Starting phenix.real_space_refine on Fri Jun 6 09:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_12776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_12776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_12776.map" model { file = "/net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_12776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oag_12776/06_2025/7oag_12776.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X Time building chain proxies: 2.25, per 1000 atoms: 0.30 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 C 4 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 15 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 15 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 15 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 15 " - pdb=" SG CYS Y 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 15 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 39 " distance=2.02 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 39 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 39 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 39 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 39 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 39 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 39 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 39 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 39 " distance=2.03 Simple disulfide: pdb=" SG CYS W 19 " - pdb=" SG CYS W 39 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 39 " distance=2.02 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 39 " distance=2.03 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: 1.72 Conformation dependent library (CDL) restraints added in 932.5 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: 0.97 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: 1.72 Time building geometry restraints manager: 2.10 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.250 Find NCS groups from input model: 0.160 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.006 0.002 TRP R 8 HIS 0.002 0.001 HIS U 16 PHE 0.008 0.001 PHE W 2 TYR 0.005 0.001 TYR F 40 Details of bonding type rmsd hydrogen bonds : bond 0.21425 ( 250) hydrogen bonds : angle 8.98794 ( 600) SS BOND : bond 0.00363 ( 75) SS BOND : angle 1.06410 ( 150) covalent geometry : bond 0.00693 ( 7825) covalent geometry : angle 0.67321 (10375) *********************** 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 : 0.974 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: 0.9073 (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: 0.8722 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3951 time to fit residues: 56.3145 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.037992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.023312 restraints weight = 38822.983| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 5.17 r_work: 0.2176 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7900 Z= 0.206 Angle : 0.600 5.108 10525 Z= 0.307 Chirality : 0.045 0.110 850 Planarity : 0.004 0.028 1350 Dihedral : 4.112 21.292 1075 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 950 helix: 1.93 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.52 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 8 HIS 0.002 0.000 HIS W 16 PHE 0.012 0.001 PHE Y 35 TYR 0.007 0.001 TYR J 25 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 250) hydrogen bonds : angle 6.70893 ( 600) SS BOND : bond 0.00196 ( 75) SS BOND : angle 0.63083 ( 150) covalent geometry : bond 0.00440 ( 7825) covalent geometry : angle 0.59966 (10375) *********************** 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 : 0.934 Fit side-chains REVERT: C 26 LYS cc_start: 0.9376 (ptmm) cc_final: 0.9072 (ptmm) REVERT: I 13 MET cc_start: 0.8574 (mpp) cc_final: 0.8045 (mpp) REVERT: P 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9333 (mmmm) REVERT: T 5 ASN cc_start: 0.9493 (t0) cc_final: 0.9028 (t0) REVERT: V 5 ASN cc_start: 0.9522 (t0) cc_final: 0.8964 (t0) REVERT: V 32 LYS cc_start: 0.9707 (mmtt) cc_final: 0.9042 (mtpt) REVERT: W 25 TYR cc_start: 0.9424 (m-80) cc_final: 0.9114 (m-80) REVERT: W 26 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8842 (ptmm) REVERT: X 5 ASN cc_start: 0.9428 (t0) cc_final: 0.8962 (t0) REVERT: X 32 LYS cc_start: 0.9676 (mmtt) cc_final: 0.9033 (mtpt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3928 time to fit residues: 54.6112 Evaluate side-chains 112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.2982 r_free = 0.2982 target = 0.037445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.023103 restraints weight = 37974.407| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 5.13 r_work: 0.2173 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7900 Z= 0.163 Angle : 0.537 4.993 10525 Z= 0.273 Chirality : 0.042 0.107 850 Planarity : 0.004 0.027 1350 Dihedral : 3.695 18.919 1075 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 950 helix: 2.21 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 8 HIS 0.002 0.000 HIS B 16 PHE 0.005 0.001 PHE Y 35 TYR 0.013 0.001 TYR F 25 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 250) hydrogen bonds : angle 6.29873 ( 600) SS BOND : bond 0.00222 ( 75) SS BOND : angle 0.52250 ( 150) covalent geometry : bond 0.00351 ( 7825) covalent geometry : angle 0.53690 (10375) *********************** 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 : 0.881 Fit side-chains REVERT: C 26 LYS cc_start: 0.9416 (ptmm) cc_final: 0.9132 (ptmm) REVERT: G 11 ASP cc_start: 0.8229 (t0) cc_final: 0.7895 (t0) REVERT: I 20 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9360 (mmmm) REVERT: K 5 ASN cc_start: 0.9380 (t0) cc_final: 0.8717 (t0) REVERT: M 10 GLU cc_start: 0.9008 (pm20) cc_final: 0.8743 (pm20) REVERT: M 26 LYS cc_start: 0.9359 (ptmt) cc_final: 0.9032 (ptmm) REVERT: N 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9428 (mmmm) REVERT: O 5 ASN cc_start: 0.9385 (t0) cc_final: 0.8741 (t0) REVERT: O 10 GLU cc_start: 0.9006 (pm20) cc_final: 0.8679 (pm20) REVERT: P 20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9286 (mmmm) REVERT: R 5 ASN cc_start: 0.9515 (t0) cc_final: 0.8935 (t0) REVERT: T 5 ASN cc_start: 0.9483 (t0) cc_final: 0.8916 (t0) REVERT: T 20 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9328 (mmmm) REVERT: V 5 ASN cc_start: 0.9529 (t0) cc_final: 0.8917 (t0) REVERT: V 32 LYS cc_start: 0.9626 (mmtt) cc_final: 0.8887 (mtpt) REVERT: W 25 TYR cc_start: 0.9492 (m-80) cc_final: 0.9217 (m-80) REVERT: W 26 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8838 (ptmm) REVERT: X 5 ASN cc_start: 0.9425 (t0) cc_final: 0.8926 (t0) REVERT: X 32 LYS cc_start: 0.9639 (mmtt) cc_final: 0.8786 (ttpt) REVERT: Y 13 MET cc_start: 0.8534 (mmt) cc_final: 0.8196 (mmm) REVERT: Y 25 TYR cc_start: 0.9560 (m-80) cc_final: 0.9024 (m-80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3864 time to fit residues: 59.3009 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 : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.022857 restraints weight = 37030.575| |-----------------------------------------------------------------------------| r_work (start): 0.2333 rms_B_bonded: 5.16 r_work: 0.2175 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3799 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= 0.134 Angle : 0.523 5.149 10525 Z= 0.264 Chirality : 0.041 0.107 850 Planarity : 0.003 0.026 1350 Dihedral : 3.545 17.940 1075 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 10.32 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 950 helix: 2.13 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 8 HIS 0.001 0.000 HIS X 16 PHE 0.004 0.001 PHE Y 35 TYR 0.010 0.001 TYR D 25 Details of bonding type rmsd hydrogen bonds : bond 0.02456 ( 250) hydrogen bonds : angle 6.06398 ( 600) SS BOND : bond 0.00183 ( 75) SS BOND : angle 0.47674 ( 150) covalent geometry : bond 0.00293 ( 7825) covalent geometry : angle 0.52343 (10375) *********************** 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 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.862 Fit side-chains REVERT: A 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9396 (mmmm) REVERT: C 26 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9084 (ptmm) REVERT: D 20 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9379 (mmmm) REVERT: G 11 ASP cc_start: 0.8250 (t0) cc_final: 0.7871 (t0) REVERT: H 10 GLU cc_start: 0.8968 (pm20) cc_final: 0.8692 (pm20) REVERT: I 5 ASN cc_start: 0.9372 (t0) cc_final: 0.8661 (t0) REVERT: I 20 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9365 (mmmm) REVERT: J 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9348 (mmmm) REVERT: K 5 ASN cc_start: 0.9352 (t0) cc_final: 0.8620 (t0) REVERT: M 10 GLU cc_start: 0.9043 (pm20) cc_final: 0.8782 (pm20) REVERT: M 26 LYS cc_start: 0.9371 (ptmt) cc_final: 0.9033 (ptmm) REVERT: N 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9414 (mmmm) REVERT: O 5 ASN cc_start: 0.9354 (t0) cc_final: 0.8700 (t0) REVERT: O 10 GLU cc_start: 0.9038 (pm20) cc_final: 0.8748 (pm20) REVERT: P 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9282 (mmmm) REVERT: R 5 ASN cc_start: 0.9462 (t0) cc_final: 0.8818 (t0) REVERT: T 5 ASN cc_start: 0.9459 (t0) cc_final: 0.8868 (t0) REVERT: T 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9317 (mmmm) REVERT: V 5 ASN cc_start: 0.9515 (t0) cc_final: 0.8899 (t0) REVERT: V 20 LYS cc_start: 0.9658 (mmmt) cc_final: 0.9433 (mmmm) REVERT: V 32 LYS cc_start: 0.9616 (mmtt) cc_final: 0.8877 (mtpt) REVERT: W 25 TYR cc_start: 0.9511 (m-80) cc_final: 0.9309 (m-80) REVERT: W 26 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8744 (ptmm) REVERT: X 5 ASN cc_start: 0.9352 (t0) cc_final: 0.8771 (t0) REVERT: X 26 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9111 (ptpp) REVERT: X 32 LYS cc_start: 0.9629 (mmtt) cc_final: 0.8790 (ttpt) REVERT: Y 13 MET cc_start: 0.8451 (mmt) cc_final: 0.8111 (mmm) REVERT: Y 25 TYR cc_start: 0.9567 (m-80) cc_final: 0.9000 (m-80) outliers start: 2 outliers final: 1 residues processed: 135 average time/residue: 0.3981 time to fit residues: 64.0778 Evaluate side-chains 132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 13 MET 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 91 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 = 0.2973 r_free = 0.2973 target = 0.037394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.022772 restraints weight = 37536.284| |-----------------------------------------------------------------------------| r_work (start): 0.2308 rms_B_bonded: 5.16 r_work: 0.2156 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7900 Z= 0.151 Angle : 0.539 5.664 10525 Z= 0.271 Chirality : 0.042 0.108 850 Planarity : 0.003 0.026 1350 Dihedral : 3.530 18.552 1075 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.39 % Allowed : 11.23 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 950 helix: 2.15 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 8 HIS 0.001 0.000 HIS C 16 PHE 0.003 0.001 PHE Y 35 TYR 0.011 0.001 TYR D 25 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 250) hydrogen bonds : angle 6.02609 ( 600) SS BOND : bond 0.00203 ( 75) SS BOND : angle 0.48491 ( 150) covalent geometry : bond 0.00327 ( 7825) covalent geometry : angle 0.53997 (10375) *********************** 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 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.923 Fit side-chains REVERT: A 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9385 (mmmm) REVERT: D 20 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9353 (mmmm) REVERT: G 11 ASP cc_start: 0.8229 (t0) cc_final: 0.7973 (t0) REVERT: H 10 GLU cc_start: 0.8960 (pm20) cc_final: 0.8634 (pm20) REVERT: I 5 ASN cc_start: 0.9382 (t0) cc_final: 0.8650 (t0) REVERT: I 20 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9339 (mmmm) REVERT: J 20 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9344 (mmmm) REVERT: K 5 ASN cc_start: 0.9366 (t0) cc_final: 0.8657 (t0) REVERT: L 20 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9434 (mmmm) REVERT: M 10 GLU cc_start: 0.9060 (pm20) cc_final: 0.8827 (pm20) REVERT: M 26 LYS cc_start: 0.9306 (ptmt) cc_final: 0.8917 (ptmm) REVERT: N 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9412 (mmmm) REVERT: O 5 ASN cc_start: 0.9336 (t0) cc_final: 0.8689 (t0) REVERT: P 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9291 (mmmm) REVERT: R 5 ASN cc_start: 0.9467 (t0) cc_final: 0.8821 (t0) REVERT: T 5 ASN cc_start: 0.9470 (t0) cc_final: 0.8923 (t0) REVERT: T 20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9320 (mmmm) REVERT: V 5 ASN cc_start: 0.9526 (t0) cc_final: 0.8913 (t0) REVERT: V 20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9430 (mmmm) REVERT: V 32 LYS cc_start: 0.9633 (mmtt) cc_final: 0.8921 (mtpt) REVERT: X 5 ASN cc_start: 0.9375 (t0) cc_final: 0.8804 (t0) REVERT: X 26 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9082 (ptpp) REVERT: X 32 LYS cc_start: 0.9644 (mmtt) cc_final: 0.8850 (ttpt) REVERT: Y 13 MET cc_start: 0.8420 (mmt) cc_final: 0.8103 (mmm) outliers start: 3 outliers final: 1 residues processed: 135 average time/residue: 0.3826 time to fit residues: 61.1616 Evaluate side-chains 133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- 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 = 0.2988 r_free = 0.2988 target = 0.037892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.023062 restraints weight = 37379.457| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 5.21 r_work: 0.2175 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7900 Z= 0.111 Angle : 0.525 6.129 10525 Z= 0.265 Chirality : 0.041 0.112 850 Planarity : 0.003 0.025 1350 Dihedral : 3.399 19.417 1075 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 11.61 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 950 helix: 2.21 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.52 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 8 HIS 0.001 0.000 HIS Y 18 PHE 0.003 0.001 PHE Y 35 TYR 0.015 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02228 ( 250) hydrogen bonds : angle 5.80350 ( 600) SS BOND : bond 0.00169 ( 75) SS BOND : angle 0.46741 ( 150) covalent geometry : bond 0.00255 ( 7825) covalent geometry : angle 0.52581 (10375) *********************** 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 147 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.866 Fit side-chains REVERT: A 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9418 (mmmm) REVERT: D 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9383 (mmmm) REVERT: E 20 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9367 (mmmm) REVERT: G 5 ASN cc_start: 0.9285 (t0) cc_final: 0.8541 (t0) REVERT: G 11 ASP cc_start: 0.8199 (t0) cc_final: 0.7734 (t0) REVERT: G 13 MET cc_start: 0.8644 (mmt) cc_final: 0.8256 (mmt) REVERT: H 10 GLU cc_start: 0.8964 (pm20) cc_final: 0.8656 (pm20) REVERT: I 5 ASN cc_start: 0.9302 (t0) cc_final: 0.8535 (t0) REVERT: I 10 GLU cc_start: 0.8886 (pm20) cc_final: 0.8667 (pm20) REVERT: I 20 LYS cc_start: 0.9578 (mmmt) cc_final: 0.9346 (mmmm) REVERT: J 20 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9340 (mmmm) REVERT: K 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8591 (t0) REVERT: K 10 GLU cc_start: 0.8946 (pm20) cc_final: 0.8725 (pm20) REVERT: L 20 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9444 (mmmm) REVERT: M 5 ASN cc_start: 0.9355 (t0) cc_final: 0.8662 (t0) REVERT: M 10 GLU cc_start: 0.9058 (pm20) cc_final: 0.8850 (pm20) REVERT: M 26 LYS cc_start: 0.9305 (ptmt) cc_final: 0.8899 (ptmm) REVERT: N 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9418 (mmmm) REVERT: O 5 ASN cc_start: 0.9294 (t0) cc_final: 0.8605 (t0) REVERT: O 10 GLU cc_start: 0.8959 (pm20) cc_final: 0.8648 (pm20) REVERT: P 5 ASN cc_start: 0.9409 (t0) cc_final: 0.9048 (t0) REVERT: P 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9310 (mmmm) REVERT: Q 20 LYS cc_start: 0.9671 (mmmt) cc_final: 0.9453 (mmmm) REVERT: R 5 ASN cc_start: 0.9385 (t0) cc_final: 0.8927 (t0) REVERT: S 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9411 (mmmm) REVERT: T 5 ASN cc_start: 0.9415 (t0) cc_final: 0.9026 (t0) REVERT: T 20 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9290 (mmmm) REVERT: T 25 TYR cc_start: 0.9490 (m-80) cc_final: 0.9127 (m-80) REVERT: U 20 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9437 (mmmm) REVERT: V 5 ASN cc_start: 0.9439 (t0) cc_final: 0.8769 (t0) REVERT: V 20 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9451 (mmmm) REVERT: V 32 LYS cc_start: 0.9616 (mmtt) cc_final: 0.8920 (mtpt) REVERT: X 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8717 (t0) REVERT: X 26 LYS cc_start: 0.9415 (pttm) cc_final: 0.9078 (ptpp) REVERT: X 32 LYS cc_start: 0.9631 (mmtt) cc_final: 0.8801 (ttpt) REVERT: Y 25 TYR cc_start: 0.9592 (m-80) cc_final: 0.9056 (m-80) outliers start: 2 outliers final: 0 residues processed: 145 average time/residue: 0.3800 time to fit residues: 65.1040 Evaluate side-chains 140 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.022851 restraints weight = 37215.933| |-----------------------------------------------------------------------------| r_work (start): 0.2314 rms_B_bonded: 5.14 r_work: 0.2158 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7900 Z= 0.154 Angle : 0.552 6.713 10525 Z= 0.279 Chirality : 0.042 0.111 850 Planarity : 0.003 0.025 1350 Dihedral : 3.487 20.037 1075 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 11.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 950 helix: 2.31 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 8 HIS 0.001 0.000 HIS B 16 PHE 0.003 0.001 PHE U 2 TYR 0.014 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02402 ( 250) hydrogen bonds : angle 5.89677 ( 600) SS BOND : bond 0.00210 ( 75) SS BOND : angle 0.49976 ( 150) covalent geometry : bond 0.00336 ( 7825) covalent geometry : angle 0.55255 (10375) *********************** 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 142 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.997 Fit side-chains REVERT: A 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9415 (mmmm) REVERT: D 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9377 (mmmm) REVERT: E 20 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9389 (mmmm) REVERT: G 11 ASP cc_start: 0.8229 (t0) cc_final: 0.7754 (t0) REVERT: G 13 MET cc_start: 0.8657 (mmt) cc_final: 0.8262 (mmt) REVERT: H 10 GLU cc_start: 0.8946 (pm20) cc_final: 0.8703 (pm20) REVERT: I 5 ASN cc_start: 0.9360 (t0) cc_final: 0.8626 (t0) REVERT: I 10 GLU cc_start: 0.8929 (pm20) cc_final: 0.8710 (pm20) REVERT: I 20 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9342 (mmmm) REVERT: J 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9337 (mmmm) REVERT: K 5 ASN cc_start: 0.9365 (t0) cc_final: 0.8680 (t0) REVERT: L 20 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9447 (mmmm) REVERT: M 5 ASN cc_start: 0.9384 (t0) cc_final: 0.8734 (t0) REVERT: M 10 GLU cc_start: 0.9112 (pm20) cc_final: 0.8898 (pm20) REVERT: M 26 LYS cc_start: 0.9277 (ptmt) cc_final: 0.8855 (ptmm) REVERT: N 20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9421 (mmmm) REVERT: O 5 ASN cc_start: 0.9316 (t0) cc_final: 0.8661 (t0) REVERT: O 10 GLU cc_start: 0.9044 (pm20) cc_final: 0.8747 (pm20) REVERT: P 20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9286 (mmmm) REVERT: Q 20 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9446 (mmmm) REVERT: R 5 ASN cc_start: 0.9466 (t0) cc_final: 0.8980 (t0) REVERT: T 5 ASN cc_start: 0.9468 (t0) cc_final: 0.8916 (t0) REVERT: T 20 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9301 (mmmm) REVERT: T 25 TYR cc_start: 0.9481 (m-80) cc_final: 0.9117 (m-80) REVERT: U 20 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9435 (mmmm) REVERT: V 5 ASN cc_start: 0.9481 (t0) cc_final: 0.8854 (t0) REVERT: V 20 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9414 (mmmm) REVERT: V 32 LYS cc_start: 0.9639 (mmtt) cc_final: 0.8939 (mtpt) REVERT: X 5 ASN cc_start: 0.9364 (t0) cc_final: 0.8744 (t0) REVERT: X 26 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9051 (ptpp) REVERT: X 32 LYS cc_start: 0.9655 (mmtt) cc_final: 0.8868 (ttpt) REVERT: Y 13 MET cc_start: 0.8437 (mmt) cc_final: 0.8144 (mmm) REVERT: Y 25 TYR cc_start: 0.9578 (m-80) cc_final: 0.9033 (m-80) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.3779 time to fit residues: 62.9723 Evaluate side-chains 140 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.037701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.022908 restraints weight = 37739.643| |-----------------------------------------------------------------------------| r_work (start): 0.2315 rms_B_bonded: 5.20 r_work: 0.2159 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7900 Z= 0.138 Angle : 0.570 7.200 10525 Z= 0.288 Chirality : 0.041 0.112 850 Planarity : 0.003 0.025 1350 Dihedral : 3.455 21.458 1075 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 12.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 950 helix: 2.32 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 8 HIS 0.001 0.000 HIS N 18 PHE 0.003 0.001 PHE Y 35 TYR 0.014 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02259 ( 250) hydrogen bonds : angle 5.81061 ( 600) SS BOND : bond 0.00191 ( 75) SS BOND : angle 0.47357 ( 150) covalent geometry : bond 0.00311 ( 7825) covalent geometry : angle 0.57130 (10375) *********************** 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 145 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.868 Fit side-chains REVERT: A 20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9420 (mmmm) REVERT: D 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9438 (mmmm) REVERT: E 20 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9393 (mmmm) REVERT: G 5 ASN cc_start: 0.9307 (t0) cc_final: 0.8595 (t0) REVERT: G 11 ASP cc_start: 0.8202 (t0) cc_final: 0.7678 (t0) REVERT: G 13 MET cc_start: 0.8634 (mmt) cc_final: 0.8222 (mmt) REVERT: H 10 GLU cc_start: 0.8959 (pm20) cc_final: 0.8718 (pm20) REVERT: I 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8581 (t0) REVERT: I 10 GLU cc_start: 0.8954 (pm20) cc_final: 0.8753 (pm20) REVERT: I 20 LYS cc_start: 0.9585 (mmmt) cc_final: 0.9340 (mmmm) REVERT: J 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9337 (mmmm) REVERT: K 5 ASN cc_start: 0.9342 (t0) cc_final: 0.8631 (t0) REVERT: K 10 GLU cc_start: 0.8922 (pm20) cc_final: 0.8624 (pm20) REVERT: L 20 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9441 (mmmm) REVERT: M 5 ASN cc_start: 0.9378 (t0) cc_final: 0.8692 (t0) REVERT: M 26 LYS cc_start: 0.9269 (ptmt) cc_final: 0.8834 (ptmm) REVERT: N 20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9410 (mmmm) REVERT: O 5 ASN cc_start: 0.9301 (t0) cc_final: 0.8642 (t0) REVERT: O 10 GLU cc_start: 0.9099 (pm20) cc_final: 0.8809 (pm20) REVERT: P 20 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9275 (mmmm) REVERT: Q 20 LYS cc_start: 0.9681 (mmmt) cc_final: 0.9452 (mmmm) REVERT: R 5 ASN cc_start: 0.9427 (t0) cc_final: 0.8974 (t0) REVERT: S 20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9407 (mmmm) REVERT: T 5 ASN cc_start: 0.9448 (t0) cc_final: 0.9053 (t0) REVERT: T 10 GLU cc_start: 0.8809 (pm20) cc_final: 0.8569 (pm20) REVERT: T 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9310 (mmmm) REVERT: T 25 TYR cc_start: 0.9470 (m-80) cc_final: 0.9123 (m-80) REVERT: U 20 LYS cc_start: 0.9687 (mmmt) cc_final: 0.9438 (mmmm) REVERT: V 5 ASN cc_start: 0.9463 (t0) cc_final: 0.8796 (t0) REVERT: V 10 GLU cc_start: 0.8741 (pm20) cc_final: 0.8410 (pm20) REVERT: V 20 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9408 (mmmm) REVERT: V 32 LYS cc_start: 0.9619 (mmtt) cc_final: 0.8926 (mtpt) REVERT: X 5 ASN cc_start: 0.9343 (t0) cc_final: 0.8727 (t0) REVERT: X 26 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.9056 (ptpp) REVERT: X 32 LYS cc_start: 0.9640 (mmtt) cc_final: 0.8850 (ttpt) REVERT: Y 13 MET cc_start: 0.8403 (mmt) cc_final: 0.8105 (mmm) REVERT: Y 25 TYR cc_start: 0.9589 (m-80) cc_final: 0.9063 (m-80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.3821 time to fit residues: 64.9012 Evaluate side-chains 142 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 0.0070 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.038403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.023423 restraints weight = 37985.989| |-----------------------------------------------------------------------------| r_work (start): 0.2345 rms_B_bonded: 5.29 r_work: 0.2191 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7900 Z= 0.097 Angle : 0.566 7.829 10525 Z= 0.283 Chirality : 0.040 0.115 850 Planarity : 0.003 0.025 1350 Dihedral : 3.185 20.156 1075 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 950 helix: 2.30 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 8 HIS 0.001 0.000 HIS M 18 PHE 0.003 0.000 PHE A 2 TYR 0.015 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02015 ( 250) hydrogen bonds : angle 5.56646 ( 600) SS BOND : bond 0.00137 ( 75) SS BOND : angle 0.44851 ( 150) covalent geometry : bond 0.00241 ( 7825) covalent geometry : angle 0.56764 (10375) *********************** 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 152 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.883 Fit side-chains REVERT: A 5 ASN cc_start: 0.9151 (t0) cc_final: 0.8389 (t0) REVERT: A 20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9440 (mmmm) REVERT: C 10 GLU cc_start: 0.8872 (pm20) cc_final: 0.8525 (pm20) REVERT: D 20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9411 (mmmm) REVERT: E 20 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9400 (mmmm) REVERT: F 20 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9347 (mmmm) REVERT: G 5 ASN cc_start: 0.9210 (t0) cc_final: 0.8441 (t0) REVERT: G 11 ASP cc_start: 0.8260 (t0) cc_final: 0.7786 (t0) REVERT: G 13 MET cc_start: 0.8574 (mmt) cc_final: 0.8174 (mmt) REVERT: G 25 TYR cc_start: 0.9517 (m-80) cc_final: 0.9197 (m-80) REVERT: H 10 GLU cc_start: 0.8946 (pm20) cc_final: 0.8697 (pm20) REVERT: H 20 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9337 (mmmm) REVERT: I 5 ASN cc_start: 0.9194 (t0) cc_final: 0.8393 (t0) REVERT: I 20 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9393 (mmmm) REVERT: J 20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9367 (mmmm) REVERT: K 5 ASN cc_start: 0.9235 (t0) cc_final: 0.8493 (t0) REVERT: K 10 GLU cc_start: 0.8974 (pm20) cc_final: 0.8693 (pm20) REVERT: L 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9419 (mmmm) REVERT: M 5 ASN cc_start: 0.9273 (t0) cc_final: 0.8546 (t0) REVERT: M 10 GLU cc_start: 0.8975 (pm20) cc_final: 0.8664 (pm20) REVERT: M 26 LYS cc_start: 0.9240 (ptmt) cc_final: 0.8786 (ptmm) REVERT: N 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9404 (mmmm) REVERT: O 5 ASN cc_start: 0.9202 (t0) cc_final: 0.8481 (t0) REVERT: O 10 GLU cc_start: 0.9098 (pm20) cc_final: 0.8858 (pm20) REVERT: P 5 ASN cc_start: 0.9342 (t0) cc_final: 0.8966 (t0) REVERT: P 20 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9276 (mmmm) REVERT: Q 10 GLU cc_start: 0.9016 (pm20) cc_final: 0.8727 (pm20) REVERT: Q 20 LYS cc_start: 0.9683 (mmmt) cc_final: 0.9458 (mmmm) REVERT: R 5 ASN cc_start: 0.9314 (t0) cc_final: 0.8872 (t0) REVERT: S 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9437 (mmmm) REVERT: T 5 ASN cc_start: 0.9358 (t0) cc_final: 0.8909 (t0) REVERT: T 10 GLU cc_start: 0.8833 (pm20) cc_final: 0.8612 (pm20) REVERT: T 20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9324 (mmmm) REVERT: T 25 TYR cc_start: 0.9458 (m-80) cc_final: 0.9082 (m-80) REVERT: U 20 LYS cc_start: 0.9692 (mmmt) cc_final: 0.9454 (mmmm) REVERT: V 5 ASN cc_start: 0.9387 (t0) cc_final: 0.8693 (t0) REVERT: V 10 GLU cc_start: 0.8784 (pm20) cc_final: 0.8462 (pm20) REVERT: V 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9415 (mmmm) REVERT: V 32 LYS cc_start: 0.9593 (mmtt) cc_final: 0.8889 (mtpt) REVERT: W 5 ASN cc_start: 0.9196 (t0) cc_final: 0.8568 (t0) REVERT: X 5 ASN cc_start: 0.9270 (t0) cc_final: 0.8615 (t0) REVERT: X 26 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9047 (ptpp) REVERT: X 32 LYS cc_start: 0.9622 (mmtt) cc_final: 0.8855 (ttpt) REVERT: Y 25 TYR cc_start: 0.9596 (m-80) cc_final: 0.9119 (m-80) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.3767 time to fit residues: 67.3452 Evaluate side-chains 147 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 91 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.037599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.022805 restraints weight = 38117.894| |-----------------------------------------------------------------------------| r_work (start): 0.2317 rms_B_bonded: 5.20 r_work: 0.2160 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7900 Z= 0.156 Angle : 0.612 8.415 10525 Z= 0.307 Chirality : 0.041 0.111 850 Planarity : 0.003 0.025 1350 Dihedral : 3.310 21.370 1075 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 950 helix: 2.47 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 8 HIS 0.001 0.000 HIS T 18 PHE 0.003 0.001 PHE Y 35 TYR 0.014 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02269 ( 250) hydrogen bonds : angle 5.73406 ( 600) SS BOND : bond 0.00206 ( 75) SS BOND : angle 0.48112 ( 150) covalent geometry : bond 0.00346 ( 7825) covalent geometry : angle 0.61402 (10375) ********************** 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 148 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.884 Fit side-chains REVERT: A 20 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9426 (mmmm) REVERT: D 20 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9396 (mmmm) REVERT: E 20 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9416 (mmmm) REVERT: F 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9363 (mmmm) REVERT: G 5 ASN cc_start: 0.9305 (t0) cc_final: 0.8589 (t0) REVERT: G 11 ASP cc_start: 0.8264 (t0) cc_final: 0.7790 (t0) REVERT: G 13 MET cc_start: 0.8654 (mmt) cc_final: 0.8258 (mmt) REVERT: I 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8567 (t0) REVERT: I 10 GLU cc_start: 0.8898 (pm20) cc_final: 0.8587 (pm20) REVERT: I 20 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9364 (mmmm) REVERT: J 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9359 (mmmm) REVERT: K 5 ASN cc_start: 0.9358 (t0) cc_final: 0.8673 (t0) REVERT: K 10 GLU cc_start: 0.8980 (pm20) cc_final: 0.8698 (pm20) REVERT: L 20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9423 (mmmm) REVERT: M 5 ASN cc_start: 0.9381 (t0) cc_final: 0.8712 (t0) REVERT: M 10 GLU cc_start: 0.9042 (pm20) cc_final: 0.8743 (pm20) REVERT: M 26 LYS cc_start: 0.9259 (ptmt) cc_final: 0.8821 (ptmm) REVERT: N 20 LYS cc_start: 0.9669 (mmmt) cc_final: 0.9419 (mmmm) REVERT: O 5 ASN cc_start: 0.9302 (t0) cc_final: 0.8617 (t0) REVERT: P 5 ASN cc_start: 0.9431 (t0) cc_final: 0.8705 (t0) REVERT: P 20 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9296 (mmmm) REVERT: Q 10 GLU cc_start: 0.9065 (pm20) cc_final: 0.8785 (pm20) REVERT: Q 20 LYS cc_start: 0.9701 (mmmt) cc_final: 0.9471 (mmmm) REVERT: R 5 ASN cc_start: 0.9433 (t0) cc_final: 0.8985 (t0) REVERT: S 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9411 (mmmm) REVERT: T 5 ASN cc_start: 0.9452 (t0) cc_final: 0.9071 (t0) REVERT: T 10 GLU cc_start: 0.8838 (pm20) cc_final: 0.8587 (pm20) REVERT: T 20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9328 (mmmm) REVERT: T 25 TYR cc_start: 0.9463 (m-80) cc_final: 0.9109 (m-80) REVERT: U 20 LYS cc_start: 0.9691 (mmmt) cc_final: 0.9447 (mmmm) REVERT: V 5 ASN cc_start: 0.9456 (t0) cc_final: 0.8787 (t0) REVERT: V 10 GLU cc_start: 0.8782 (pm20) cc_final: 0.8452 (pm20) REVERT: V 20 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9411 (mmmm) REVERT: V 32 LYS cc_start: 0.9636 (mmtt) cc_final: 0.8949 (mtpt) REVERT: X 5 ASN cc_start: 0.9353 (t0) cc_final: 0.8729 (t0) REVERT: X 26 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9066 (ptpp) REVERT: X 32 LYS cc_start: 0.9655 (mmtt) cc_final: 0.8877 (ttpt) REVERT: Y 13 MET cc_start: 0.8438 (mmt) cc_final: 0.8161 (mmm) REVERT: Y 25 TYR cc_start: 0.9602 (m-80) cc_final: 0.9105 (m-80) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.3909 time to fit residues: 67.7692 Evaluate side-chains 146 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.038292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023510 restraints weight = 36998.717| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 5.19 r_work: 0.2196 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7900 Z= 0.109 Angle : 0.620 9.156 10525 Z= 0.308 Chirality : 0.040 0.112 850 Planarity : 0.003 0.025 1350 Dihedral : 3.265 20.981 1075 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 12.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 950 helix: 2.31 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 8 HIS 0.001 0.000 HIS T 18 PHE 0.004 0.000 PHE Y 35 TYR 0.015 0.001 TYR W 25 Details of bonding type rmsd hydrogen bonds : bond 0.02050 ( 250) hydrogen bonds : angle 5.52783 ( 600) SS BOND : bond 0.00148 ( 75) SS BOND : angle 0.43943 ( 150) covalent geometry : bond 0.00271 ( 7825) covalent geometry : angle 0.62263 (10375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.93 seconds wall clock time: 62 minutes 55.03 seconds (3775.03 seconds total)