Starting phenix.real_space_refine on Tue Mar 3 17:22:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2026/7oag_12776.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 4750 2.51 5 N 1325 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7600 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y Time building chain proxies: 0.76, per 1000 atoms: 0.10 Number of scatterers: 7600 At special positions: 0 Unit cell: (76.911, 76.911, 124.877, 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 175 16.00 O 1350 8.00 N 1325 7.00 C 4750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 15 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 15 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 15 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 15 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 15 " - pdb=" SG CYS Y 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 39 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 39 " distance=2.02 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 39 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 39 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 39 " distance=2.02 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 39 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 39 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 39 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 39 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 39 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 39 " distance=2.03 Simple disulfide: pdb=" SG CYS W 19 " - pdb=" SG CYS W 39 " distance=2.03 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 39 " distance=2.02 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: 0.65 Conformation dependent library (CDL) restraints added in 259.6 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 25 sheets defined 47.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 31 through 35 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 13 through 21 Processing helix chain 'M' and resid 31 through 35 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 13 through 21 Processing helix chain 'N' and resid 31 through 35 Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 13 through 21 Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 13 through 21 Processing helix chain 'P' and resid 31 through 35 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 21 Processing helix chain 'Q' and resid 31 through 35 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 31 through 35 Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 13 through 21 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 13 through 21 Processing helix chain 'T' and resid 31 through 35 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 13 through 21 Processing helix chain 'U' and resid 31 through 35 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 13 through 21 Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 13 through 21 Processing helix chain 'W' and resid 31 through 35 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 13 through 21 Processing helix chain 'Y' and resid 31 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AB5, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30 250 hydrogen bonds defined for protein. 600 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: 1.02 Time building geometry restraints manager: 0.89 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: 2350 1.34 - 1.46: 2020 1.46 - 1.57: 3255 1.57 - 1.69: 0 1.69 - 1.80: 200 Bond restraints: 7825 Sorted by residual: bond pdb=" CB TRP V 8 " pdb=" CG TRP V 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP P 8 " pdb=" CG TRP P 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP M 8 " pdb=" CG TRP M 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP R 8 " pdb=" CG TRP R 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP J 8 " pdb=" CG TRP J 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 ... (remaining 7820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 8591 0.74 - 1.48: 1283 1.48 - 2.22: 351 2.22 - 2.97: 100 2.97 - 3.71: 50 Bond angle restraints: 10375 Sorted by residual: angle pdb=" CA LYS U 26 " pdb=" CB LYS U 26 " pdb=" CG LYS U 26 " ideal model delta sigma weight residual 114.10 117.63 -3.53 2.00e+00 2.50e-01 3.11e+00 angle pdb=" C LEU Q 36 " pdb=" N CYS Q 37 " pdb=" CA CYS Q 37 " ideal model delta sigma weight residual 122.17 119.31 2.86 1.62e+00 3.81e-01 3.11e+00 angle pdb=" CA LYS B 26 " pdb=" CB LYS B 26 " pdb=" CG LYS B 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA LYS F 26 " pdb=" CB LYS F 26 " pdb=" CG LYS F 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 angle pdb=" CA LYS G 26 " pdb=" CB LYS G 26 " pdb=" CG LYS G 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 ... (remaining 10370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.37: 3548 8.37 - 16.74: 702 16.74 - 25.11: 175 25.11 - 33.48: 100 33.48 - 41.84: 100 Dihedral angle restraints: 4625 sinusoidal: 1975 harmonic: 2650 Sorted by residual: dihedral pdb=" CA ILE N 22 " pdb=" CB ILE N 22 " pdb=" CG1 ILE N 22 " pdb=" CD1 ILE N 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.05 -38.05 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE W 22 " pdb=" CB ILE W 22 " pdb=" CG1 ILE W 22 " pdb=" CD1 ILE W 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.04 -38.04 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE U 22 " pdb=" CB ILE U 22 " pdb=" CG1 ILE U 22 " pdb=" CD1 ILE U 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.03 -38.03 3 1.50e+01 4.44e-03 6.68e+00 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 463 0.025 - 0.049: 148 0.049 - 0.074: 89 0.074 - 0.098: 95 0.098 - 0.123: 55 Chirality restraints: 850 Sorted by residual: chirality pdb=" CA LYS K 26 " pdb=" N LYS K 26 " pdb=" C LYS K 26 " pdb=" CB LYS K 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA LYS N 26 " pdb=" N LYS N 26 " pdb=" C LYS N 26 " pdb=" CB LYS N 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA LYS L 26 " pdb=" N LYS L 26 " pdb=" C LYS L 26 " pdb=" CB LYS L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 847 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO C 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO Q 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO Q 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO Q 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.48e-01 pdb=" N PRO H 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO H 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 7 " 0.013 5.00e-02 4.00e+02 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2997 2.84 - 3.35: 7691 3.35 - 3.87: 13985 3.87 - 4.38: 16356 4.38 - 4.90: 25243 Nonbonded interactions: 66272 Sorted by model distance: nonbonded pdb=" N PHE L 2 " pdb=" OD2 ASP P 11 " model vdw 2.321 3.120 nonbonded pdb=" OD2 ASP Q 11 " pdb=" N PHE U 2 " model vdw 2.358 3.120 nonbonded pdb=" O HIS K 18 " pdb=" OG SER K 21 " model vdw 2.401 3.040 nonbonded pdb=" O HIS E 18 " pdb=" OG SER E 21 " model vdw 2.402 3.040 nonbonded pdb=" O HIS M 18 " pdb=" OG SER M 21 " model vdw 2.402 3.040 ... (remaining 66267 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 1.860 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 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 : 0.007 0.038 7900 Z= 0.335 Angle : 0.680 3.707 10525 Z= 0.383 Chirality : 0.049 0.123 850 Planarity : 0.004 0.023 1350 Dihedral : 10.390 38.045 2800 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 950 helix: 1.41 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR F 40 PHE 0.008 0.001 PHE W 2 TRP 0.006 0.002 TRP R 8 HIS 0.002 0.001 HIS U 16 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 7825) covalent geometry : angle 0.67321 (10375) SS BOND : bond 0.00363 ( 75) SS BOND : angle 1.06410 ( 150) hydrogen bonds : bond 0.21425 ( 250) hydrogen bonds : angle 8.98794 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.228 Fit side-chains REVERT: L 23 LYS cc_start: 0.9235 (mppt) cc_final: 0.9034 (mmtm) REVERT: L 25 TYR cc_start: 0.9451 (m-80) cc_final: 0.9074 (m-80) REVERT: V 5 ASN cc_start: 0.9346 (t0) cc_final: 0.9021 (t0) REVERT: V 32 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8150 (ttpt) REVERT: X 5 ASN cc_start: 0.9226 (t0) cc_final: 0.8941 (t0) REVERT: X 32 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8137 (mtpt) REVERT: Y 5 ASN cc_start: 0.8723 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1730 time to fit residues: 24.5587 Evaluate side-chains 104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.023239 restraints weight = 38883.034| |-----------------------------------------------------------------------------| r_work (start): 0.2331 rms_B_bonded: 5.19 r_work: 0.2172 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7900 Z= 0.222 Angle : 0.617 5.265 10525 Z= 0.315 Chirality : 0.045 0.106 850 Planarity : 0.004 0.029 1350 Dihedral : 4.104 20.605 1075 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: 0.18 (0.28), residues: 950 helix: 1.98 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -0.51 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 25 PHE 0.011 0.001 PHE Y 35 TRP 0.014 0.002 TRP W 8 HIS 0.002 0.000 HIS W 16 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 7825) covalent geometry : angle 0.61653 (10375) SS BOND : bond 0.00210 ( 75) SS BOND : angle 0.63357 ( 150) hydrogen bonds : bond 0.03573 ( 250) hydrogen bonds : angle 6.81648 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.245 Fit side-chains REVERT: C 26 LYS cc_start: 0.9418 (ptmm) cc_final: 0.9128 (ptmm) REVERT: I 13 MET cc_start: 0.8644 (mpp) cc_final: 0.8094 (mpp) REVERT: O 10 GLU cc_start: 0.8985 (pm20) cc_final: 0.8668 (pm20) REVERT: T 5 ASN cc_start: 0.9528 (t0) cc_final: 0.9059 (t0) REVERT: V 5 ASN cc_start: 0.9552 (t0) cc_final: 0.8979 (t0) REVERT: V 32 LYS cc_start: 0.9653 (mmtt) cc_final: 0.8931 (mtpt) REVERT: W 25 TYR cc_start: 0.9418 (m-80) cc_final: 0.9033 (m-80) REVERT: W 26 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8871 (ptmm) REVERT: X 5 ASN cc_start: 0.9447 (t0) cc_final: 0.8996 (t0) REVERT: X 32 LYS cc_start: 0.9650 (mmtt) cc_final: 0.8926 (mtpt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1696 time to fit residues: 23.7411 Evaluate side-chains 110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.037729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.022942 restraints weight = 38283.545| |-----------------------------------------------------------------------------| r_work (start): 0.2324 rms_B_bonded: 5.25 r_work: 0.2169 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7900 Z= 0.141 Angle : 0.526 4.475 10525 Z= 0.268 Chirality : 0.042 0.108 850 Planarity : 0.003 0.027 1350 Dihedral : 3.644 19.097 1075 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.28), residues: 950 helix: 2.21 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR F 25 PHE 0.005 0.001 PHE Y 35 TRP 0.010 0.002 TRP A 8 HIS 0.002 0.000 HIS R 16 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7825) covalent geometry : angle 0.52652 (10375) SS BOND : bond 0.00193 ( 75) SS BOND : angle 0.51260 ( 150) hydrogen bonds : bond 0.02610 ( 250) hydrogen bonds : angle 6.24966 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.296 Fit side-chains REVERT: C 26 LYS cc_start: 0.9418 (ptmm) cc_final: 0.9131 (ptmm) REVERT: G 11 ASP cc_start: 0.8251 (t0) cc_final: 0.7912 (t0) REVERT: K 5 ASN cc_start: 0.9359 (t0) cc_final: 0.8660 (t0) REVERT: M 10 GLU cc_start: 0.9004 (pm20) cc_final: 0.8746 (pm20) REVERT: M 26 LYS cc_start: 0.9357 (ptmt) cc_final: 0.9025 (ptmm) REVERT: N 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9430 (mmmm) REVERT: O 5 ASN cc_start: 0.9375 (t0) cc_final: 0.8752 (t0) REVERT: O 10 GLU cc_start: 0.9022 (pm20) cc_final: 0.8754 (pm20) REVERT: P 20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9278 (mmmm) REVERT: R 5 ASN cc_start: 0.9494 (t0) cc_final: 0.8893 (t0) REVERT: T 5 ASN cc_start: 0.9473 (t0) cc_final: 0.8903 (t0) REVERT: V 5 ASN cc_start: 0.9518 (t0) cc_final: 0.8899 (t0) REVERT: V 32 LYS cc_start: 0.9628 (mmtt) cc_final: 0.8900 (mtpt) REVERT: W 25 TYR cc_start: 0.9465 (m-80) cc_final: 0.9152 (m-80) REVERT: W 26 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8863 (ptmm) REVERT: X 5 ASN cc_start: 0.9357 (t0) cc_final: 0.8791 (t0) REVERT: X 32 LYS cc_start: 0.9635 (mmtt) cc_final: 0.8778 (ttpt) REVERT: Y 25 TYR cc_start: 0.9566 (m-80) cc_final: 0.9012 (m-80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1732 time to fit residues: 26.5678 Evaluate side-chains 119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 chunk 21 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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 = 0.2956 r_free = 0.2956 target = 0.036897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.022544 restraints weight = 37658.360| |-----------------------------------------------------------------------------| r_work (start): 0.2304 rms_B_bonded: 5.12 r_work: 0.2142 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7900 Z= 0.228 Angle : 0.592 5.438 10525 Z= 0.299 Chirality : 0.043 0.110 850 Planarity : 0.004 0.027 1350 Dihedral : 3.918 19.459 1075 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.39 % Allowed : 10.84 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.28), residues: 950 helix: 2.19 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR D 25 PHE 0.005 0.001 PHE U 2 TRP 0.013 0.002 TRP Y 8 HIS 0.002 0.000 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 7825) covalent geometry : angle 0.59243 (10375) SS BOND : bond 0.00269 ( 75) SS BOND : angle 0.57841 ( 150) hydrogen bonds : bond 0.02881 ( 250) hydrogen bonds : angle 6.36475 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.305 Fit side-chains REVERT: C 26 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9097 (ptmm) REVERT: G 11 ASP cc_start: 0.8252 (t0) cc_final: 0.7875 (t0) REVERT: M 10 GLU cc_start: 0.9096 (pm20) cc_final: 0.8842 (pm20) REVERT: M 26 LYS cc_start: 0.9364 (ptmt) cc_final: 0.9025 (ptmm) REVERT: N 20 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9428 (mmmm) REVERT: O 10 GLU cc_start: 0.9094 (pm20) cc_final: 0.8858 (pm20) REVERT: P 20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9285 (mmmm) REVERT: P 26 LYS cc_start: 0.9386 (ptpp) cc_final: 0.9173 (ptmm) REVERT: T 5 ASN cc_start: 0.9539 (t0) cc_final: 0.9098 (t0) REVERT: T 11 ASP cc_start: 0.8367 (t0) cc_final: 0.8124 (t0) REVERT: T 13 MET cc_start: 0.8987 (mmm) cc_final: 0.8778 (mmm) REVERT: V 5 ASN cc_start: 0.9573 (t0) cc_final: 0.8969 (t0) REVERT: V 32 LYS cc_start: 0.9654 (mmtt) cc_final: 0.8920 (mtpt) REVERT: W 26 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8800 (ptmm) REVERT: X 5 ASN cc_start: 0.9499 (t0) cc_final: 0.9028 (t0) REVERT: X 26 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9130 (ptpp) REVERT: X 32 LYS cc_start: 0.9664 (mmtt) cc_final: 0.8871 (ttpt) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.1603 time to fit residues: 22.6019 Evaluate side-chains 121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.037965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.023145 restraints weight = 37793.216| |-----------------------------------------------------------------------------| r_work (start): 0.2328 rms_B_bonded: 5.22 r_work: 0.2176 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7900 Z= 0.099 Angle : 0.506 5.768 10525 Z= 0.256 Chirality : 0.041 0.110 850 Planarity : 0.003 0.025 1350 Dihedral : 3.559 20.632 1075 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 11.23 % Favored : 88.52 % 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: 0.20 (0.28), residues: 950 helix: 2.15 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR W 25 PHE 0.003 0.001 PHE Y 35 TRP 0.011 0.002 TRP K 8 HIS 0.001 0.000 HIS Y 18 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7825) covalent geometry : angle 0.50678 (10375) SS BOND : bond 0.00158 ( 75) SS BOND : angle 0.47458 ( 150) hydrogen bonds : bond 0.02254 ( 250) hydrogen bonds : angle 5.87446 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.339 Fit side-chains REVERT: A 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9410 (mmmm) REVERT: C 26 LYS cc_start: 0.9324 (ptmm) cc_final: 0.8879 (ptmm) REVERT: D 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9378 (mmmm) REVERT: G 11 ASP cc_start: 0.8203 (t0) cc_final: 0.7883 (t0) REVERT: I 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8591 (t0) REVERT: J 20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9350 (mmmm) REVERT: K 5 ASN cc_start: 0.9319 (t0) cc_final: 0.8593 (t0) REVERT: L 20 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9425 (mmmm) REVERT: M 5 ASN cc_start: 0.9361 (t0) cc_final: 0.8667 (t0) REVERT: M 10 GLU cc_start: 0.9076 (pm20) cc_final: 0.8859 (pm20) REVERT: M 26 LYS cc_start: 0.9320 (ptmt) cc_final: 0.8926 (ptmm) REVERT: N 20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9423 (mmmm) REVERT: O 5 ASN cc_start: 0.9300 (t0) cc_final: 0.8650 (t0) REVERT: P 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9273 (mmmm) REVERT: P 26 LYS cc_start: 0.9358 (ptpp) cc_final: 0.9148 (ptmm) REVERT: Q 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9418 (mmmm) REVERT: R 5 ASN cc_start: 0.9405 (t0) cc_final: 0.8749 (t0) REVERT: T 5 ASN cc_start: 0.9410 (t0) cc_final: 0.8791 (t0) REVERT: T 20 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9310 (mmmm) REVERT: V 5 ASN cc_start: 0.9448 (t0) cc_final: 0.8812 (t0) REVERT: V 20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9442 (mmmm) REVERT: V 32 LYS cc_start: 0.9610 (mmtt) cc_final: 0.8892 (mtpt) REVERT: W 25 TYR cc_start: 0.9480 (m-80) cc_final: 0.9225 (m-80) REVERT: W 26 LYS cc_start: 0.9073 (ptmm) cc_final: 0.8723 (ptmm) REVERT: X 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8735 (t0) REVERT: X 26 LYS cc_start: 0.9446 (pttm) cc_final: 0.9076 (ptpp) REVERT: X 32 LYS cc_start: 0.9618 (mmtt) cc_final: 0.8787 (ttpt) REVERT: Y 20 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9374 (mmmm) REVERT: Y 25 TYR cc_start: 0.9600 (m-80) cc_final: 0.9178 (m-80) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1769 time to fit residues: 28.4229 Evaluate side-chains 131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.022643 restraints weight = 37366.055| |-----------------------------------------------------------------------------| r_work (start): 0.2311 rms_B_bonded: 5.10 r_work: 0.2151 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7900 Z= 0.213 Angle : 0.599 6.260 10525 Z= 0.299 Chirality : 0.043 0.110 850 Planarity : 0.003 0.026 1350 Dihedral : 3.723 20.831 1075 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % 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: 0.23 (0.28), residues: 950 helix: 2.31 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR W 25 PHE 0.004 0.001 PHE P 2 TRP 0.012 0.002 TRP Y 8 HIS 0.001 0.000 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7825) covalent geometry : angle 0.59935 (10375) SS BOND : bond 0.00251 ( 75) SS BOND : angle 0.56214 ( 150) hydrogen bonds : bond 0.02650 ( 250) hydrogen bonds : angle 6.12344 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.319 Fit side-chains REVERT: C 10 GLU cc_start: 0.8931 (pm20) cc_final: 0.8646 (pm20) REVERT: C 26 LYS cc_start: 0.9363 (ptmm) cc_final: 0.8903 (ptmm) REVERT: D 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9390 (mmmm) REVERT: G 11 ASP cc_start: 0.8214 (t0) cc_final: 0.7845 (t0) REVERT: J 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9369 (mmmm) REVERT: K 10 GLU cc_start: 0.9002 (pm20) cc_final: 0.8770 (pm20) REVERT: M 10 GLU cc_start: 0.9124 (pm20) cc_final: 0.8906 (pm20) REVERT: M 26 LYS cc_start: 0.9309 (ptmt) cc_final: 0.8902 (ptmm) REVERT: N 20 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9422 (mmmm) REVERT: O 5 ASN cc_start: 0.9382 (t0) cc_final: 0.8762 (t0) REVERT: P 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9279 (mmmm) REVERT: P 26 LYS cc_start: 0.9367 (ptpp) cc_final: 0.9163 (ptmm) REVERT: T 5 ASN cc_start: 0.9527 (t0) cc_final: 0.9027 (t0) REVERT: T 20 LYS cc_start: 0.9658 (mmmt) cc_final: 0.9353 (mmmm) REVERT: V 5 ASN cc_start: 0.9557 (t0) cc_final: 0.8939 (t0) REVERT: V 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9414 (mmmm) REVERT: V 32 LYS cc_start: 0.9635 (mmtt) cc_final: 0.8909 (mtpt) REVERT: W 26 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8658 (ptmm) REVERT: X 5 ASN cc_start: 0.9458 (t0) cc_final: 0.8847 (t0) REVERT: X 11 ASP cc_start: 0.8110 (t0) cc_final: 0.7773 (t0) REVERT: X 26 LYS cc_start: 0.9436 (pttm) cc_final: 0.9054 (ptpp) REVERT: X 32 LYS cc_start: 0.9658 (mmtt) cc_final: 0.8868 (ttpt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1705 time to fit residues: 25.7460 Evaluate side-chains 126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.2981 r_free = 0.2981 target = 0.037595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.022933 restraints weight = 37253.673| |-----------------------------------------------------------------------------| r_work (start): 0.2331 rms_B_bonded: 5.19 r_work: 0.2169 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7900 Z= 0.119 Angle : 0.561 7.643 10525 Z= 0.280 Chirality : 0.041 0.111 850 Planarity : 0.003 0.025 1350 Dihedral : 3.552 21.238 1075 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 11.87 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.28), residues: 950 helix: 2.29 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR W 25 PHE 0.003 0.001 PHE Y 35 TRP 0.010 0.002 TRP T 8 HIS 0.001 0.000 HIS W 18 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7825) covalent geometry : angle 0.56235 (10375) SS BOND : bond 0.00178 ( 75) SS BOND : angle 0.46243 ( 150) hydrogen bonds : bond 0.02212 ( 250) hydrogen bonds : angle 5.81335 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.289 Fit side-chains REVERT: A 20 LYS cc_start: 0.9639 (mmmt) cc_final: 0.9411 (mmmm) REVERT: C 10 GLU cc_start: 0.8957 (pm20) cc_final: 0.8720 (pm20) REVERT: C 26 LYS cc_start: 0.9337 (ptmm) cc_final: 0.8863 (ptmm) REVERT: D 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9367 (mmmm) REVERT: G 5 ASN cc_start: 0.9310 (t0) cc_final: 0.8571 (t0) REVERT: G 11 ASP cc_start: 0.8149 (t0) cc_final: 0.7804 (t0) REVERT: G 20 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9366 (mmmm) REVERT: I 5 ASN cc_start: 0.9312 (t0) cc_final: 0.8532 (t0) REVERT: I 10 GLU cc_start: 0.8917 (pm20) cc_final: 0.8688 (pm20) REVERT: J 20 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9373 (mmmm) REVERT: K 5 ASN cc_start: 0.9325 (t0) cc_final: 0.8579 (t0) REVERT: K 10 GLU cc_start: 0.9024 (pm20) cc_final: 0.8810 (pm20) REVERT: L 20 LYS cc_start: 0.9665 (mmmt) cc_final: 0.9421 (mmmm) REVERT: M 5 ASN cc_start: 0.9371 (t0) cc_final: 0.8661 (t0) REVERT: M 10 GLU cc_start: 0.9126 (pm20) cc_final: 0.8916 (pm20) REVERT: M 26 LYS cc_start: 0.9308 (ptmt) cc_final: 0.8889 (ptmm) REVERT: N 20 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9419 (mmmm) REVERT: O 5 ASN cc_start: 0.9304 (t0) cc_final: 0.8600 (t0) REVERT: O 10 GLU cc_start: 0.8935 (pm20) cc_final: 0.8569 (pm20) REVERT: P 20 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9326 (mmmm) REVERT: P 26 LYS cc_start: 0.9352 (ptpp) cc_final: 0.9152 (ptmm) REVERT: Q 20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9448 (mmmm) REVERT: R 5 ASN cc_start: 0.9420 (t0) cc_final: 0.8952 (t0) REVERT: T 5 ASN cc_start: 0.9438 (t0) cc_final: 0.9022 (t0) REVERT: T 10 GLU cc_start: 0.8795 (pm20) cc_final: 0.8564 (pm20) REVERT: T 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9310 (mmmm) REVERT: T 25 TYR cc_start: 0.9488 (m-80) cc_final: 0.9165 (m-80) REVERT: U 20 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9420 (mmmm) REVERT: V 5 ASN cc_start: 0.9447 (t0) cc_final: 0.8763 (t0) REVERT: V 10 GLU cc_start: 0.8776 (pm20) cc_final: 0.8410 (pm20) REVERT: V 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9406 (mmmm) REVERT: V 32 LYS cc_start: 0.9593 (mmtt) cc_final: 0.8856 (mtpt) REVERT: W 26 LYS cc_start: 0.9043 (ptmm) cc_final: 0.8676 (ptmm) REVERT: X 5 ASN cc_start: 0.9325 (t0) cc_final: 0.8676 (t0) REVERT: X 26 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: X 32 LYS cc_start: 0.9614 (mmtt) cc_final: 0.8777 (ttpt) REVERT: Y 25 TYR cc_start: 0.9587 (m-80) cc_final: 0.9122 (m-80) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1673 time to fit residues: 27.7529 Evaluate side-chains 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3025 r_free = 0.3025 target = 0.038622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.023495 restraints weight = 38668.947| |-----------------------------------------------------------------------------| r_work (start): 0.2349 rms_B_bonded: 5.24 r_work: 0.2201 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7900 Z= 0.095 Angle : 0.556 7.603 10525 Z= 0.275 Chirality : 0.040 0.116 850 Planarity : 0.003 0.024 1350 Dihedral : 3.181 20.040 1075 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 12.00 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.28), residues: 950 helix: 2.29 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR W 25 PHE 0.002 0.000 PHE A 2 TRP 0.010 0.002 TRP B 8 HIS 0.001 0.000 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7825) covalent geometry : angle 0.55777 (10375) SS BOND : bond 0.00135 ( 75) SS BOND : angle 0.44557 ( 150) hydrogen bonds : bond 0.02014 ( 250) hydrogen bonds : angle 5.59042 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.330 Fit side-chains REVERT: A 5 ASN cc_start: 0.9147 (t0) cc_final: 0.8439 (t0) REVERT: A 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9433 (mmmm) REVERT: C 26 LYS cc_start: 0.9272 (ptmm) cc_final: 0.8819 (ptmm) REVERT: D 20 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9387 (mmmm) REVERT: E 20 LYS cc_start: 0.9590 (mmmt) cc_final: 0.9378 (mmmm) REVERT: F 20 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9344 (mmmm) REVERT: G 5 ASN cc_start: 0.9212 (t0) cc_final: 0.8472 (t0) REVERT: G 11 ASP cc_start: 0.8111 (t0) cc_final: 0.7790 (t0) REVERT: G 20 LYS cc_start: 0.9575 (mmmt) cc_final: 0.9275 (mmmm) REVERT: H 10 GLU cc_start: 0.8934 (pm20) cc_final: 0.8657 (pm20) REVERT: H 20 LYS cc_start: 0.9559 (mmmt) cc_final: 0.9345 (mmmm) REVERT: I 5 ASN cc_start: 0.9188 (t0) cc_final: 0.8414 (t0) REVERT: J 20 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9372 (mmmm) REVERT: K 5 ASN cc_start: 0.9224 (t0) cc_final: 0.8502 (t0) REVERT: L 20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9428 (mmmm) REVERT: M 5 ASN cc_start: 0.9272 (t0) cc_final: 0.8571 (t0) REVERT: M 26 LYS cc_start: 0.9247 (ptmt) cc_final: 0.8803 (ptmm) REVERT: N 20 LYS cc_start: 0.9661 (mmmt) cc_final: 0.9435 (mmmm) REVERT: O 5 ASN cc_start: 0.9199 (t0) cc_final: 0.8495 (t0) REVERT: O 10 GLU cc_start: 0.8929 (pm20) cc_final: 0.8579 (pm20) REVERT: P 5 ASN cc_start: 0.9358 (t0) cc_final: 0.8988 (t0) REVERT: P 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9346 (mmmm) REVERT: Q 20 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9458 (mmmm) REVERT: R 5 ASN cc_start: 0.9313 (t0) cc_final: 0.8889 (t0) REVERT: S 20 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9409 (mmmm) REVERT: S 25 TYR cc_start: 0.9446 (m-80) cc_final: 0.9153 (m-10) REVERT: T 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8939 (t0) REVERT: T 20 LYS cc_start: 0.9639 (mmmt) cc_final: 0.9327 (mmmm) REVERT: T 25 TYR cc_start: 0.9464 (m-80) cc_final: 0.9058 (m-80) REVERT: U 20 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9451 (mmmm) REVERT: V 5 ASN cc_start: 0.9397 (t0) cc_final: 0.8728 (t0) REVERT: V 10 GLU cc_start: 0.8796 (pm20) cc_final: 0.8449 (pm20) REVERT: V 20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9405 (mmmm) REVERT: V 32 LYS cc_start: 0.9606 (mmtt) cc_final: 0.8913 (mtpt) REVERT: W 26 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8691 (ptmm) REVERT: X 5 ASN cc_start: 0.9254 (t0) cc_final: 0.8613 (t0) REVERT: X 26 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9001 (ptpp) REVERT: X 32 LYS cc_start: 0.9626 (mmtt) cc_final: 0.8867 (ttpt) REVERT: Y 25 TYR cc_start: 0.9600 (m-80) cc_final: 0.9109 (m-80) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1677 time to fit residues: 29.3058 Evaluate side-chains 145 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.022939 restraints weight = 38887.111| |-----------------------------------------------------------------------------| r_work (start): 0.2309 rms_B_bonded: 5.09 r_work: 0.2159 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7900 Z= 0.236 Angle : 0.666 8.384 10525 Z= 0.332 Chirality : 0.044 0.110 850 Planarity : 0.003 0.025 1350 Dihedral : 3.680 23.019 1075 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.13 % Allowed : 12.39 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.28), residues: 950 helix: 2.57 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.61 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR W 25 PHE 0.006 0.001 PHE Q 2 TRP 0.012 0.002 TRP M 8 HIS 0.001 0.000 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7825) covalent geometry : angle 0.66667 (10375) SS BOND : bond 0.00295 ( 75) SS BOND : angle 0.61349 ( 150) hydrogen bonds : bond 0.02640 ( 250) hydrogen bonds : angle 6.03795 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.248 Fit side-chains REVERT: A 20 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9412 (mmmm) REVERT: C 10 GLU cc_start: 0.8914 (pm20) cc_final: 0.8671 (pm20) REVERT: C 26 LYS cc_start: 0.9260 (ptmm) cc_final: 0.8837 (ptmm) REVERT: D 20 LYS cc_start: 0.9656 (mmmt) cc_final: 0.9395 (mmmm) REVERT: G 11 ASP cc_start: 0.8107 (t0) cc_final: 0.7747 (t0) REVERT: G 20 LYS cc_start: 0.9605 (mmmt) cc_final: 0.9327 (mmmm) REVERT: J 20 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9382 (mmmm) REVERT: K 5 ASN cc_start: 0.9420 (t0) cc_final: 0.8791 (t0) REVERT: K 10 GLU cc_start: 0.8916 (pm20) cc_final: 0.8606 (pm20) REVERT: M 10 GLU cc_start: 0.9029 (pm20) cc_final: 0.8697 (pm20) REVERT: M 26 LYS cc_start: 0.9261 (ptmt) cc_final: 0.8829 (ptmm) REVERT: N 20 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9410 (mmmm) REVERT: O 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8780 (t0) REVERT: O 10 GLU cc_start: 0.8991 (pm20) cc_final: 0.8635 (pm20) REVERT: P 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9300 (mmmm) REVERT: T 5 ASN cc_start: 0.9501 (t0) cc_final: 0.9019 (t0) REVERT: T 10 GLU cc_start: 0.8855 (pm20) cc_final: 0.8564 (pm20) REVERT: T 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9344 (mmmm) REVERT: T 25 TYR cc_start: 0.9466 (m-80) cc_final: 0.9136 (m-80) REVERT: V 5 ASN cc_start: 0.9547 (t0) cc_final: 0.8948 (t0) REVERT: V 10 GLU cc_start: 0.8830 (pm20) cc_final: 0.8479 (pm20) REVERT: V 20 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9418 (mmmm) REVERT: V 32 LYS cc_start: 0.9663 (mmtt) cc_final: 0.8967 (mtpt) REVERT: X 5 ASN cc_start: 0.9457 (t0) cc_final: 0.9005 (t0) REVERT: X 26 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: X 32 LYS cc_start: 0.9679 (mmtt) cc_final: 0.8920 (ttpt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1729 time to fit residues: 26.9432 Evaluate side-chains 131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3006 r_free = 0.3006 target = 0.038109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.023134 restraints weight = 38466.963| |-----------------------------------------------------------------------------| r_work (start): 0.2328 rms_B_bonded: 5.17 r_work: 0.2179 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7900 Z= 0.137 Angle : 0.626 9.326 10525 Z= 0.311 Chirality : 0.041 0.110 850 Planarity : 0.003 0.025 1350 Dihedral : 3.627 22.757 1075 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 12.26 % Favored : 87.61 % 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: 0.29 (0.28), residues: 950 helix: 2.48 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.59 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR W 25 PHE 0.005 0.001 PHE Y 35 TRP 0.010 0.002 TRP K 8 HIS 0.001 0.000 HIS S 18 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7825) covalent geometry : angle 0.62763 (10375) SS BOND : bond 0.00198 ( 75) SS BOND : angle 0.47456 ( 150) hydrogen bonds : bond 0.02242 ( 250) hydrogen bonds : angle 5.75524 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.376 Fit side-chains REVERT: A 20 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9415 (mmmm) REVERT: C 26 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8808 (ptmm) REVERT: G 11 ASP cc_start: 0.8039 (t0) cc_final: 0.7685 (t0) REVERT: G 20 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9281 (mmmm) REVERT: H 10 GLU cc_start: 0.8933 (pm20) cc_final: 0.8715 (pm20) REVERT: I 5 ASN cc_start: 0.9320 (t0) cc_final: 0.8640 (t0) REVERT: I 10 GLU cc_start: 0.8926 (pm20) cc_final: 0.8608 (pm20) REVERT: J 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9374 (mmmm) REVERT: K 5 ASN cc_start: 0.9337 (t0) cc_final: 0.8665 (t0) REVERT: K 10 GLU cc_start: 0.8921 (pm20) cc_final: 0.8636 (pm20) REVERT: L 20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9421 (mmmm) REVERT: M 5 ASN cc_start: 0.9367 (t0) cc_final: 0.8725 (t0) REVERT: M 10 GLU cc_start: 0.9054 (pm20) cc_final: 0.8743 (pm20) REVERT: M 26 LYS cc_start: 0.9268 (ptmt) cc_final: 0.8824 (ptmm) REVERT: N 20 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9429 (mmmm) REVERT: O 5 ASN cc_start: 0.9285 (t0) cc_final: 0.8665 (t0) REVERT: O 10 GLU cc_start: 0.8964 (pm20) cc_final: 0.8623 (pm20) REVERT: P 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9297 (mmmm) REVERT: Q 10 GLU cc_start: 0.9086 (pm20) cc_final: 0.8824 (pm20) REVERT: Q 20 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9457 (mmmm) REVERT: R 5 ASN cc_start: 0.9407 (t0) cc_final: 0.8984 (t0) REVERT: R 25 TYR cc_start: 0.9502 (m-80) cc_final: 0.9274 (m-80) REVERT: S 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9430 (mmmm) REVERT: T 5 ASN cc_start: 0.9431 (t0) cc_final: 0.8842 (t0) REVERT: T 10 GLU cc_start: 0.8871 (pm20) cc_final: 0.8608 (pm20) REVERT: T 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9306 (mmmm) REVERT: T 25 TYR cc_start: 0.9458 (m-80) cc_final: 0.9125 (m-80) REVERT: U 20 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9437 (mmmm) REVERT: V 5 ASN cc_start: 0.9451 (t0) cc_final: 0.8835 (t0) REVERT: V 10 GLU cc_start: 0.8823 (pm20) cc_final: 0.8480 (pm20) REVERT: V 20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9408 (mmmm) REVERT: V 32 LYS cc_start: 0.9625 (mmtt) cc_final: 0.8921 (mtpt) REVERT: X 5 ASN cc_start: 0.9346 (t0) cc_final: 0.8750 (t0) REVERT: X 26 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9056 (ptpp) REVERT: X 32 LYS cc_start: 0.9644 (mmtt) cc_final: 0.8869 (ttpt) REVERT: Y 25 TYR cc_start: 0.9595 (m-80) cc_final: 0.9133 (m-80) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1675 time to fit residues: 28.1548 Evaluate side-chains 139 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.2994 r_free = 0.2994 target = 0.037704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.022808 restraints weight = 38393.253| |-----------------------------------------------------------------------------| r_work (start): 0.2308 rms_B_bonded: 5.19 r_work: 0.2156 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7900 Z= 0.196 Angle : 0.647 9.037 10525 Z= 0.323 Chirality : 0.042 0.113 850 Planarity : 0.003 0.025 1350 Dihedral : 3.715 22.366 1075 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 0.26 % Allowed : 12.00 % Favored : 87.74 % 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: 0.28 (0.28), residues: 950 helix: 2.60 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.65 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR W 25 PHE 0.005 0.001 PHE H 2 TRP 0.011 0.002 TRP Y 8 HIS 0.001 0.000 HIS L 18 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7825) covalent geometry : angle 0.64846 (10375) SS BOND : bond 0.00250 ( 75) SS BOND : angle 0.54430 ( 150) hydrogen bonds : bond 0.02452 ( 250) hydrogen bonds : angle 5.93347 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.60 seconds wall clock time: 30 minutes 45.85 seconds (1845.85 seconds total)