43935 (20223) hydrogen bonds : bond 0.02547 ( 840) hydrogen bonds : angle 4.68278 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 0.688 Fit side-chains REVERT: R 8 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7339 (mt) REVERT: R 42 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8071 (mm-30) REVERT: R 53 GLU cc_start: 0.8432 (tt0) cc_final: 0.8083 (tt0) REVERT: A 4 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7221 (tptp) REVERT: A 15 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 42 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: A 50 ASP cc_start: 0.8471 (m-30) cc_final: 0.8023 (m-30) REVERT: A 52 MET cc_start: 0.8693 (mtp) cc_final: 0.8438 (mtp) REVERT: A 59 ASP cc_start: 0.8548 (t0) cc_final: 0.8154 (t0) REVERT: A 67 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8232 (mtmt) REVERT: B 4 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.6988 (mmtm) REVERT: B 67 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7801 (mtmm) REVERT: C 41 GLU cc_start: 0.8574 (tp30) cc_final: 0.8333 (mm-30) REVERT: C 42 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: C 59 ASP cc_start: 0.8579 (t0) cc_final: 0.8056 (t0) REVERT: C 67 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7961 (mtmt) REVERT: D 4 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7655 (tptm) REVERT: D 8 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7827 (mt) REVERT: D 24 MET cc_start: 0.9060 (mtm) cc_final: 0.8804 (mtp) REVERT: D 84 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8142 (ttmm) REVERT: E 40 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8180 (ttm-80) REVERT: E 42 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: E 53 GLU cc_start: 0.8480 (tt0) cc_final: 0.8264 (tt0) REVERT: E 57 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7567 (mmt-90) REVERT: E 67 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7916 (mttp) REVERT: F 15 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8777 (mm-30) REVERT: G 8 ILE cc_start: 0.8224 (mt) cc_final: 0.7956 (mt) REVERT: G 67 LYS cc_start: 0.8228 (mtmm) cc_final: 0.8003 (mtmt) REVERT: G 84 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8283 (ttmm) REVERT: H 24 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8660 (mtp) REVERT: H 42 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8325 (mm-30) REVERT: H 52 MET cc_start: 0.8566 (mtm) cc_final: 0.8246 (mtm) REVERT: H 71 ASP cc_start: 0.8417 (m-30) cc_final: 0.8136 (m-30) REVERT: H 84 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8036 (mtmm) REVERT: I 42 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: I 67 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7991 (mtpt) REVERT: I 70 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8460 (mt-10) REVERT: I 84 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8227 (ttmm) REVERT: J 4 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7484 (tppt) REVERT: J 24 MET cc_start: 0.8883 (mtm) cc_final: 0.8489 (mtm) REVERT: J 27 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8651 (p) REVERT: J 57 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6998 (mtp85) REVERT: J 67 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8042 (mtmm) REVERT: J 71 ASP cc_start: 0.8705 (m-30) cc_final: 0.8307 (m-30) REVERT: K 4 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7457 (mmtm) REVERT: K 54 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7061 (mt-10) REVERT: K 71 ASP cc_start: 0.8590 (m-30) cc_final: 0.8282 (m-30) REVERT: L 8 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7695 (mt) REVERT: L 42 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: L 67 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7788 (mtpt) REVERT: M 4 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7063 (tppt) REVERT: M 6 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (tttt) REVERT: M 8 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7529 (mt) REVERT: M 50 ASP cc_start: 0.8217 (m-30) cc_final: 0.7702 (m-30) REVERT: M 59 ASP cc_start: 0.8245 (t70) cc_final: 0.7696 (t0) REVERT: M 84 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7828 (ttmm) REVERT: N 39 MET cc_start: 0.9122 (mtm) cc_final: 0.8888 (mtm) REVERT: N 54 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7064 (mt-10) REVERT: N 59 ASP cc_start: 0.8438 (t0) cc_final: 0.8030 (t0) REVERT: O 42 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: O 67 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7719 (mtmt) REVERT: P 4 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8068 (tppp) REVERT: P 39 MET cc_start: 0.9102 (mtp) cc_final: 0.8766 (mtm) REVERT: Q 40 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8501 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8326 (tp30) cc_final: 0.7998 (tp30) REVERT: Q 59 ASP cc_start: 0.8461 (t0) cc_final: 0.8093 (t0) REVERT: Q 67 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7682 (mtmt) REVERT: S 8 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7692 (mt) REVERT: S 9 VAL cc_start: 0.7822 (t) cc_final: 0.7432 (t) REVERT: S 52 MET cc_start: 0.8703 (mtp) cc_final: 0.8297 (mtm) REVERT: S 67 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8010 (mtpt) REVERT: T 4 LYS cc_start: 0.7657 (tptm) cc_final: 0.7089 (tppt) REVERT: T 24 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: U 4 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7170 (mmtm) REVERT: U 6 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7717 (tttt) REVERT: U 8 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7490 (mt) REVERT: U 9 VAL cc_start: 0.7858 (t) cc_final: 0.7338 (t) REVERT: U 42 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: U 52 MET cc_start: 0.8687 (mtp) cc_final: 0.8414 (mtm) REVERT: U 71 ASP cc_start: 0.8584 (m-30) cc_final: 0.8253 (m-30) outliers start: 43 outliers final: 14 residues processed: 419 average time/residue: 0.7577 time to fit residues: 339.7268 Evaluate side-chains 432 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Chi-restraints excluded: chain U residue 84 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.096615 restraints weight = 16900.569| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.66 r_work: 0.2879 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15204 Z= 0.112 Angle : 0.429 6.999 20223 Z= 0.234 Chirality : 0.037 0.135 2331 Planarity : 0.002 0.015 2478 Dihedral : 3.168 12.095 1932 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.56 % Allowed : 29.70 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1785 helix: 1.37 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 40 TYR 0.006 0.000 TYR I 20 PHE 0.005 0.001 PHE R 22 HIS 0.001 0.000 HIS K 21 Details of bonding type rmsd covalent geometry : bond 0.00272 (15204) covalent geometry : angle 0.42948 (20223) hydrogen bonds : bond 0.02421 ( 840) hydrogen bonds : angle 4.64138 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 395 time to evaluate : 0.546 Fit side-chains REVERT: R 8 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7342 (mt) REVERT: R 42 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8046 (mm-30) REVERT: R 53 GLU cc_start: 0.8487 (tt0) cc_final: 0.8177 (tt0) REVERT: A 4 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7225 (tptp) REVERT: A 15 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 42 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 50 ASP cc_start: 0.8452 (m-30) cc_final: 0.8000 (m-30) REVERT: A 52 MET cc_start: 0.8694 (mtp) cc_final: 0.8447 (mtp) REVERT: A 59 ASP cc_start: 0.8537 (t0) cc_final: 0.8145 (t0) REVERT: A 67 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8217 (mtmt) REVERT: B 4 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7054 (tppp) REVERT: B 67 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7831 (mtmm) REVERT: B 84 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7518 (mtmm) REVERT: C 41 GLU cc_start: 0.8563 (tp30) cc_final: 0.8317 (mm-30) REVERT: C 42 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: C 59 ASP cc_start: 0.8613 (t0) cc_final: 0.8098 (t0) REVERT: C 67 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7970 (mtmt) REVERT: D 4 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7602 (tptm) REVERT: D 8 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7737 (mt) REVERT: D 24 MET cc_start: 0.9061 (mtm) cc_final: 0.8804 (mtp) REVERT: D 84 LYS cc_start: 0.8387 (ptpt) cc_final: 0.8139 (ttmm) REVERT: E 40 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8179 (ttm-80) REVERT: E 42 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: E 53 GLU cc_start: 0.8466 (tt0) cc_final: 0.8213 (tt0) REVERT: F 15 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8750 (mm-30) REVERT: F 84 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7923 (mtmm) REVERT: G 8 ILE cc_start: 0.8199 (mt) cc_final: 0.7923 (mt) REVERT: G 67 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7992 (mtmt) REVERT: G 84 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8379 (ttmm) REVERT: H 24 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8665 (mtp) REVERT: H 42 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8355 (mm-30) REVERT: H 52 MET cc_start: 0.8602 (mtm) cc_final: 0.8294 (mtm) REVERT: H 71 ASP cc_start: 0.8418 (m-30) cc_final: 0.8132 (m-30) REVERT: H 84 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8046 (mtmm) REVERT: I 42 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: I 67 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7992 (mtpt) REVERT: I 70 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8454 (mt-10) REVERT: J 4 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7489 (tppt) REVERT: J 24 MET cc_start: 0.8903 (mtm) cc_final: 0.8515 (mtm) REVERT: J 27 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8656 (p) REVERT: J 67 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7943 (mtmm) REVERT: J 71 ASP cc_start: 0.8722 (m-30) cc_final: 0.8312 (m-30) REVERT: K 4 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7471 (mmtm) REVERT: K 71 ASP cc_start: 0.8569 (m-30) cc_final: 0.8261 (m-30) REVERT: L 8 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7691 (mt) REVERT: L 42 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: L 67 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7782 (mtpt) REVERT: M 4 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7064 (tppt) REVERT: M 6 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (tttt) REVERT: M 8 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7567 (mt) REVERT: M 50 ASP cc_start: 0.8203 (m-30) cc_final: 0.7648 (m-30) REVERT: M 59 ASP cc_start: 0.8232 (t70) cc_final: 0.7691 (t0) REVERT: M 84 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7953 (ttmm) REVERT: N 39 MET cc_start: 0.9135 (mtm) cc_final: 0.8889 (mtm) REVERT: N 54 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7107 (mt-10) REVERT: N 59 ASP cc_start: 0.8426 (t0) cc_final: 0.8007 (t0) REVERT: O 42 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8189 (mm-30) REVERT: O 67 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7746 (mtmt) REVERT: P 4 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7564 (tmtp) REVERT: P 39 MET cc_start: 0.9103 (mtp) cc_final: 0.8779 (mtm) REVERT: Q 40 ARG cc_start: 0.8737 (ttm110) cc_final: 0.8466 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8319 (tp30) cc_final: 0.7989 (tp30) REVERT: Q 59 ASP cc_start: 0.8456 (t0) cc_final: 0.8090 (t0) REVERT: Q 67 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7778 (mtmt) REVERT: S 8 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7467 (mt) REVERT: S 52 MET cc_start: 0.8695 (mtp) cc_final: 0.8278 (mtm) REVERT: S 67 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7991 (mtpt) REVERT: T 4 LYS cc_start: 0.7670 (tptm) cc_final: 0.7280 (tppt) REVERT: T 24 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: U 4 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7182 (mmtm) REVERT: U 6 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7685 (tttt) REVERT: U 8 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7473 (mt) REVERT: U 9 VAL cc_start: 0.7908 (t) cc_final: 0.7412 (t) REVERT: U 42 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: U 52 MET cc_start: 0.8695 (mtp) cc_final: 0.8427 (mtm) REVERT: U 71 ASP cc_start: 0.8585 (m-30) cc_final: 0.8254 (m-30) outliers start: 43 outliers final: 16 residues processed: 417 average time/residue: 0.7538 time to fit residues: 337.1506 Evaluate side-chains 433 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 392 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Chi-restraints excluded: chain U residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.111572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094584 restraints weight = 17009.654| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.66 r_work: 0.2875 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15204 Z= 0.157 Angle : 0.487 6.967 20223 Z= 0.257 Chirality : 0.039 0.135 2331 Planarity : 0.003 0.019 2478 Dihedral : 3.318 12.122 1932 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.80 % Allowed : 29.29 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1785 helix: 1.24 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.21 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 40 TYR 0.005 0.001 TYR A 5 PHE 0.008 0.001 PHE R 22 HIS 0.002 0.001 HIS J 21 Details of bonding type rmsd covalent geometry : bond 0.00391 (15204) covalent geometry : angle 0.48746 (20223) hydrogen bonds : bond 0.02751 ( 840) hydrogen bonds : angle 4.73698 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3570 Ramachandran restraints generated. 1785 Oldfield, 0 Emsley, 1785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 396 time to evaluate : 0.640 Fit side-chains REVERT: R 8 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7378 (mt) REVERT: R 42 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8060 (mm-30) REVERT: R 53 GLU cc_start: 0.8478 (tt0) cc_final: 0.8108 (tt0) REVERT: A 4 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7267 (tptp) REVERT: A 15 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 42 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: A 50 ASP cc_start: 0.8482 (m-30) cc_final: 0.8053 (m-30) REVERT: A 52 MET cc_start: 0.8707 (mtp) cc_final: 0.8412 (mtp) REVERT: A 59 ASP cc_start: 0.8562 (t0) cc_final: 0.8164 (t0) REVERT: A 67 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8215 (mtmt) REVERT: B 4 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7050 (tppp) REVERT: B 67 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7834 (mtmm) REVERT: B 84 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7538 (mtmm) REVERT: C 41 GLU cc_start: 0.8610 (tp30) cc_final: 0.8323 (mm-30) REVERT: C 42 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: C 59 ASP cc_start: 0.8574 (t0) cc_final: 0.8030 (t0) REVERT: C 67 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7993 (mtmt) REVERT: D 4 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7569 (tptm) REVERT: D 8 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7828 (mt) REVERT: D 24 MET cc_start: 0.9076 (mtm) cc_final: 0.8824 (mtp) REVERT: D 84 LYS cc_start: 0.8422 (ptpt) cc_final: 0.8173 (ttmm) REVERT: E 40 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8194 (ttm-80) REVERT: E 53 GLU cc_start: 0.8492 (tt0) cc_final: 0.8249 (tt0) REVERT: E 57 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7600 (mmt-90) REVERT: E 84 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8035 (ptpp) REVERT: F 15 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8668 (mm-30) REVERT: F 84 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7931 (mtmm) REVERT: G 8 ILE cc_start: 0.8269 (mt) cc_final: 0.7988 (mt) REVERT: G 67 LYS cc_start: 0.8237 (mtmm) cc_final: 0.8016 (mtmt) REVERT: G 84 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8378 (ttmm) REVERT: H 24 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (mtp) REVERT: H 42 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8245 (mm-30) REVERT: H 52 MET cc_start: 0.8613 (mtm) cc_final: 0.8316 (mtm) REVERT: H 71 ASP cc_start: 0.8429 (m-30) cc_final: 0.8127 (m-30) REVERT: H 84 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8076 (mtmm) REVERT: I 42 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: I 67 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7947 (mtpt) REVERT: J 4 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7432 (tppt) REVERT: J 24 MET cc_start: 0.8863 (mtm) cc_final: 0.8437 (mtm) REVERT: J 27 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8539 (p) REVERT: J 67 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8142 (mtmm) REVERT: J 71 ASP cc_start: 0.8683 (m-30) cc_final: 0.8263 (m-30) REVERT: K 4 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7490 (mmtm) REVERT: K 54 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6896 (mt-10) REVERT: K 71 ASP cc_start: 0.8602 (m-30) cc_final: 0.8280 (m-30) REVERT: L 8 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7711 (mt) REVERT: L 42 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: L 67 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7779 (mtpt) REVERT: M 4 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7196 (tppt) REVERT: M 6 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8089 (tttt) REVERT: M 8 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7543 (mt) REVERT: M 42 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: M 50 ASP cc_start: 0.8256 (m-30) cc_final: 0.7744 (m-30) REVERT: M 59 ASP cc_start: 0.8243 (t70) cc_final: 0.7630 (t0) REVERT: M 84 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7955 (ttmm) REVERT: N 39 MET cc_start: 0.9150 (mtm) cc_final: 0.8903 (mtm) REVERT: N 54 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7110 (mt-10) REVERT: N 59 ASP cc_start: 0.8457 (t0) cc_final: 0.8077 (t0) REVERT: O 42 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: O 67 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7638 (mtmt) REVERT: O 84 LYS cc_start: 0.8511 (ttmm) cc_final: 0.7957 (mtmt) REVERT: P 4 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7449 (tmtp) REVERT: P 23 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8243 (mtm110) REVERT: P 39 MET cc_start: 0.9083 (mtp) cc_final: 0.8735 (mtm) REVERT: P 84 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7785 (ptpp) REVERT: Q 40 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8452 (ttp-170) REVERT: Q 41 GLU cc_start: 0.8314 (tp30) cc_final: 0.8002 (tp30) REVERT: Q 59 ASP cc_start: 0.8483 (t0) cc_final: 0.8095 (t0) REVERT: Q 67 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7793 (mtmt) REVERT: S 8 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7692 (mt) REVERT: S 9 VAL cc_start: 0.7819 (t) cc_final: 0.7439 (t) REVERT: S 52 MET cc_start: 0.8756 (mtp) cc_final: 0.8387 (mtm) REVERT: S 67 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8024 (mtpt) REVERT: T 4 LYS cc_start: 0.7790 (tptm) cc_final: 0.7461 (tppt) REVERT: T 24 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8554 (mtp) REVERT: U 4 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7292 (mmtm) REVERT: U 6 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7750 (tttt) REVERT: U 8 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7475 (mt) REVERT: U 9 VAL cc_start: 0.7921 (t) cc_final: 0.7441 (t) REVERT: U 42 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: U 52 MET cc_start: 0.8655 (mtp) cc_final: 0.8397 (mtm) REVERT: U 71 ASP cc_start: 0.8607 (m-30) cc_final: 0.8277 (m-30) outliers start: 47 outliers final: 14 residues processed: 419 average time/residue: 0.7723 time to fit residues: 346.3255 Evaluate side-chains 438 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 395 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain J residue 4 LYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 6 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain U residue 42 GLU Chi-restraints excluded: chain U residue 84 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.113688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096851 restraints weight = 16829.106| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.66 r_work: 0.2895 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15204 Z= 0.105 Angle : 0.428 8.079 20223 Z= 0.233 Chirality : 0.037 0.132 2331 Planarity : 0.002 0.015 2478 Dihedral : 3.164 12.059 1932 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.38 % Allowed : 29.82 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1785 helix: 1.38 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -1.22 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 40 TYR 0.006 0.000 TYR I 20 PHE 0.005 0.001 PHE B 22 HIS 0.001 0.000 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00252 (15204) covalent geometry : angle 0.42838 (20223) hydrogen bonds : bond 0.02351 ( 840) hydrogen bonds : angle 4.64550 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5935.74 seconds wall clock time: 101 minutes 42.45 seconds (6102.45 seconds total)