Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 6DKZ_complete.pdb Found miller_array, 6DKZ.mtz Found phil, 6DKZ.edits Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ 6DKZ.edits Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "6DKZ_complete.pdb" } default_model = "6DKZ_complete.pdb" miller_array { file = "6DKZ.mtz" } default_miller_array = "6DKZ.mtz" phil_files = "6DKZ.edits" default_phil = "6DKZ.edits" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 8 and name C atom_selection_2 = chain A and resseq 1 and name N distance_ideal = 1.4 sigma = 0.02 } bond { atom_selection_1 = chain A and resseq 6 and name O atom_selection_2 = chain A and resseq 1 and name H3 distance_ideal = 1.9 sigma = 0.2 } } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Classifications: {'peptide': 8} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 0.06, per 1000 atoms: 0.48 Number of scatterers: 126 At special positions: 0 Unit cell: (14.061, 19.862, 18.632, 90, 91.699, 90) Space group: P 1 21/n 1 (No. 14) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 11 8.00 N 8 7.00 C 37 6.00 H 70 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 116 C GLY A 8 .*. C " atom 2: "ATOM 1 N SER A 1 .*. N " symmetry operation: x,y,z distance_model: 1.332 distance_ideal: 1.400 ideal - model: 0.068 slack: 0.000 delta_slack: 0.068 sigma: 0.0200 bond: atom 1: "ATOM 79 O ILE A 6 .*. O " atom 2: "ATOM 7 H3 SER A 1 .*. H " symmetry operation: x,y,z distance_model: 3.041 distance_ideal: 1.900 ideal - model: -1.141 slack: 0.000 delta_slack: -1.141 sigma: 0.2000 Total number of added/changed bonds: 2 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.04 Conformation dependent library (CDL) restraints added in 4.8 milliseconds Time building geometry restraints manager: 0.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 0.99: 6 0.99 - 1.13: 64 1.13 - 1.28: 8 1.28 - 1.42: 8 1.42 - 1.56: 37 Bond restraints: 123 Sorted by residual: bond pdb=" N LEU A 4 " pdb=" H LEU A 4 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 8 " pdb=" H GLY A 8 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N ILE A 6 " pdb=" H ILE A 6 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" N LEU A 7 " pdb=" H LEU A 7 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" N ILE A 3 " pdb=" H ILE A 3 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 118 not shown) Histogram of bond angle deviations from ideal: 103.91 - 108.12: 37 108.12 - 112.33: 131 112.33 - 116.54: 18 116.54 - 120.75: 13 120.75 - 124.96: 22 Bond angle restraints: 221 Sorted by residual: angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" C LEU A 4 " ideal model delta sigma weight residual 112.23 114.29 -2.06 1.26e+00 6.30e-01 2.67e+00 angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" HA LEU A 4 " ideal model delta sigma weight residual 110.00 105.45 4.55 3.00e+00 1.11e-01 2.30e+00 angle pdb=" C LEU A 4 " pdb=" CA LEU A 4 " pdb=" CB LEU A 4 " ideal model delta sigma weight residual 110.38 107.45 2.93 2.04e+00 2.40e-01 2.07e+00 angle pdb=" N ILE A 3 " pdb=" CA ILE A 3 " pdb=" C ILE A 3 " ideal model delta sigma weight residual 110.53 111.71 -1.18 9.40e-01 1.13e+00 1.56e+00 angle pdb=" CA ILE A 2 " pdb=" C ILE A 2 " pdb=" N ILE A 3 " ideal model delta sigma weight residual 117.15 118.53 -1.38 1.14e+00 7.69e-01 1.47e+00 ... (remaining 216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.37: 28 7.37 - 14.74: 5 14.74 - 22.11: 2 22.11 - 29.48: 1 29.48 - 36.84: 2 Dihedral angle restraints: 38 sinusoidal: 31 harmonic: 7 Sorted by residual: dihedral pdb=" N ILE A 6 " pdb=" CA ILE A 6 " pdb=" CB ILE A 6 " pdb=" CG1 ILE A 6 " ideal model delta sinusoidal sigma weight residual -180.00 -153.87 -26.13 3 1.50e+01 4.44e-03 3.79e+00 dihedral pdb=" CA LEU A 4 " pdb=" C LEU A 4 " pdb=" N GLY A 5 " pdb=" CA GLY A 5 " ideal model delta harmonic sigma weight residual -180.00 -171.77 -8.23 0 5.00e+00 4.00e-02 2.71e+00 dihedral pdb=" N SER A 1 " pdb=" CA SER A 1 " pdb=" CB SER A 1 " pdb=" OG SER A 1 " ideal model delta sinusoidal sigma weight residual 180.00 162.44 17.56 3 1.50e+01 4.44e-03 1.87e+00 ... (remaining 35 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.045: 6 0.045 - 0.090: 3 0.090 - 0.134: 1 0.134 - 0.178: 0 0.178 - 0.222: 1 Chirality restraints: 11 Sorted by residual: chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU A 7 " pdb=" N LEU A 7 " pdb=" C LEU A 7 " pdb=" CB LEU A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.72e-01 ... (remaining 8 not shown) Planarity restraints: 14 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 4 " 0.005 2.00e-02 2.50e+03 9.12e-03 8.32e-01 pdb=" C LEU A 4 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU A 4 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY A 5 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 7 " 0.002 2.00e-02 2.50e+03 4.45e-03 1.98e-01 pdb=" C LEU A 7 " -0.008 2.00e-02 2.50e+03 pdb=" O LEU A 7 " 0.003 2.00e-02 2.50e+03 pdb=" N GLY A 8 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 1 " -0.002 2.00e-02 2.50e+03 4.41e-03 1.94e-01 pdb=" C SER A 1 " 0.008 2.00e-02 2.50e+03 pdb=" O SER A 1 " -0.003 2.00e-02 2.50e+03 pdb=" N ILE A 2 " -0.003 2.00e-02 2.50e+03 ... (remaining 11 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.30: 36 2.30 - 2.82: 319 2.82 - 3.35: 427 3.35 - 3.87: 638 3.87 - 4.40: 911 Nonbonded interactions: 2331 Sorted by model distance: nonbonded pdb=" HG SER A 1 " pdb=" O HOH A 101 " model vdw 1.771 1.850 nonbonded pdb=" O ILE A 2 " pdb=" H LEU A 7 " model vdw sym.op. 1.878 1.850 -x+1/2,y-1/2,-z+1/2 nonbonded pdb=" H ILE A 2 " pdb=" O GLY A 8 " model vdw sym.op. 1.893 1.850 -x+1,-y+2,-z+1 nonbonded pdb=" O GLY A 8 " pdb=" H ILE A 2 " model vdw sym.op. 1.893 1.850 -x+1,-y+2,-z+1 nonbonded pdb=" H1 HOH A 101 " pdb=" O GLY A 8 " model vdw sym.op. 1.926 1.850 -x+1,-y+2,-z+1 ... (remaining 2326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 4 Type Number sf(0) Gaussians O 11 7.97 2 N 8 6.98 3 C 37 5.99 3 H 70 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== n_use = 126 n_use_u_iso = 72 n_use_u_aniso = 54 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 126 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (126 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 70 aniso = 56) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 8 and name C atom_selection_2 = chain A and resseq 1 and name N distance_ideal = 1.4 sigma = 0.02 } bond { atom_selection_1 = chain A and resseq 6 and name O atom_selection_2 = chain A and resseq 1 and name H3 distance_ideal = 1.9 sigma = 0.2 } } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "6DKZ_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 70 occupancy sum: 70.00 (% of total atoms 55.56) Rotatable: count: 31 occupancy sum: 31.00 (% of total atoms 24.60) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.99 - 11.47 A, n_refl.=5296 (all), 9.84 % free)-------------| | | | r_work= 0.1909 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.749423 | | target function (ml) not normalized (work): 13128.495967 | | target function (ml) not normalized (free): 1444.486855 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.47 - 1.57 0.97 1223 137 0.2135 0.2081 3.52 3.5012| | 2: 1.57 - 1.25 0.97 1223 133 0.1789 0.1739 2.7828 2.7739| | 3: 1.25 - 1.09 0.93 1186 120 0.1626 0.1858 2.4225 2.4636| | 4: 1.09 - 0.99 0.90 1143 131 0.1839 0.1994 2.2285 2.2921| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 11.47 - 1.57 1223 137 0.82 15.93 0.99 0.79 94.30| | 2: 1.57 - 1.25 1223 133 0.78 19.50 1.03 0.79 39.67| | 3: 1.25 - 1.09 1186 120 0.87 11.31 1.01 0.78 10.57| | 4: 1.09 - 0.99 1143 131 0.85 13.55 0.99 0.75 6.98| |alpha: min = 0.75 max = 0.79 mean = 0.78| |beta: min = 6.98 max = 94.30 mean = 38.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 90.00 mean = 15.13| |phase err.(test): min = 0.00 max = 89.60 mean = 14.90| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.017 53 Z= 0.499 Angle : 1.046 3.297 70 Z= 0.641 Chirality : 0.089 0.222 11 Planarity : 0.005 0.009 7 Dihedral : 10.290 26.133 18 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -2.81 (2.93), residues: 6 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (2.23), residues: 6 Individual atomic B min max mean iso aniso Overall: 1.87 7.91 3.11 0.68 0 56 Protein: 1.87 7.91 3.10 0.68 0 54 Water: 2.52 3.97 3.25 N/A 0 2 Chain A: 1.87 7.91 3.11 N/A 0 56 Histogram: Values Number of atoms 1.87 - 2.47 24 2.47 - 3.08 11 3.08 - 3.68 7 3.68 - 4.29 6 4.29 - 4.89 2 4.89 - 5.50 2 5.50 - 6.10 1 6.10 - 6.71 1 6.71 - 7.31 1 7.31 - 7.91 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.99 - 11.47 A, n_refl.=5296 (all), 9.84 % free)-------------| | | | r_work= 0.1909 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.749423 | | target function (ml) not normalized (work): 13128.495967 | | target function (ml) not normalized (free): 1444.486855 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1913 0.1909 0.1951 n_refl.: 5296 re-set all scales: r(all,work,free)=0.1913 0.1909 0.1951 n_refl.: 5296 remove outliers: r(all,work,free)=0.1913 0.1909 0.1951 n_refl.: 5296 overall B=0.04 to atoms: r(all,work,free)=0.1915 0.1911 0.1949 n_refl.: 5296 bulk-solvent and scaling: r(all,work,free)=0.1768 0.1760 0.1837 n_refl.: 5296 remove outliers: r(all,work,free)=0.1758 0.1749 0.1837 n_refl.: 5293 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 75.38 86 12 0.3425 48.467 44.243 0.923 0.997 0.162 3.422-2.852 98.04 93 7 0.1520 56.416 55.525 0.961 1.001 0.000 2.845-2.368 99.42 156 15 0.1698 47.060 46.122 0.995 1.000 0.000 2.365-1.967 99.36 280 29 0.1924 40.402 39.443 1.021 1.000 0.000 1.967-1.635 98.49 463 58 0.1907 28.573 28.202 1.018 1.001 0.000 1.635-1.360 97.27 805 87 0.1721 21.714 21.446 1.029 1.002 0.000 1.359-1.131 95.05 1385 151 0.1575 18.568 18.310 1.008 1.004 0.000 1.130-0.990 90.69 1504 162 0.1532 14.105 14.117 0.981 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0643 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1749 r_free=0.1837 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1749 r_free=0.1837 ========================= Local real-space refinement ========================= Before: r_work=0.1749 r_free=0.1837 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0677 time to fit residues: 0.1438 After: r_work=0.1755 r_free=0.1845 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.655226 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 6.341774 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1750 0.1815 0.0065 0.006 0.9 0.0 0.0 0.0 0 4.328 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1750 r_free=0.1815 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 After: r_work=0.1750 r_free=0.1815 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.50 18.15 0.65 0.448 3.438 6.342 0.037 17.40 18.29 0.89 0.466 3.405 6.342 0.037 Individual atomic B min max mean iso aniso Overall: 1.81 8.57 3.08 0.67 0 56 Protein: 1.81 8.57 3.07 0.67 0 54 Water: 2.44 3.92 3.18 N/A 0 2 Chain A: 1.81 8.57 3.08 N/A 0 56 Histogram: Values Number of atoms 1.81 - 2.48 26 2.48 - 3.16 12 3.16 - 3.84 7 3.84 - 4.51 5 4.51 - 5.19 1 5.19 - 5.87 2 5.87 - 6.54 1 6.54 - 7.22 0 7.22 - 7.89 1 7.89 - 8.57 1 =========================== Idealize ADP of riding H ========================== r_work=0.1740 r_free=0.1829 r_work=0.1738 r_free=0.1834 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.99 - 11.47 A, n_refl.=5293 (all), 9.84 % free)-------------| | | | r_work= 0.1738 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ls_wunit_k1) (work): 0.036679 | | target function (ls_wunit_k1) not normalized (work): 175.032734 | | target function (ls_wunit_k1) not normalized (free): 22.805968 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1748 0.1738 0.1834 n_refl.: 5293 re-set all scales: r(all,work,free)=0.1889 0.1882 0.1956 n_refl.: 5293 remove outliers: r(all,work,free)=0.1889 0.1882 0.1956 n_refl.: 5293 overall B=0.03 to atoms: r(all,work,free)=0.1890 0.1883 0.1955 n_refl.: 5293 bulk-solvent and scaling: r(all,work,free)=0.1748 0.1738 0.1835 n_refl.: 5293 remove outliers: r(all,work,free)=0.1746 0.1738 0.1816 n_refl.: 5291 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 75.38 86 12 0.3424 48.467 44.439 0.918 0.997 0.166 3.422-2.852 98.04 93 7 0.1536 56.416 55.492 0.975 0.999 0.000 2.845-2.368 99.42 156 15 0.1565 47.060 46.341 0.994 0.998 0.000 2.365-1.967 99.36 280 29 0.1917 40.402 39.448 1.026 0.998 0.000 1.967-1.635 98.49 463 58 0.1831 28.573 28.232 1.025 0.997 0.000 1.635-1.360 97.27 805 87 0.1687 21.714 21.446 1.035 0.997 0.000 1.359-1.131 94.99 1385 150 0.1583 18.553 18.315 1.017 0.997 0.000 1.130-0.990 90.64 1504 161 0.1588 14.111 14.132 0.997 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0431 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1738 r_free=0.1816 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1738 r_free=0.1816 ========================= Local real-space refinement ========================= Before: r_work=0.1738 r_free=0.1816 3 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0684 time to fit residues: 0.2145 After: r_work=0.1777 r_free=0.1885 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.026592 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 5.221212 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2193 0.2225 0.0032 0.003 0.5 0.0 0.0 0.0 0 0.125 0.2067 0.2097 0.0030 0.003 0.5 0.0 0.0 0.0 0 0.250 0.1893 0.1929 0.0036 0.003 0.6 0.0 0.0 0.0 0 0.500 0.1829 0.1867 0.0038 0.003 0.7 0.0 0.0 0.0 0 1.000 0.1766 0.1817 0.0051 0.004 0.8 0.0 0.0 0.0 0 2.000 0.1744 0.1810 0.0065 0.004 0.8 0.0 0.0 0.0 0 3.000 0.1733 0.1801 0.0068 0.004 0.9 0.0 0.0 0.0 0 4.000 0.1725 0.1800 0.0075 0.005 0.9 0.0 0.0 0.0 0 5.000 0.1721 0.1801 0.0080 0.005 0.9 0.0 0.0 0.0 0 6.000 0.1718 0.1799 0.0081 0.005 1.0 0.0 0.0 0.0 0 7.000 0.1715 0.1799 0.0084 0.005 1.0 0.0 0.0 0.0 0 8.000 0.1712 0.1799 0.0087 0.005 1.0 0.0 0.0 0.0 0 9.000 0.1710 0.1799 0.0089 0.006 1.0 0.0 0.0 0.0 0 10.000 0.1738 0.1803 0.0065 0.004 0.9 0.0 0.0 0.0 0 3.513 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1712 0.1799 0.0087 0.005 1.0 0.0 0.0 0.0 0 9.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1712 r_free=0.1799 3 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 After: r_work=0.1712 r_free=0.1799 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.12 17.99 0.87 0.741 3.802 5.221 0.036 17.12 17.98 0.87 0.741 3.802 5.221 0.036 Individual atomic B min max mean iso aniso Overall: 1.84 8.60 3.10 0.67 0 56 Protein: 1.84 8.60 3.10 0.67 0 54 Water: 2.47 3.95 3.21 N/A 0 2 Chain A: 1.84 8.60 3.10 N/A 0 56 Histogram: Values Number of atoms 1.84 - 2.51 26 2.51 - 3.19 12 3.19 - 3.87 7 3.87 - 4.54 5 4.54 - 5.22 1 5.22 - 5.89 2 5.89 - 6.57 1 6.57 - 7.25 0 7.25 - 7.92 1 7.92 - 8.60 1 =========================== Idealize ADP of riding H ========================== r_work=0.1712 r_free=0.1798 r_work=0.1712 r_free=0.1798 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.99 - 11.47 A, n_refl.=5291 (all), 9.81 % free)-------------| | | | r_work= 0.1712 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ls_wunit_k1) (work): 0.035769 | | target function (ls_wunit_k1) not normalized (work): 170.689903 | | target function (ls_wunit_k1) not normalized (free): 22.575536 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1720 0.1712 0.1798 n_refl.: 5291 re-set all scales: r(all,work,free)=0.1867 0.1861 0.1920 n_refl.: 5291 remove outliers: r(all,work,free)=0.1867 0.1861 0.1920 n_refl.: 5291 overall B=0.02 to atoms: r(all,work,free)=0.1868 0.1862 0.1919 n_refl.: 5291 bulk-solvent and scaling: r(all,work,free)=0.1720 0.1712 0.1799 n_refl.: 5291 remove outliers: r(all,work,free)=0.1720 0.1712 0.1799 n_refl.: 5291 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 75.38 86 12 0.3422 48.467 44.476 0.913 1.003 0.162 3.422-2.852 98.04 93 7 0.1505 56.416 55.533 0.969 1.005 0.000 2.845-2.368 99.42 156 15 0.1574 47.060 46.292 0.989 1.004 0.000 2.365-1.967 99.36 280 29 0.1898 40.402 39.460 1.022 1.003 0.000 1.967-1.635 98.49 463 58 0.1823 28.573 28.213 1.022 1.002 0.000 1.635-1.360 97.27 805 87 0.1666 21.714 21.444 1.031 1.002 0.000 1.359-1.131 94.99 1385 150 0.1549 18.553 18.319 1.015 1.001 0.000 1.130-0.990 90.64 1504 161 0.1537 14.111 14.157 0.997 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0259 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1712 r_free=0.1799 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1712 r_free=0.1799 ========================= Local real-space refinement ========================= Before: r_work=0.1712 r_free=0.1799 3 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0641 time to fit residues: 0.2012 After: r_work=0.1749 r_free=0.1849 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.078740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.381284 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1716 0.1783 0.0067 0.005 1.0 0.0 0.0 0.0 0 0.539 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1716 r_free=0.1783 3 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0047 After: r_work=0.1716 r_free=0.1783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.16 17.83 0.67 0.744 3.822 0.381 2.877 17.14 17.69 0.56 0.803 3.802 0.381 2.864 Individual atomic B min max mean iso aniso Overall: 1.84 8.11 3.08 0.66 0 56 Protein: 1.84 8.11 3.08 0.66 0 54 Water: 2.36 3.78 3.07 N/A 0 2 Chain A: 1.84 8.11 3.08 N/A 0 56 Histogram: Values Number of atoms 1.84 - 2.47 26 2.47 - 3.10 10 3.10 - 3.72 7 3.72 - 4.35 7 4.35 - 4.98 1 4.98 - 5.60 2 5.60 - 6.23 1 6.23 - 6.86 0 6.86 - 7.48 1 7.48 - 8.11 1 =========================== Idealize ADP of riding H ========================== r_work=0.1714 r_free=0.1769 r_work=0.1714 r_free=0.1770 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.99 - 11.47 A, n_refl.=5291 (all), 9.81 % free)-------------| | | | r_work= 0.1714 r_free= 0.1770 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.864464 | | target function (ml) not normalized (work): 13669.222133 | | target function (ml) not normalized (free): 1509.583075 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1720 0.1714 0.1770 n_refl.: 5291 re-set all scales: r(all,work,free)=0.1863 0.1860 0.1888 n_refl.: 5291 remove outliers: r(all,work,free)=0.1863 0.1860 0.1888 n_refl.: 5291 overall B=0.02 to atoms: r(all,work,free)=0.1864 0.1861 0.1888 n_refl.: 5291 bulk-solvent and scaling: r(all,work,free)=0.1720 0.1715 0.1768 n_refl.: 5291 remove outliers: r(all,work,free)=0.1717 0.1710 0.1768 n_refl.: 5290 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 74.62 85 12 0.3379 48.414 44.685 0.916 1.002 0.161 3.422-2.852 98.04 93 7 0.1518 56.416 55.580 0.968 1.004 0.000 2.845-2.368 99.42 156 15 0.1635 47.060 46.120 0.991 1.003 0.000 2.365-1.967 99.36 280 29 0.1933 40.402 39.397 1.022 1.004 0.000 1.967-1.635 98.49 463 58 0.1863 28.573 28.160 1.021 1.004 0.000 1.635-1.360 97.27 805 87 0.1696 21.714 21.444 1.027 1.005 0.000 1.359-1.131 94.99 1385 150 0.1531 18.553 18.303 1.009 1.007 0.000 1.130-0.990 90.64 1504 161 0.1472 14.111 14.158 0.991 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0245 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1710 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1710 r_free=0.1768 ========================= Local real-space refinement ========================= Before: r_work=0.1710 r_free=0.1768 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.006 outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0669 time to fit residues: 0.1428 After: r_work=0.1717 r_free=0.1775 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.078599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.447918 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1709 0.1767 0.0058 0.005 1.0 0.0 0.0 0.0 0 0.539 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1709 r_free=0.1767 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 After: r_work=0.1709 r_free=0.1767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.09 17.67 0.58 0.731 3.782 0.448 2.862 17.04 17.67 0.63 0.764 3.767 0.448 2.859 Individual atomic B min max mean iso aniso Overall: 1.82 7.89 3.06 0.67 0 56 Protein: 1.82 7.89 3.06 0.67 0 54 Water: 2.34 3.76 3.05 N/A 0 2 Chain A: 1.82 7.89 3.06 N/A 0 56 Histogram: Values Number of atoms 1.82 - 2.43 26 2.43 - 3.04 9 3.04 - 3.64 7 3.64 - 4.25 7 4.25 - 4.86 1 4.86 - 5.46 3 5.46 - 6.07 0 6.07 - 6.67 1 6.67 - 7.28 1 7.28 - 7.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.1704 r_free=0.1767 r_work=0.1704 r_free=0.1766 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.99 - 11.47 A, n_refl.=5290 (all), 9.81 % free)-------------| | | | r_work= 0.1704 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.858599 | | target function (ml) not normalized (work): 13638.375597 | | target function (ml) not normalized (free): 1508.674758 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1711 0.1704 0.1766 n_refl.: 5290 re-set all scales: r(all,work,free)=0.1852 0.1849 0.1883 n_refl.: 5290 remove outliers: r(all,work,free)=0.1852 0.1849 0.1883 n_refl.: 5290 overall B=0.00 to atoms: r(all,work,free)=0.1852 0.1849 0.1883 n_refl.: 5290 bulk-solvent and scaling: r(all,work,free)=0.1711 0.1704 0.1762 n_refl.: 5290 remove outliers: r(all,work,free)=0.1711 0.1704 0.1762 n_refl.: 5290 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 74.62 85 12 0.3385 48.414 44.702 0.898 1.003 0.161 3.422-2.852 98.04 93 7 0.1525 56.416 55.576 0.950 1.005 0.000 2.845-2.368 99.42 156 15 0.1628 47.060 46.108 0.971 1.004 0.000 2.365-1.967 99.36 280 29 0.1927 40.402 39.397 1.001 1.005 0.000 1.967-1.635 98.49 463 58 0.1860 28.573 28.175 1.001 1.005 0.000 1.635-1.360 97.27 805 87 0.1691 21.714 21.444 1.005 1.006 0.000 1.359-1.131 94.99 1385 150 0.1521 18.553 18.302 0.986 1.007 0.000 1.130-0.990 90.64 1504 161 0.1464 14.111 14.155 0.966 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0632 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1704 r_free=0.1762 After: r_work=0.1705 r_free=0.1760 ================================== NQH flips ================================== r_work=0.1705 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1705 r_free=0.1760 ========================= Local real-space refinement ========================= Before: r_work=0.1705 r_free=0.1760 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0645 time to fit residues: 0.1373 After: r_work=0.1711 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.004152 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.446781 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1713 0.1757 0.0044 0.004 1.0 0.0 0.0 0.0 0 0.502 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1713 r_free=0.1757 2 residues out of total 6 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 After: r_work=0.1713 r_free=0.1757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.13 17.57 0.44 0.732 3.745 0.447 2.862 17.12 17.59 0.47 0.742 3.735 0.447 2.861 Individual atomic B min max mean iso aniso Overall: 1.80 7.86 3.03 0.67 0 56 Protein: 1.80 7.86 3.03 0.67 0 54 Water: 2.31 3.75 3.03 N/A 0 2 Chain A: 1.80 7.86 3.03 N/A 0 56 Histogram: Values Number of atoms 1.80 - 2.41 26 2.41 - 3.01 9 3.01 - 3.62 7 3.62 - 4.23 7 4.23 - 4.83 1 4.83 - 5.44 2 5.44 - 6.04 1 6.04 - 6.65 1 6.65 - 7.25 1 7.25 - 7.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.1712 r_free=0.1759 r_work=0.1712 r_free=0.1759 ----------X-ray data---------- |--(resolution: 0.99 - 11.47 A, n_refl.=5290 (all), 9.81 % free)-------------| | | | r_work= 0.1712 r_free= 0.1759 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.861059 | | target function (ml) not normalized (work): 13650.112569 | | target function (ml) not normalized (free): 1506.666534 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.47 - 1.57 0.97 1220 137 0.1944 0.1900 3.6105 3.6514| | 2: 1.57 - 1.25 0.97 1223 133 0.1658 0.1593 2.9466 2.9288| | 3: 1.25 - 1.09 0.93 1186 119 0.1424 0.1695 2.5517 2.5761| | 4: 1.09 - 0.99 0.90 1142 130 0.1522 0.1670 2.2901 2.3871| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 11.47 - 1.57 1220 137 0.84 14.32 1.00 1.04 124.28| | 2: 1.57 - 1.25 1223 133 0.81 17.41 1.00 1.02 51.54| | 3: 1.25 - 1.09 1186 119 0.89 9.57 1.00 1.00 12.89| | 4: 1.09 - 0.99 1142 130 0.88 11.11 0.99 0.99 8.34| |alpha: min = 0.99 max = 1.04 mean = 1.01| |beta: min = 8.34 max = 124.28 mean = 50.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 13.16| |phase err.(test): min = 0.00 max = 89.82 mean = 12.82| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1717 0.1712 0.1759 n_refl.: 5290 re-set all scales: r(all,work,free)=0.1856 0.1853 0.1879 n_refl.: 5290 remove outliers: r(all,work,free)=0.1856 0.1853 0.1879 n_refl.: 5290 overall B=0.00 to atoms: r(all,work,free)=0.1856 0.1853 0.1879 n_refl.: 5290 bulk-solvent and scaling: r(all,work,free)=0.1716 0.1712 0.1757 n_refl.: 5290 remove outliers: r(all,work,free)=0.1716 0.1712 0.1757 n_refl.: 5290 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 11.473-3.457 74.62 85 12 0.3374 48.414 44.635 0.895 1.005 0.165 3.422-2.852 98.04 93 7 0.1508 56.416 55.530 0.947 1.007 0.000 2.845-2.368 99.42 156 15 0.1631 47.060 46.119 0.969 1.006 0.000 2.365-1.967 99.36 280 29 0.1933 40.402 39.392 1.000 1.006 0.000 1.967-1.635 98.49 463 58 0.1885 28.573 28.169 0.995 1.006 0.000 1.635-1.360 97.27 805 87 0.1693 21.714 21.441 1.002 1.006 0.000 1.359-1.131 94.99 1385 150 0.1528 18.553 18.299 0.981 1.006 0.000 1.130-0.990 90.64 1504 161 0.1475 14.111 14.155 0.960 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0983 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.1909 0.1951 0.008 1.046 1.9 7.9 3.1 6 0.000 1_bss: 0.1749 0.1837 0.008 1.046 1.9 8.0 3.1 6 0.000 1_settarget: 0.1749 0.1837 0.008 1.046 1.9 8.0 3.1 6 0.000 1_nqh: 0.1749 0.1837 0.008 1.046 1.9 8.0 3.1 6 0.000 1_realsrl: 0.1755 0.1845 0.008 1.046 1.9 8.0 3.1 6 0.008 1_weight: 0.1755 0.1845 0.008 1.046 1.9 8.0 3.1 6 0.008 1_xyzrec: 0.1750 0.1815 0.006 0.916 1.9 8.0 3.1 6 0.088 1_realsrl2: 0.1750 0.1815 0.006 0.916 1.9 8.0 3.1 6 0.088 1_adp: 0.1740 0.1829 0.006 0.916 1.8 8.6 3.1 6 0.088 1_regHadp: 0.1738 0.1834 0.006 0.916 1.8 8.6 3.1 6 0.088 2_bss: 0.1738 0.1816 0.006 0.916 1.8 8.6 3.1 6 0.088 2_settarget: 0.1738 0.1816 0.006 0.916 1.8 8.6 3.1 6 0.088 2_updatecdl: 0.1738 0.1816 0.006 0.916 1.8 8.6 3.1 6 0.088 2_nqh: 0.1738 0.1816 0.006 0.916 1.8 8.6 3.1 6 0.088 2_realsrl: 0.1777 0.1885 0.006 0.916 1.8 8.6 3.1 6 0.093 2_weight: 0.1777 0.1885 0.006 0.916 1.8 8.6 3.1 6 0.093 2_xyzrec: 0.1712 0.1799 0.005 0.990 1.8 8.6 3.1 6 0.093 2_realsrl2: 0.1712 0.1799 0.005 0.990 1.8 8.6 3.1 6 0.093 2_adp: 0.1712 0.1798 0.005 0.990 1.8 8.6 3.1 6 0.093 2_regHadp: 0.1712 0.1798 0.005 0.990 1.8 8.6 3.1 6 0.093 3_bss: 0.1712 0.1799 0.005 0.990 1.9 8.6 3.1 6 0.093 3_settarget: 0.1712 0.1799 0.005 0.990 1.9 8.6 3.1 6 0.093 3_updatecdl: 0.1712 0.1799 0.005 0.990 1.9 8.6 3.1 6 0.093 3_nqh: 0.1712 0.1799 0.005 0.990 1.9 8.6 3.1 6 0.093 3_realsrl: 0.1749 0.1849 0.005 0.990 1.9 8.6 3.1 6 0.096 3_weight: 0.1749 0.1849 0.005 0.990 1.9 8.6 3.1 6 0.096 3_xyzrec: 0.1716 0.1783 0.005 0.979 1.9 8.6 3.1 6 0.090 3_realsrl2: 0.1716 0.1783 0.005 0.979 1.9 8.6 3.1 6 0.090 3_adp: 0.1714 0.1769 0.005 0.979 1.8 8.1 3.1 6 0.090 3_regHadp: 0.1714 0.1770 0.005 0.979 1.8 8.1 3.1 6 0.090 4_bss: 0.1710 0.1768 0.005 0.979 1.9 8.1 3.1 6 0.090 4_settarget: 0.1710 0.1768 0.005 0.979 1.9 8.1 3.1 6 0.090 4_updatecdl: 0.1710 0.1768 0.005 0.979 1.9 8.1 3.1 6 0.090 4_nqh: 0.1710 0.1768 0.005 0.979 1.9 8.1 3.1 6 0.090 4_realsrl: 0.1717 0.1775 0.005 0.979 1.9 8.1 3.1 6 0.092 4_weight: 0.1717 0.1775 0.005 0.979 1.9 8.1 3.1 6 0.092 4_xyzrec: 0.1709 0.1767 0.005 0.988 1.9 8.1 3.1 6 0.092 4_realsrl2: 0.1709 0.1767 0.005 0.988 1.9 8.1 3.1 6 0.092 4_adp: 0.1704 0.1767 0.005 0.988 1.8 7.9 3.1 6 0.092 4_regHadp: 0.1704 0.1766 0.005 0.988 1.8 7.9 3.1 6 0.092 5_bss: 0.1704 0.1762 0.005 0.988 1.8 7.9 3.1 6 0.092 5_settarget: 0.1704 0.1762 0.005 0.988 1.8 7.9 3.1 6 0.092 5_updatecdl: 0.1704 0.1762 0.005 0.988 1.8 7.9 3.1 6 0.092 5_setrh: 0.1705 0.1760 0.005 0.988 1.8 7.9 3.1 6 0.091 5_nqh: 0.1705 0.1760 0.005 0.988 1.8 7.9 3.1 6 0.091 5_realsrl: 0.1711 0.1764 0.005 0.988 1.8 7.9 3.1 6 0.092 5_weight: 0.1711 0.1764 0.005 0.988 1.8 7.9 3.1 6 0.092 5_xyzrec: 0.1713 0.1757 0.004 1.020 1.8 7.9 3.1 6 0.093 5_realsrl2: 0.1713 0.1757 0.004 1.020 1.8 7.9 3.1 6 0.093 5_adp: 0.1712 0.1759 0.004 1.020 1.8 7.9 3.0 6 0.093 5_regHadp: 0.1712 0.1759 0.004 1.020 1.8 7.9 3.0 6 0.093 end: 0.1712 0.1757 0.004 1.020 1.8 7.9 3.0 6 0.093 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6DKZ_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6DKZ_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 0.1300 Refinement macro-cycles (run) : 90.3400 Write final files (write_after_run_outputs) : 5.5000 Total : 95.9700 Total CPU time: 103.15 seconds =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:01:15 PDT -0700 (1712790075.11 s) Start R-work = 0.1749, R-free = 0.1837 Final R-work = 0.1712, R-free = 0.1757 =============================================================================== Job complete usr+sys time: 107.17 seconds wall clock time: 2 minutes 1.23 seconds (121.23 seconds total)